4V7I

Ribosome-SecY complex.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.6 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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

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

(2009) Structure 17: 1453-1464

  • DOI: 10.1016/j.str.2009.09.010
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 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 com ...

    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.


    Organizational Affiliation

    Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PREPROTEIN TRANSLOCASE SECY SUBUNIT
AA
442N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
PREPROTEIN TRANSLOCASE SECE SUBUNIT
AB
65N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Preprotein translocase subunit secG
AC
53Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)Mutation(s): 0 
Gene Names: secG
Find proteins for P60460 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Go to UniProtKB:  P60460
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L1
A5
234Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplA
Find proteins for P0A7L0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L0
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
A6
273Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplB
Find proteins for P60422 (Escherichia coli (strain K12))
Go to UniProtKB:  P60422
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
AD
209Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplC
Find proteins for P60438 (Escherichia coli (strain K12))
Go to UniProtKB:  P60438
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
AE
201Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplD (eryA)
Find proteins for P60723 (Escherichia coli (strain K12))
Go to UniProtKB:  P60723
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
AF
179Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplE
Find proteins for P62399 (Escherichia coli (strain K12))
Go to UniProtKB:  P62399
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
AG
177Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplF
Find proteins for P0AG55 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG55
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
AH
149Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplI
Find proteins for P0A7R1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R1
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
AI
142Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplK (relC)
Find proteins for P0A7J7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7J7
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
AJ
142Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplM
Find proteins for P0AA10 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AA10
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
AK
123Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplN
Find proteins for P0ADY3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY3
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
AL
144Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplO
Find proteins for P02413 (Escherichia coli (strain K12))
Go to UniProtKB:  P02413
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
AM
136Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplP
Find proteins for P0ADY7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY7
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
AN
127Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplQ
Find proteins for P0AG44 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG44
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
AO
117Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplR
Find proteins for P0C018 (Escherichia coli (strain K12))
Go to UniProtKB:  P0C018
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
AP
115Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplS
Find proteins for P0A7K6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7K6
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
AQ
118Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplT (pdzA)
Find proteins for P0A7L3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L3
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
AR
103Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplU
Find proteins for P0AG48 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG48
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
AS
110Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplV (eryB)
Find proteins for P61175 (Escherichia coli (strain K12))
Go to UniProtKB:  P61175
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
AT
100Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplW
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ0
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
AU
104Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplX
Find proteins for P60624 (Escherichia coli (strain K12))
Go to UniProtKB:  P60624
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
AV
94Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplY
Find proteins for P68919 (Escherichia coli (strain K12))
Go to UniProtKB:  P68919
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
AW
85Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmA
Find proteins for P0A7L8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L8
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
AX
78Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmB
Find proteins for P0A7M2 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M2
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
AY
63Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmC
Find proteins for P0A7M6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M6
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
AZ
59Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmD
Find proteins for P0AG51 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG51
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
A0
57Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmF
Find proteins for P0A7N4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N4
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
A1
55Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmG
Find proteins for P0A7N9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N9
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
A2
46Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmH (rimA, ssaF)
Find proteins for P0A7P5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7P5
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
A3
65Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmI
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q1
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
A4
38Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmJ
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q6
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
BB
241Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsB
Find proteins for P0A7V0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V0
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
BC
233Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsC
Find proteins for P0A7V3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V3
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
BD
206Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsD (ramA)
Find proteins for P0A7V8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V8
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
BE
167Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsE (spc)
Find proteins for P0A7W1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W1
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
BF
135Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsF
Find proteins for P02358 (Escherichia coli (strain K12))
Go to UniProtKB:  P02358
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
BG
179Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsG
Find proteins for P02359 (Escherichia coli (strain K12))
Go to UniProtKB:  P02359
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
BH
130Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsH
Find proteins for P0A7W7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W7
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
BI
130Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsI
Find proteins for P0A7X3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7X3
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
BJ
103Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsJ (nusE)
Find proteins for P0A7R5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R5
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
BK
129Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsK
Find proteins for P0A7R9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R9
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
BL
124Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsL (strA)
Find proteins for P0A7S3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S3
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
BM
118Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsM
Find proteins for P0A7S9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S9
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
BN
101Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsN
Find proteins for P0AG59 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG59
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
BO
89Escherichia coli O157:H7Mutation(s): 0 
Gene Names: rpsO
Find proteins for Q8X9M2 (Escherichia coli O157:H7)
Go to UniProtKB:  Q8X9M2
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
BP
82Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsP
Find proteins for P0A7T3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T3
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
BQ
84Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsQ (neaA)
Find proteins for P0AG63 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG63
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
BR
75Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsR
Find proteins for P0A7T7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T7
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
BS
92Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsS
Find proteins for P0A7U3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U3
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
BT
87Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsT
Find proteins for P0A7U7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U7
Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
BU
71Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsU
Find proteins for P68679 (Escherichia coli (strain K12))
Go to UniProtKB:  P68679
Entity ID: 1
MoleculeChainsLengthOrganism
5S ribosomal RNAA7120Escherichia coli
Entity ID: 2
MoleculeChainsLengthOrganism
23S ribosomal RNAA82904Escherichia coli
Entity ID: 36
MoleculeChainsLengthOrganism
16S ribosomal RNABA1542Escherichia coli
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.6 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Type: Other
  • Version 1.2: 2015-04-22
    Type: Other
  • Version 1.3: 2018-07-18
    Type: Data collection, Other