ISDA: 4V7I

Deposition Date 2009-10-21

Release Date 2014-07-09

Last Version Date 2024-02-28

Entry Detail

PDB ID:

4V7I

Keywords:

RIBOSOME

Title:

Ribosome-SecY complex.

Biological Source:

Source Organism:

Escherichia coli (Taxon ID: 562)
Methanocaldococcus jannaschii (Taxon ID: 2190)
Escherichia coli K-12 (Taxon ID: 83333)
Escherichia coli (Taxon ID: 83334)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

9.60 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

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Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:EA (auth: A0)
Chain Length:57
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P0A7N4 Pfam ID:PF01783

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Gene (Uniprot):rpmG
Chain IDs:FA (auth: A1)
Chain Length:55
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P0A7N9 Pfam ID:PF00471

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:GA (auth: A2)
Chain Length:46
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P0A7P5 Pfam ID:PF00468

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:HA (auth: A3)
Chain Length:65
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P0A7Q1 Pfam ID:PF01632

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:IA (auth: A4)
Chain Length:38
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P0A7Q6 Pfam ID:PF00444

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L1
Gene (Uniprot):rplA
Chain IDs:F (auth: A5)
Chain Length:234
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P0A7L0 Pfam ID:PF00687

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:G (auth: A6)
Chain Length:273
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P60422 Pfam ID:PF00181, PF03947

Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:A (auth: A7)
Chain Length:120
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:B (auth: A8)
Chain Length:2904
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:PREPROTEIN TRANSLOCASE SECY SUBUNIT
Chain IDs:C (auth: AA)
Chain Length:442
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:PREPROTEIN TRANSLOCASE SECE SUBUNIT
Chain IDs:D (auth: AB)
Chain Length:65
Number of Molecules:1
Biological Source:Escherichia coli

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Preprotein translocase subunit secG
Gene (Uniprot):secG
Chain IDs:E (auth: AC)
Chain Length:53
Number of Molecules:1
Biological Source:Methanocaldococcus jannaschii

UniProt ID:P60460 Pfam ID:PF03911

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:H (auth: AD)
Chain Length:209
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P60438 Pfam ID:PF00297

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:I (auth: AE)
Chain Length:201
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P60723 Pfam ID:PF00573

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:J (auth: AF)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P62399 Pfam ID:PF00281, PF00673

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Gene (Uniprot):rplF
Chain IDs:K (auth: AG)
Chain Length:177
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P0AG55 Pfam ID:PF00347

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:L (auth: AH)
Chain Length:149
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P0A7R1 Pfam ID:PF01281, PF03948

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L11
Gene (Uniprot):rplK
Chain IDs:M (auth: AI)
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P0A7J7 Pfam ID:PF03946, PF00298

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:N (auth: AJ)
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P0AA10 Pfam ID:PF00572

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:O (auth: AK)
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P0ADY3 Pfam ID:PF00238

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:P (auth: AL)
Chain Length:144
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P02413 Pfam ID:PF00828

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:Q (auth: AM)
Chain Length:136
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P0ADY7 Pfam ID:PF00252

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:R (auth: AN)
Chain Length:127
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P0AG44 Pfam ID:PF01196

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:S (auth: AO)
Chain Length:117
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P0C018 Pfam ID:PF00861

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:T (auth: AP)
Chain Length:115
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P0A7K6 Pfam ID:PF01245

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:U (auth: AQ)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P0A7L3 Pfam ID:PF00453

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:V (auth: AR)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P0AG48 Pfam ID:PF00829

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:W (auth: AS)
Chain Length:110
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P61175 Pfam ID:PF00237

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:X (auth: AT)
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P0ADZ0 Pfam ID:PF00276

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:Y (auth: AU)
Chain Length:104
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P60624 Pfam ID:PF00467, PF17136

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:Z (auth: AV)
Chain Length:94
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P68919 Pfam ID:PF01386

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:AA (auth: AW)
Chain Length:85
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P0A7L8 Pfam ID:PF01016

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:BA (auth: AX)
Chain Length:78
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P0A7M2 Pfam ID:PF00830

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:CA (auth: AY)
Chain Length:63
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P0A7M6 Pfam ID:PF00831

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:DA (auth: AZ)
Chain Length:59
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P0AG51 Pfam ID:PF00327

Polymer Type:polyribonucleotide
Molecule:16S ribosomal RNA
Chain IDs:JA (auth: BA)
Chain Length:1542
Number of Molecules:1
Biological Source:Escherichia coli

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:KA (auth: BB)
Chain Length:241
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P0A7V0 Pfam ID:PF00318

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:LA (auth: BC)
Chain Length:233
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P0A7V3 Pfam ID:PF07650, PF00189

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:MA (auth: BD)
Chain Length:206
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P0A7V8 Pfam ID:PF00163, PF01479

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Gene (Uniprot):rpsE
Chain IDs:NA (auth: BE)
Chain Length:167
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P0A7W1 Pfam ID:PF00333, PF03719

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:OA (auth: BF)
Chain Length:135
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P02358 Pfam ID:PF01250

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:PA (auth: BG)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P02359 Pfam ID:PF00177

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Gene (Uniprot):rpsH
Chain IDs:QA (auth: BH)
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P0A7W7 Pfam ID:PF00410

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:RA (auth: BI)
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P0A7X3 Pfam ID:PF00380

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Gene (Uniprot):rpsJ
Chain IDs:SA (auth: BJ)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P0A7R5 Pfam ID:PF00338

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:TA (auth: BK)
Chain Length:129
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P0A7R9 Pfam ID:PF00411

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Gene (Uniprot):rpsL
Chain IDs:UA (auth: BL)
Chain Length:124
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P0A7S3 Pfam ID:PF00164

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:VA (auth: BM)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P0A7S9 Pfam ID:PF00416

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14
Gene (Uniprot):rpsN
Chain IDs:WA (auth: BN)
Chain Length:101
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P0AG59 Pfam ID:PF00253

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:XA (auth: BO)
Chain Length:89
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:Q8X9M2 Pfam ID:PF00312

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:YA (auth: BP)
Chain Length:82
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P0A7T3 Pfam ID:PF00886

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Gene (Uniprot):rpsQ
Chain IDs:ZA (auth: BQ)
Chain Length:84
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P0AG63 Pfam ID:PF00366

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:AB (auth: BR)
Chain Length:75
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P0A7T7 Pfam ID:PF01084

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:BB (auth: BS)
Chain Length:92
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P0A7U3 Pfam ID:PF00203

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:CB (auth: BT)
Chain Length:87
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P0A7U7 Pfam ID:PF01649

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S21
Gene (Uniprot):rpsU
Chain IDs:DB (auth: BU)
Chain Length:71
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P68679 Pfam ID:PF01165

Ligand Molecules

Primary Citation

Regulation of the protein-conducting channel by a bound ribosome.

Gumbart, J, Trabuco, L.G, Schreiner, E, Villa, E, Schulten, K.Show

Structure 17 1453 1464 (2009)

PMID: 19913480 DOI: 10.1016/j.str.2009.09.010

Abstact

During protein synthesis, it is often necessary for the ribosome to form a complex with a membrane-bound channel, the SecY/Sec61 complex, in order to translocate nascent proteins across a cellular membrane. Structural data on the ribosome-channel complex are currently limited to low-resolution cryo-electron microscopy maps, including one showing a bacterial ribosome bound to a monomeric SecY complex. Using that map along with available atomic-level models of the ribosome and SecY, we have determined, through molecular dynamics flexible fitting (MDFF), an atomic-resolution model of the ribosome-channel complex. We characterized computationally the sites of ribosome-SecY interaction within the complex and determined the effect of ribosome binding on the SecY channel. We also constructed a model of a ribosome in complex with a SecY dimer by adding a second copy of SecY to the MDFF-derived model. The study involved 2.7-million-atom simulations over altogether nearly 50 ns.

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Protein

Chemical

Disease

Primary Citation of related structures