ISDA

Deposition Date 2013-11-22

Release Date 2014-07-09

Last Version Date 2024-11-20

Entry Detail

PDB ID:

4V7E

Keywords:

RIBOSOME

Title:

Model of the small subunit RNA based on a 5.5 A cryo-EM map of Triticum aestivum translating 80S ribosome

Biological Source:

Source Organism:

Triticum aestivum (Taxon ID: 4565)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

5.50 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:60S ribosomal RNA
Chain IDs:HC (auth: Aa)
Chain Length:3391
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:JC (auth: Ab)
Chain Length:120
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polyribonucleotide
Molecule:5.8S ribosomal RNA
Chain IDs:IC (auth: Ac)
Chain Length:160
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polyribonucleotide
Molecule:18S ribosomal RNA
Chain IDs:A (auth: Ad)
Chain Length:1810
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polyribonucleotide
Molecule:P-site tRNA
Chain IDs:B (auth: Ae)
Chain Length:75
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polyribonucleotide
Molecule:5'-R(*AP*AP*AP*AP*GP*AP*CP*UP*UP*CP*A)-3'
Chain IDs:C (auth: Af)
Chain Length:11
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S2
Chain IDs:BA
Chain Length:133
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S1E
Chain IDs:DA (auth: BB)
Chain Length:86
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S5
Chain IDs:HA (auth: BC)
Chain Length:263
Number of Molecules:1
Biological Source:Triticum aestivum

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S3
Chain IDs:K (auth: BD)
Chain Length:208
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:Q8L804 Pfam ID:PF07650, PF00189

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S4E
Chain IDs:L (auth: BE)
Chain Length:265
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S7
Chain IDs:M (auth: BF)
Chain Length:191
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S6
Chain IDs:IA (auth: BG)
Chain Length:380
Number of Molecules:1
Biological Source:Triticum aestivum

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S7E
Gene (Uniprot):LOC123085612
Chain IDs:JA (auth: BH)
Chain Length:189
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:Q5I7K2 Pfam ID:PF01251

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S8E
Chain IDs:E (auth: BI)
Chain Length:220
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S4
Chain IDs:GA (auth: BJ)
Chain Length:195
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S10E
Chain IDs:F (auth: BK)
Chain Length:183
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S17
Chain IDs:S (auth: BL)
Chain Length:160
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S12E
Chain IDs:G (auth: BM)
Chain Length:171
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S15
Chain IDs:R (auth: BN)
Chain Length:151
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S11
Chain IDs:P (auth: BO)
Chain Length:151
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S19
Chain IDs:U (auth: BP)
Chain Length:154
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S9
Chain IDs:N (auth: BQ)
Chain Length:149
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S17E
Chain IDs:CA (auth: BR)
Chain Length:141
Number of Molecules:1
Biological Source:Triticum aestivum

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S13
Gene (Uniprot):LOC123105378
Chain IDs:Q (auth: BS)
Chain Length:152
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:Q8L806 Pfam ID:PF00416

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S19E
Chain IDs:T (auth: BT)
Chain Length:146
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S10
Chain IDs:O (auth: BU)
Chain Length:128
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S21E
Chain IDs:EA (auth: BV)
Chain Length:82
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S8
Chain IDs:X (auth: BW)
Chain Length:130
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S12
Chain IDs:I (auth: BX)
Chain Length:142
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S24E
Chain IDs:D (auth: BY)
Chain Length:138
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S25E
Chain IDs:V (auth: BZ)
Chain Length:108
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S26E
Chain IDs:FA (auth: Ba)
Chain Length:133
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S27E
Chain IDs:Z (auth: Bb)
Chain Length:86
Number of Molecules:1
Biological Source:Triticum aestivum

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S28E
Chain IDs:W (auth: Bc)
Chain Length:263
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:Q7X9K4 Pfam ID:PF01200

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S14
Gene (Uniprot):RPS29
Chain IDs:Y (auth: Bd)
Chain Length:208
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:Q5I7K3 Pfam ID:PF00253

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S30E
Chain IDs:AA (auth: Be)
Chain Length:265
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S31e
Chain IDs:H (auth: Bf)
Chain Length:191
Number of Molecules:1
Biological Source:Triticum aestivum

Protein Blast

Polymer Type:polypeptide(L)
Molecule:RACK1
Gene (Uniprot):TaGB1
Chain IDs:J (auth: Bg)
Chain Length:380
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:Q8LNY6 Pfam ID:PF00400

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L2
Chain IDs:OA (auth: CA)
Chain Length:261
Number of Molecules:1
Biological Source:Triticum aestivum

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L3
Gene (Uniprot):LOC123120076
Chain IDs:UB (auth: CB)
Chain Length:389
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:Q7X744 Pfam ID:PF00297

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L4
Chain IDs:VB (auth: CC)
Chain Length:112
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18
Chain IDs:VA (auth: CD)
Chain Length:304
Number of Molecules:1
Biological Source:Triticum aestivum

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L6E
Chain IDs:CC (auth: CE)
Chain Length:219
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:Q5I7L4 Pfam ID:PF01159

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L30
Chain IDs:SB (auth: CF)
Chain Length:111
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:Q5I7K6 Pfam ID:PF08079, PF00327

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L8E
Chain IDs:KA (auth: CG)
Chain Length:119
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L6
Chain IDs:QA (auth: CH)
Chain Length:190
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L16
Chain IDs:YB (auth: CI)
Chain Length:224
Number of Molecules:1
Biological Source:Triticum aestivum

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L5
Chain IDs:PA (auth: CJ)
Chain Length:94
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:Q5I7L2 Pfam ID:PF00281, PF00673

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L11
Chain IDs:MB (auth: CK)
Chain Length:166
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13E
Chain IDs:BC (auth: CL)
Chain Length:208
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L14E
Chain IDs:IB (auth: CM)
Chain Length:134
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L15E
Chain IDs:SA (auth: CN)
Chain Length:25
Number of Molecules:1
Biological Source:Triticum aestivum

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13
Chain IDs:WB (auth: CO)
Chain Length:206
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:Q5I7L1 Pfam ID:PF00572

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L22
Chain IDs:XA (auth: CP)
Chain Length:171
Number of Molecules:1
Biological Source:Triticum aestivum

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18E
Chain IDs:UA (auth: CQ)
Chain Length:319
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:Q5I7L0 Pfam ID:PF17135

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L19E
Chain IDs:WA (auth: CR)
Chain Length:209
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:Q7XY20 Pfam ID:PF01280

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L20
Chain IDs:JB (auth: CS)
Chain Length:178
Number of Molecules:1
Biological Source:Triticum aestivum

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L21E
Chain IDs:LA (auth: CT)
Chain Length:164
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:A0A9R1HBE9

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L22E
Chain IDs:KB (auth: CU)
Chain Length:110
Number of Molecules:1
Biological Source:Triticum aestivum

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L14
Chain IDs:RA (auth: CV)
Chain Length:140
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:Q5I7K4 Pfam ID:PF00238

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L24E
Chain IDs:ZA (auth: CW)
Chain Length:162
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23
Chain IDs:YA (auth: CX)
Chain Length:152
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L24
Chain IDs:AB (auth: CY)
Chain Length:150
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27E
Chain IDs:MA (auth: CZ)
Chain Length:216
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L15
Chain IDs:TA (auth: Ca)
Chain Length:261
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L29E
Chain IDs:FC (auth: Cb)
Chain Length:389
Number of Molecules:1
Biological Source:Triticum aestivum

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L30E
Chain IDs:CB (auth: Cc)
Chain Length:112
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:Q5I7K9 Pfam ID:PF01248

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L31E
Chain IDs:DB (auth: Cd)
Chain Length:304
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L32E
Chain IDs:EB (auth: Ce)
Chain Length:219
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L33E
Chain IDs:DC (auth: Cf)
Chain Length:111
Number of Molecules:1
Biological Source:Triticum aestivum

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L34E
Chain IDs:GC (auth: Cg)
Chain Length:119
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:Q5I7K8 Pfam ID:PF01199

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L29
Gene (Uniprot):RPL35
Chain IDs:RB (auth: Ch)
Chain Length:190
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:Q8L805 Pfam ID:PF00831

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L36E
Chain IDs:LB (auth: Ci)
Chain Length:224
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:A0A9R1H1R6

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L37E
Chain IDs:FB (auth: Cj)
Chain Length:94
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L38E
Chain IDs:EC (auth: Ck)
Chain Length:166
Number of Molecules:1
Biological Source:Triticum aestivum

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L39E
Gene (Uniprot):LOC123167131
Chain IDs:GB (auth: Cl)
Chain Length:208
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:Q5I7K7 Pfam ID:PF00832

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L40E
Chain IDs:AC (auth: Cm)
Chain Length:134
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L41E
Chain IDs:ZB (auth: Cn)
Chain Length:25
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L44E
Chain IDs:HB (auth: Co)
Chain Length:206
Number of Molecules:1
Biological Source:Triticum aestivum

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L43E
Gene (Uniprot):TAA_ctg0616b.00240.1, TRAES_3BF073800030CFD_c1
Chain IDs:XB (auth: Cp)
Chain Length:171
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:D8L9P6 Pfam ID:PF01780

Polymer Type:polypeptide(L)
Molecule:60S acidic ribosomal protein P0
Chain IDs:TB (auth: Cq)
Chain Length:319
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L28E
Chain IDs:BB (auth: Cr)
Chain Length:209
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polypeptide(L)
Molecule:Acidic ribosomal protein P2
Chain IDs:PB (auth: Cs), QB (auth: Ct)
Chain Length:178
Number of Molecules:2
Biological Source:Triticum aestivum

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein P1
Gene (Uniprot):LOC606341
Chain IDs:NB (auth: Cu), OB (auth: Cv)
Chain Length:110
Number of Molecules:2
Biological Source:Triticum aestivum

UniProt ID:Q5I7K5 Pfam ID:PF00428

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L1
Chain IDs:NA (auth: Cz)
Chain Length:216
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:Q5I7L3 Pfam ID:PF00687

Ligand Molecules

Primary Citation

Structures of the Sec61 complex engaged in nascent peptide translocation or membrane insertion.

Gogala, M, Becker, T, Beatrix, B, Armache, J.-P, Barrio-Garcia, C, Berninghausen, O, Beckmann, R, Armache, J.-P, Jarasch, A, Anger, A.M, Villa, E, Becker, T, Bhushan, S, Jossinet, F, Habeck, M, Dindar, G, Franckenberg, S, Marquez, V, Mielke, T, Thomm, M, Berninghausen, O, Beatrix, B, Soding, J, Westhof, E, Wilson, D.N, Beckmann, R, Armache, J.-P, Jarasch, A, Anger, A.M, Villa, E, Becker, T, Bhushan, S, Jossinet, F, Habeck, M, Dindar, G, Franckenberg, S, Marquez, V, Mielke, T, Thomm, M, Berninghausen, O, Beatrix, B, Soding, J, Westhof, E, Wilson, D.N, Beckmann, R.Show

Nature 506 107 110 (2014)

PMID: 24499919 DOI: 10.1038/nature12950

Abstact

The biogenesis of secretory as well as transmembrane proteins requires the activity of the universally conserved protein-conducting channel (PCC), the Sec61 complex (SecY complex in bacteria). In eukaryotic cells the PCC is located in the membrane of the endoplasmic reticulum where it can bind to translating ribosomes for co-translational protein transport. The Sec complex consists of three subunits (Sec61α, β and γ) and provides an aqueous environment for the translocation of hydrophilic peptides as well as a lateral opening in the Sec61α subunit that has been proposed to act as a gate for the membrane partitioning of hydrophobic domains. A plug helix and a so-called pore ring are believed to seal the PCC against ion flow and are proposed to rearrange for accommodation of translocating peptides. Several crystal and cryo-electron microscopy structures revealed different conformations of closed and partially open Sec61 and SecY complexes. However, in none of these samples has the translocation state been unambiguously defined biochemically. Here we present cryo-electron microscopy structures of ribosome-bound Sec61 complexes engaged in translocation or membrane insertion of nascent peptides. Our data show that a hydrophilic peptide can translocate through the Sec complex with an essentially closed lateral gate and an only slightly rearranged central channel. Membrane insertion of a hydrophobic domain seems to occur with the Sec complex opening the proposed lateral gate while rearranging the plug to maintain an ion permeability barrier. Taken together, we provide a structural model for the basic activities of the Sec61 complex as a protein-conducting channel.

Legend

Protein

Chemical

Disease

Primary Citation of related structures