ISDA

Deposition Date 2014-08-01

Release Date 2014-09-03

Last Version Date 2024-11-20

Entry Detail

PDB ID:

3J7R

Keywords:

RIBOSOME

Title:

Structure of the translating mammalian ribosome-Sec61 complex

Biological Source:

Source Organism:

Sus scrofa (Taxon ID: 9823)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.90 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Sec61 alpha subunit
Gene (Uniprot):SEC61A1
Chain IDs:UA (auth: 1)
Chain Length:393
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:A0A4X1TV07 Pfam ID:PF10559, PF00344

Polymer Type:polypeptide(L)
Molecule:Sec61 gamma subunit
Chain IDs:VA (auth: 2)
Chain Length:68
Number of Molecules:1
Biological Source:Sus scrofa

Polymer Type:polypeptide(L)
Molecule:Sec61 beta subunit
Chain IDs:WA (auth: 3)
Chain Length:36
Number of Molecules:1
Biological Source:Sus scrofa

Polymer Type:polyribonucleotide
Molecule:28S ribosomal RNA
Chain IDs:A (auth: 5)
Chain Length:3722
Number of Molecules:1
Biological Source:Sus scrofa

Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:B (auth: 7)
Chain Length:120
Number of Molecules:1
Biological Source:Sus scrofa

Polymer Type:polyribonucleotide
Molecule:5.8S ribosomal RNA
Chain IDs:C (auth: 8)
Chain Length:156
Number of Molecules:1
Biological Source:Sus scrofa

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL2
Chain IDs:D (auth: A)
Chain Length:257
Number of Molecules:1
Biological Source:Sus scrofa

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL3
Chain IDs:E (auth: B)
Chain Length:394
Number of Molecules:1
Biological Source:Sus scrofa

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL4
Chain IDs:F (auth: C)
Chain Length:115
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:F1SJJ5 Pfam ID:PF00573, PF14374

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL18
Gene (Uniprot):RPL5
Chain IDs:G (auth: D)
Chain Length:125
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:A0A287ASD0 Pfam ID:PF17144, PF14204

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL6
Gene (Uniprot):RPL6
Chain IDs:H (auth: E)
Chain Length:135
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:Q2YGT9 Pfam ID:PF03868, PF01159

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL30
Chain IDs:I (auth: F)
Chain Length:110
Number of Molecules:1
Biological Source:Sus scrofa

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL8
Chain IDs:J (auth: G)
Chain Length:266
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:A0A4X1W808 Pfam ID:PF01248

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL6
Gene (Uniprot):RPL9
Chain IDs:K (auth: H)
Chain Length:192
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:I3LP78 Pfam ID:PF00347

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL16
Gene (Uniprot):RPL10
Chain IDs:L (auth: I)
Chain Length:213
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:Q29195 Pfam ID:PF00252

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL5
Gene (Uniprot):RPL11
Chain IDs:M (auth: J)
Chain Length:178
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:Q29205 Pfam ID:PF00281, PF00673

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL13
Gene (Uniprot):RPL13
Chain IDs:N (auth: L)
Chain Length:51
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:A0A4X1TBV3 Pfam ID:PF01294

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL14
Gene (Uniprot):RPL14
Chain IDs:O (auth: M)
Chain Length:128
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:A1XQU3 Pfam ID:PF01929

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL15
Gene (Uniprot):RPL15
Chain IDs:P (auth: N)
Chain Length:204
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:A0A286ZL65 Pfam ID:PF00827

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL13
Chain IDs:Q (auth: O)
Chain Length:106
Number of Molecules:1
Biological Source:Sus scrofa

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL22
Gene (Uniprot):RPL17
Chain IDs:R (auth: P)
Chain Length:153
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:A0A287B386 Pfam ID:PF00237

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL18
Chain IDs:S (auth: Q)
Chain Length:188
Number of Molecules:1
Biological Source:Sus scrofa

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL19
Chain IDs:T (auth: R)
Chain Length:125
Number of Molecules:1
Biological Source:Sus scrofa

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL20
Gene (Uniprot):RPL18A
Chain IDs:U (auth: S)
Chain Length:224
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:A0A287APR1 Pfam ID:PF01775

Polymer Type:polyribonucleotide
Molecule:18S ribosomal RNA
Chain IDs:XA (auth: S2)
Chain Length:1742
Number of Molecules:1
Biological Source:Sus scrofa

Polymer Type:polyribonucleotide
Molecule:Messenger RNA
Chain IDs:FC (auth: S4)
Chain Length:10
Number of Molecules:1
Biological Source:Sus scrofa

Polymer Type:polyribonucleotide
Molecule:A/P tRNA
Chain IDs:GC (auth: S5)
Chain Length:74
Number of Molecules:1
Biological Source:Sus scrofa

Polymer Type:polyribonucleotide
Molecule:P/E tRNA
Chain IDs:HC (auth: S6)
Chain Length:76
Number of Molecules:1
Biological Source:Sus scrofa

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uS2
Gene (Uniprot):RPSA
Chain IDs:YA (auth: SA)
Chain Length:295
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:Q4GWZ2 Pfam ID:PF00318, PF16122

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eS1
Gene (Uniprot):RPS3A
Chain IDs:ZA (auth: SB)
Chain Length:264
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:B6V8C8 Pfam ID:PF01015

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uS5
Gene (Uniprot):RPS2
Chain IDs:AB (auth: SC)
Chain Length:69
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:I3LJ87 Pfam ID:PF00333, PF03719

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uS3
Gene (Uniprot):RPS3
Chain IDs:BB (auth: SD)
Chain Length:56
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:Q0Z8U2 Pfam ID:PF07650, PF00189

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eS4
Chain IDs:CB (auth: SE)
Chain Length:263
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:A0A287B771 Pfam ID:PF08071, PF00900, PF00467, PF16121

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uS7
Gene (Uniprot):RPS5
Chain IDs:DB (auth: SF)
Chain Length:156
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:F2Z5E6 Pfam ID:PF00177

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eS6
Chain IDs:EB (auth: SG)
Chain Length:249
Number of Molecules:1
Biological Source:Sus scrofa

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eS7
Gene (Uniprot):RPS7
Chain IDs:FB (auth: SH)
Chain Length:194
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:A0A287A9Y6 Pfam ID:PF01251

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eS8
Chain IDs:GB (auth: SI)
Chain Length:208
Number of Molecules:1
Biological Source:Sus scrofa

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uS4
Chain IDs:HB (auth: SJ)
Chain Length:194
Number of Molecules:1
Biological Source:Sus scrofa

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eS10
Chain IDs:IB (auth: SK)
Chain Length:165
Number of Molecules:1
Biological Source:Sus scrofa

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uS17
Chain IDs:JB (auth: SL)
Chain Length:158
Number of Molecules:1
Biological Source:Sus scrofa

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eS12
Gene (Uniprot):RPS12
Chain IDs:KB (auth: SM)
Chain Length:124
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:P46405 Pfam ID:PF01248

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uS15
Chain IDs:LB (auth: SN)
Chain Length:151
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:A0A4X1TFR5 Pfam ID:PF08069, PF00312

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uS11
Chain IDs:MB (auth: SO)
Chain Length:151
Number of Molecules:1
Biological Source:Sus scrofa

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uS19
Gene (Uniprot):RPS15
Chain IDs:NB (auth: SP)
Chain Length:145
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:P62844 Pfam ID:PF00203

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uS9
Gene (Uniprot):RPS16
Chain IDs:OB (auth: SQ)
Chain Length:146
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:Q29201 Pfam ID:PF00380

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eS17
Gene (Uniprot):RPS17
Chain IDs:PB (auth: SR)
Chain Length:135
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:Q6QAP7 Pfam ID:PF00833

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uS13
Gene (Uniprot):RPS18
Chain IDs:QB (auth: SS)
Chain Length:152
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:P62272 Pfam ID:PF00416

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eS19
Chain IDs:RB (auth: ST)
Chain Length:145
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:A0A4X1SDD8 Pfam ID:PF01090

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uS10
Gene (Uniprot):RPS20
Chain IDs:SB (auth: SU)
Chain Length:119
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:A1XQU9 Pfam ID:PF00338

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eS21
Gene (Uniprot):RPS21
Chain IDs:TB (auth: SV)
Chain Length:83
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:P63221 Pfam ID:PF01249

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uS8
Chain IDs:UB (auth: SW)
Chain Length:130
Number of Molecules:1
Biological Source:Sus scrofa

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uS12
Gene (Uniprot):RPS23
Chain IDs:VB (auth: SX)
Chain Length:143
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:Q6SA96 Pfam ID:PF00164

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eS24
Gene (Uniprot):RPS24
Chain IDs:WB (auth: SY)
Chain Length:132
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:A0A4X1SJK8 Pfam ID:PF01282

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein es25
Chain IDs:XB (auth: SZ)
Chain Length:125
Number of Molecules:1
Biological Source:Sus scrofa

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eS26
Gene (Uniprot):RPS26
Chain IDs:YB (auth: Sa)
Chain Length:295
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:P49171 Pfam ID:PF01283

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eS27
Chain IDs:ZB (auth: Sb)
Chain Length:264
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:A0A4X1W2B6 Pfam ID:PF01667

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eS28
Gene (Uniprot):RPS28
Chain IDs:AC (auth: Sc)
Chain Length:69
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:Q6QAT1 Pfam ID:PF01200

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uS14
Gene (Uniprot):RPS29
Chain IDs:BC (auth: Sd)
Chain Length:56
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:Q6QAP6 Pfam ID:PF00253

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eS30
Chain IDs:CC (auth: Se)
Chain Length:263
Number of Molecules:1
Biological Source:Sus scrofa

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eS31
Gene (Uniprot):RPS27A
Chain IDs:DC (auth: Sf)
Chain Length:156
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:A0A4X1W6H9 Pfam ID:PF00240, PF01599

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein RACK1
Gene (Uniprot):RACK1
Chain IDs:EC (auth: Sg)
Chain Length:249
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:P63246 Pfam ID:PF00400

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL21
Gene (Uniprot):RPL21
Chain IDs:V (auth: T)
Chain Length:160
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:P49666 Pfam ID:PF01157

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL22
Gene (Uniprot):RPL22
Chain IDs:W (auth: U)
Chain Length:128
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:P67985 Pfam ID:PF01776

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL14
Chain IDs:X (auth: V)
Chain Length:140
Number of Molecules:1
Biological Source:Sus scrofa

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL24
Gene (Uniprot):RPL24
Chain IDs:Y (auth: W)
Chain Length:157
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:A0A4X1SH42 Pfam ID:PF01246

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL23
Chain IDs:Z (auth: X)
Chain Length:156
Number of Molecules:1
Biological Source:Sus scrofa

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL24
Gene (Uniprot):RPL26
Chain IDs:AA (auth: Y)
Chain Length:145
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:A0A4X1V977 Pfam ID:PF16906, PF00467

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL27
Gene (Uniprot):RPL27
Chain IDs:BA (auth: Z)
Chain Length:217
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:A1XQU5 Pfam ID:PF00467, PF01777

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL15
Chain IDs:CA (auth: a)
Chain Length:257
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:A0A4X1SN08 Pfam ID:PF00828

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL29
Gene (Uniprot):RPL29
Chain IDs:DA (auth: b)
Chain Length:394
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:Q95281 Pfam ID:PF01779

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL30
Gene (Uniprot):RPL30
Chain IDs:EA (auth: c)
Chain Length:115
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:A0A4X1TXJ8 Pfam ID:PF01248

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL31
Gene (Uniprot):RPL31
Chain IDs:FA (auth: d)
Chain Length:125
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:P62901 Pfam ID:PF01198

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL32
Gene (Uniprot):RPL32
Chain IDs:GA (auth: e)
Chain Length:135
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:Q6QAT0 Pfam ID:PF01655

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL33
Chain IDs:HA (auth: f)
Chain Length:110
Number of Molecules:1
Biological Source:Sus scrofa

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL34
Gene (Uniprot):RPL34
Chain IDs:IA (auth: g)
Chain Length:266
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:Q29223 Pfam ID:PF01199

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL29
Gene (Uniprot):RPL35
Chain IDs:JA (auth: h)
Chain Length:192
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:Q29361 Pfam ID:PF00831

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL36
Chain IDs:KA (auth: i)
Chain Length:213
Number of Molecules:1
Biological Source:Sus scrofa

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL37
Chain IDs:LA (auth: j)
Chain Length:178
Number of Molecules:1
Biological Source:Sus scrofa

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL38
Chain IDs:MA (auth: k)
Chain Length:70
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:A0A4X1VLH7 Pfam ID:PF01781

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL39
Chain IDs:NA (auth: l)
Chain Length:51
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:K7GP63 Pfam ID:PF00832

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL40
Gene (Uniprot):UBA52
Chain IDs:OA (auth: m)
Chain Length:128
Number of Molecules:1
Biological Source:Sus scrofa

UniProt ID:P63053 Pfam ID:PF00240, PF01020

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL41
Chain IDs:PA (auth: n)
Chain Length:204
Number of Molecules:1
Biological Source:Sus scrofa

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL42
Chain IDs:QA (auth: o)
Chain Length:106
Number of Molecules:1
Biological Source:Sus scrofa

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL43
Chain IDs:RA (auth: p)
Chain Length:153
Number of Molecules:1
Biological Source:Sus scrofa

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein eL28
Chain IDs:SA (auth: r)
Chain Length:125
Number of Molecules:1
Biological Source:Sus scrofa

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL1
Chain IDs:TA (auth: z)
Chain Length:217
Number of Molecules:1
Biological Source:Sus scrofa

Ligand Molecules

Primary Citation

Structure of the Mammalian ribosome-sec61 complex to 3.4 a resolution.

Voorhees, R.M, Fernandez, I.S, Scheres, S.H, Hegde, R.S.Show

Cell(Cambridge,Mass.) 157 1632 1643 (2014)

PMID: 24930395 DOI: 10.1016/j.cell.2014.05.024

Abstact

Cotranslational protein translocation is a universally conserved process for secretory and membrane protein biosynthesis. Nascent polypeptides emerging from a translating ribosome are either transported across or inserted into the membrane via the ribosome-bound Sec61 channel. Here, we report structures of a mammalian ribosome-Sec61 complex in both idle and translating states, determined to 3.4 and 3.9 Å resolution. The data sets permit building of a near-complete atomic model of the mammalian ribosome, visualization of A/P and P/E hybrid-state tRNAs, and analysis of a nascent polypeptide in the exit tunnel. Unprecedented chemical detail is observed for both the ribosome-Sec61 interaction and the conformational state of Sec61 upon ribosome binding. Comparison of the maps from idle and translating complexes suggests how conformational changes to the Sec61 channel could facilitate translocation of a secreted polypeptide. The high-resolution structure of the mammalian ribosome-Sec61 complex provides a valuable reference for future functional and structural studies.

Legend

Protein

Chemical

Disease

Primary Citation of related structures