4V6M

Structure of the ribosome-SecYE complex in the membrane environment


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.5 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:  
    4V6M

  • 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 present a single-particle cryo-EM structure of the SecYEG complex in a membrane environment, bound to a translating ribosome, at subnanometer resolution ...

    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

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Cell division protein FtsQD [auth AZ]98Escherichia coli O157:H7Mutation(s): 0 
Gene Names: ftsQE5F08_03860ECs_0097
Membrane Entity: Yes 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Apolipoprotein A-IE [auth A0],
F [auth A1]
200Homo sapiensMutation(s): 0 
Gene Names: APOA1
Membrane Entity: Yes 
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GTEx:  ENSG00000118137 
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Entity ID: 6
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30S ribosomal protein S2G [auth AB]240Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsBb0169JW0164
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Entity ID: 7
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30S ribosomal protein S3H [auth AC]232Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsCb3314JW3276
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30S ribosomal protein S4I [auth AD]205Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S5J [auth AE]166Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S6K [auth AF]135Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S7L [auth AG]178Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S8M [auth AH]129Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S9N [auth AI]129Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S10O [auth AJ]103Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S11P [auth AK]128Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S12Q [auth AL]123Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S13R [auth AM]117Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S14S [auth AN]100Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S15T [auth AO]88Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S16U [auth AP]82Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S17V [auth AQ]83Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S18W [auth AR]74Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S19X [auth AS]91Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S20Y [auth AT]86Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsTb0023JW0022
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30S ribosomal protein S21Z [auth AU]70Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsUb3065JW3037
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Entity ID: 28
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Preprotein translocase secY subunitCA [auth BA]435Escherichia coli 536Mutation(s): 0 
Gene Names: secYECP_3388
Membrane Entity: Yes 
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Preprotein translocase secE subunitDA [auth BB]116Escherichia coli 536Mutation(s): 0 
Gene Names: secEECP_4194
Membrane Entity: Yes 
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50S ribosomal protein L1EA [auth B5]234Escherichia coli K-12Mutation(s): 0 
Gene Names: rplAb3984JW3947
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50S ribosomal protein L2FA [auth B6]272Escherichia coli K-12Mutation(s): 0 
Gene Names: rplBb3317JW3279
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50S ribosomal protein L3GA [auth BD]209Escherichia coli K-12Mutation(s): 0 
Gene Names: rplCb3320JW3282
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50S ribosomal protein L4HA [auth BE]201Escherichia coli K-12Mutation(s): 0 
Gene Names: rplDeryAb3319JW3281
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50S ribosomal protein L5IA [auth BF]178Escherichia coli K-12Mutation(s): 0 
Gene Names: rplEb3308JW3270
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50S ribosomal protein L6JA [auth BG]176Escherichia coli K-12Mutation(s): 0 
Gene Names: rplFb3305JW3267
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50S ribosomal protein L9KA [auth BH]149Escherichia coli K-12Mutation(s): 0 
Gene Names: rplIb4203JW4161
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50S ribosomal protein L11LA [auth BI]141Escherichia coli K-12Mutation(s): 0 
Gene Names: rplKrelCb3983JW3946
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50S ribosomal protein L13MA [auth BJ]142Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L14NA [auth BK]123Escherichia coli K-12Mutation(s): 0 
Gene Names: rplNb3310JW3272
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50S ribosomal protein L15OA [auth BL]144Escherichia coli K-12Mutation(s): 0 
Gene Names: rplOb3301JW3263
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50S ribosomal protein L16PA [auth BM]136Escherichia coli K-12Mutation(s): 0 
Gene Names: rplPb3313JW3275
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50S ribosomal protein L17QA [auth BN]127Escherichia coli K-12Mutation(s): 0 
Gene Names: rplQb3294JW3256
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50S ribosomal protein L18RA [auth BO]117Escherichia coli K-12Mutation(s): 0 
Gene Names: rplRb3304JW3266
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50S ribosomal protein L19SA [auth BP]114Escherichia coli K-12Mutation(s): 0 
Gene Names: rplSb2606JW2587
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50S ribosomal protein L20TA [auth BQ]117Escherichia coli K-12Mutation(s): 0 
Gene Names: rplTpdzAb1716JW1706
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50S ribosomal protein L21UA [auth BR]103Escherichia coli K-12Mutation(s): 0 
Gene Names: rplUb3186JW3153
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UniProt GroupP0AG48
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L22VA [auth BS]110Escherichia coli K-12Mutation(s): 0 
Gene Names: rplVeryBb3315JW3277
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Entity ID: 48
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50S ribosomal protein L23WA [auth BT]100Escherichia coli K-12Mutation(s): 0 
Gene Names: rplWb3318JW3280
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Entity ID: 49
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50S ribosomal protein L24XA [auth BU]103Escherichia coli K-12Mutation(s): 0 
Gene Names: rplXb3309JW3271
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Entity ID: 50
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50S ribosomal protein L25YA [auth BV]94Escherichia coli K-12Mutation(s): 0 
Gene Names: rplYb2185JW2173
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Entity ID: 51
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50S ribosomal protein L27ZA [auth BW]84Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmAb3185JW3152
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Entity ID: 52
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50S ribosomal protein L28AB [auth BX]77Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmBb3637JW3612
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Entity ID: 53
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50S ribosomal protein L29BB [auth BY]63Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmCb3312JW3274
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Entity ID: 54
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50S ribosomal protein L30CB [auth BZ]58Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmDb3302JW3264
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Entity ID: 55
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50S ribosomal protein L32DB [auth B0]56Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmFb1089JW1075
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Entity ID: 56
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50S ribosomal protein L33EB [auth B1]54Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmGb3636JW3611
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Entity ID: 57
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50S ribosomal protein L34FB [auth B2]46Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmHrimAssaFb3703JW3680
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Entity ID: 58
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50S ribosomal protein L35GB [auth B3]64Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmIb1717JW1707
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Entity ID: 59
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50S ribosomal protein L36HB [auth B4]38Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmJb3299JW3261
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Entity ID: 1
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16S RIBOSOMAL RNAA [auth AA]1542Escherichia coli
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Entity ID: 2
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mRNAB [auth AX]11Escherichia coli
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Entity ID: 3
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FtsQ nascent chainC [auth AV]77Escherichia coli DH1
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Entity ID: 26
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5S RIBOSOMAL RNAAA [auth B7]120Escherichia coli DH1
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Entity ID: 27
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23S RIBOSOMAL RNABA [auth B8]2904Escherichia coli DH1
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PGV
Query on PGV

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AF [auth BA],
AG [auth BB],
CE [auth B8],
FC [auth A0],
FD [auth A1],
AF [auth BA],
AG [auth BB],
CE [auth B8],
FC [auth A0],
FD [auth A1],
FE [auth BA],
FG [auth BB],
GC [auth A0],
JD [auth A1],
JE [auth BA],
JG [auth BB],
MB [auth AZ],
MD [auth A1],
NC [auth A0],
OB [auth AZ],
OF [auth BA],
PC [auth A0],
QC [auth A0],
QE [auth BA],
SB [auth A0],
SF [auth BA],
TB [auth A0],
TC [auth A0],
TE [auth BA],
UB [auth A0],
UC [auth A0],
UE [auth BA],
VF [auth BB],
WF [auth BB],
XC [auth A1],
XF [auth BB],
ZF [auth BB]
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
C40 H77 O10 P
ADYWCMPUNIVOEA-GPJPVTGXSA-N
 Ligand Interaction
PEV
Query on PEV

Download Ideal Coordinates CCD File 
AC [auth A0],
AD [auth A1],
AE [auth B8],
BC [auth A0],
BD [auth A1],
AC [auth A0],
AD [auth A1],
AE [auth B8],
BC [auth A0],
BD [auth A1],
BE [auth B8],
BF [auth BA],
BG [auth BB],
CC [auth A0],
CD [auth A1],
CF [auth BA],
CG [auth BB],
DC [auth A0],
DD [auth A1],
DE [auth B8],
DF [auth BA],
DG [auth BB],
EC [auth A0],
ED [auth A1],
EE [auth B8],
EF [auth BA],
EG [auth BB],
FF [auth BA],
GD [auth A1],
GE [auth BA],
GF [auth BA],
GG [auth BB],
HC [auth A0],
HD [auth A1],
HE [auth BA],
HF [auth BA],
HG [auth BB],
IB [auth AZ],
IC [auth A0],
ID [auth A1],
IE [auth BA],
IF [auth BA],
IG [auth BB],
JB [auth AZ],
JC [auth A0],
JF [auth BA],
KB [auth AZ],
KC [auth A0],
KD [auth A1],
KE [auth BA],
KF [auth BA],
KG [auth BB],
LB [auth AZ],
LC [auth A0],
LD [auth A1],
LE [auth BA],
LF [auth BA],
MC [auth A0],
ME [auth BA],
MF [auth BA],
NB [auth AZ],
ND [auth A1],
NE [auth BA],
NF [auth BA],
OC [auth A0],
OD [auth A1],
OE [auth BA],
PB [auth A0],
PD [auth A1],
PE [auth BA],
PF [auth BA],
QB [auth A0],
QD [auth A1],
QF [auth BA],
RB [auth A0],
RC [auth A0],
RD [auth A1],
RE [auth BA],
RF [auth BA],
SC [auth A0],
SD [auth A1],
SE [auth BA],
TD [auth A1],
TF [auth BB],
UD [auth A1],
UF [auth BB],
VB [auth A0],
VC [auth A1],
VD [auth A1],
VE [auth BA],
WB [auth A0],
WC [auth A1],
WD [auth A1],
WE [auth BA],
XB [auth A0],
XD [auth A1],
XE [auth BA],
YB [auth A0],
YC [auth A1],
YD [auth B8],
YE [auth BA],
YF [auth BB],
ZB [auth A0],
ZC [auth A1],
ZD [auth B8],
ZE [auth BA]
(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
C39 H78 N O8 P
RPJZYOHZALDGKI-QNGWXLTQSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-08-20
    Changes: Database references, Structure summary
  • Version 1.2: 2014-12-10
    Changes: Other
  • Version 1.3: 2015-04-01
    Changes: Other
  • Version 1.4: 2018-07-18
    Changes: Data collection
  • Version 1.5: 2019-12-18
    Changes: Database references, Other