4V6M

Structure of the ribosome-SecYE complex in the membrane environment


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.1 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Cryo-EM structure of the ribosome-SecYE complex in the membrane environment.

Frauenfeld, J.Gumbart, J.Sluis, E.O.Funes, S.Gartmann, M.Beatrix, B.Mielke, T.Berninghausen, O.Becker, T.Schulten, K.Beckmann, R.

(2011) Nat.Struct.Mol.Biol. 18: 614-621

  • DOI: 10.1038/nsmb.2026
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The ubiquitous SecY-Sec61 complex translocates nascent secretory proteins across cellular membranes and integrates membrane proteins into lipid bilayers. Several structures of mostly detergent-solubilized Sec complexes have been reported. Here we pre ...

    The ubiquitous SecY-Sec61 complex translocates nascent secretory proteins across cellular membranes and integrates membrane proteins into lipid bilayers. Several structures of mostly detergent-solubilized Sec complexes have been reported. Here we present a single-particle cryo-EM structure of the SecYEG complex in a membrane environment, bound to a translating ribosome, at subnanometer resolution. Using the SecYEG complex reconstituted in a so-called Nanodisc, we could trace the nascent polypeptide chain from the peptidyltransferase center into the membrane. The reconstruction allowed for the identification of ribosome-lipid interactions. The rRNA helix 59 (H59) directly contacts the lipid surface and appears to modulate the membrane in immediate vicinity to the proposed lateral gate of the protein-conducting channel (PCC). On the basis of our map and molecular dynamics simulations, we present a model of a signal anchor-gated PCC in the membrane.


    Organizational Affiliation

    Gene Center, Department for Biochemistry, University of Munich, Munich, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Cell division protein FtsQ
AZ
98Escherichia coli O157:H7Mutation(s): 0 
Gene Names: ftsQ
Find proteins for Q8X9Y5 (Escherichia coli O157:H7)
Go to UniProtKB:  Q8X9Y5
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Apolipoprotein A-I
A0, A1
200Homo sapiensMutation(s): 0 
Gene Names: APOA1
Find proteins for P02647 (Homo sapiens)
Go to Gene View: APOA1
Go to UniProtKB:  P02647
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
AB
240Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsB
Find proteins for P0A7V0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V0
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
AC
232Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsC
Find proteins for P0A7V3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V3
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
AD
205Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsD (ramA)
Find proteins for P0A7V8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V8
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
AE
166Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsE (spc)
Find proteins for P0A7W1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W1
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
AF
135Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsF
Find proteins for P02358 (Escherichia coli (strain K12))
Go to UniProtKB:  P02358
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
AG
178Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsG
Find proteins for P02359 (Escherichia coli (strain K12))
Go to UniProtKB:  P02359
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
AH
129Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsH
Find proteins for P0A7W7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W7
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
AI
129Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsI
Find proteins for P0A7X3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7X3
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
AJ
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: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
AK
128Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsK
Find proteins for P0A7R9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R9
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
AL
123Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsL (strA)
Find proteins for P0A7S3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S3
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
AM
117Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsO (secC)
Find proteins for P0ADZ4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ4
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
AN
100Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsN
Find proteins for P0AG59 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG59
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
AO
88N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
AP
82Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsP
Find proteins for P0A7T3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T3
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
AQ
83Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsQ (neaA)
Find proteins for P0AG63 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG63
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
AR
74Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsR
Find proteins for P0A7T7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T7
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
AS
91Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsS
Find proteins for P0A7U3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U3
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
AT
86Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsT
Find proteins for P0A7U7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U7
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
AU
70Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsU
Find proteins for P68679 (Escherichia coli (strain K12))
Go to UniProtKB:  P68679
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
Preprotein translocase secY subunit
BA
435N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
Preprotein translocase secE subunit
BB
116N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L1
B5
234Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplA
Find proteins for P0A7L0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L0
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
B6
272Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplB
Find proteins for P60422 (Escherichia coli (strain K12))
Go to UniProtKB:  P60422
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
BD
209Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplC
Find proteins for P60438 (Escherichia coli (strain K12))
Go to UniProtKB:  P60438
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
BE
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: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
BF
178Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplE
Find proteins for P62399 (Escherichia coli (strain K12))
Go to UniProtKB:  P62399
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
BG
176Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplF
Find proteins for P0AG55 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG55
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
BH
149Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplI
Find proteins for P0A7R1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R1
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
BI
141Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplK (relC)
Find proteins for P0A7J7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7J7
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
BJ
142Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplM
Find proteins for P0AA10 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AA10
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
BK
123Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplN
Find proteins for P0ADY3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY3
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
BL
144Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplO
Find proteins for P02413 (Escherichia coli (strain K12))
Go to UniProtKB:  P02413
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
BM
136Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplP
Find proteins for P0ADY7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY7
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
BN
127Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplQ
Find proteins for P0AG44 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG44
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
BO
117Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplR
Find proteins for P0C018 (Escherichia coli (strain K12))
Go to UniProtKB:  P0C018
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
BP
114Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplS
Find proteins for P0A7K6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7K6
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
BQ
117Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplT (pdzA)
Find proteins for P0A7L3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L3
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
BR
103Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplU
Find proteins for P0AG48 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG48
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
BS
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: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
BT
100Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplW
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ0
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
BU
103Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplX
Find proteins for P60624 (Escherichia coli (strain K12))
Go to UniProtKB:  P60624
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
BV
94Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplY
Find proteins for P68919 (Escherichia coli (strain K12))
Go to UniProtKB:  P68919
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
BW
84Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmA
Find proteins for P0A7L8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L8
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
BX
77Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmB
Find proteins for P0A7M2 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M2
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
BY
63Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmC
Find proteins for P0A7M6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M6
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
BZ
58Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmD
Find proteins for P0AG51 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG51
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
B0
56Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmF
Find proteins for P0A7N4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N4
Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
B1
54Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmG
Find proteins for P0A7N9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N9
Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
B2
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: 58
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
B3
64Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmI
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q1
Entity ID: 59
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
B4
38Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmJ
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q6
Entity ID: 1
MoleculeChainsLengthOrganism
16S RIBOSOMAL RNAAA1542Escherichia coli
Entity ID: 2
MoleculeChainsLengthOrganism
mRNAAX11Escherichia coli
Entity ID: 3
MoleculeChainsLengthOrganism
FtsQ nascent chainAV77Escherichia coli DH1
Entity ID: 26
MoleculeChainsLengthOrganism
5S RIBOSOMAL RNAB7120Escherichia coli DH1
Entity ID: 27
MoleculeChainsLengthOrganism
23S RIBOSOMAL RNAB82904Escherichia coli DH1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEV
Query on PEV

Download SDF File 
Download CCD File 
A0, A1, AZ, B8, BA, BB
(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
PHOSPHATIDYLETHANOLAMINE; 1-PALMITOYL-2-OLEOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
C39 H78 N O8 P
RPJZYOHZALDGKI-QNGWXLTQSA-N
 Ligand Interaction
PGV
Query on PGV

Download SDF File 
Download CCD File 
A0, A1, AZ, B8, BA, BB
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
PHOSPHATIDYLGLYCEROL, 2-VACCENOYL-1-PALMITOYL-SN-GLYCEROL-3-PHOSPHOGLYCEROL
C40 H77 O10 P
ADYWCMPUNIVOEA-GPJPVTGXSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.1 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: 2014-08-20
    Type: Database references, Structure summary
  • Version 1.2: 2014-12-10
    Type: Other
  • Version 1.3: 2015-04-01
    Type: Other
  • Version 1.4: 2018-07-18
    Type: Data collection