Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 55-mer - A2BCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyzAB Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 55-mer -A2B2CDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyzA 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 2410929.25 
• Atom Count: 163040 
• Residue Count: 11892 
• Unique protein chains: 54
• Unique nucleic acid chains: 5

4V6M

Structure of the ribosome-SecYE complex in the membrane environment

• DOI: 10.2210/pdb4V6M/pdb
• Entry 4V6M supersedes 3J00, 3J01
• EMDataResource: EMD-1858

• Classification: RIBOSOME/RIBOSOMAL PROTEIN
• Organism(s): Escherichia coli DH1, Escherichia coli (strain K12), Escherichia coli, Homo sapiens, Escherichia coli O157:H7, Escherichia coli O6:K15:H31 (strain 536 / UPEC)


• Deposited: 2011-02-08 Released: 2014-07-09 
• Deposition Author(s): Frauenfeld, J., Gumbart, J., van der Sluis, E.O., Funes, S., Gartmann, M., Beatrix, B., Mielke, T., Berninghausen, O., Becker, T., Schulten, K., Beckmann, R.

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Experimental Data Snapshot

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

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

• PubMed: 21499241 
• DOI: 10.1038/nsmb.2026
• Primary Citation of Related Structures:  
  3J01, 3J00


• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
Cell division protein FtsQ	AZ	98	Escherichia coli O157:H7	Mutation(s): 0  Gene Names: ftsQ
Find proteins for Q8X9Y5 (Escherichia coli O157:H7) Go to UniProtKB:  Q8X9Y5

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details
Apolipoprotein A-I	A0, A1	200	Homo sapiens	Mutation(s): 0  Gene Names: APOA1
Find proteins for P02647 (Homo sapiens) Go to Gene View: APOA1 Go to UniProtKB:  P02647

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S2	AB	240	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsB
Find proteins for P0A7V0 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7V0

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S3	AC	232	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsC
Find proteins for P0A7V3 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7V3

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S4	AD	205	Escherichia 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
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S5	AE	166	Escherichia 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
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S6	AF	135	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsF
Find proteins for P02358 (Escherichia coli (strain K12)) Go to UniProtKB:  P02358

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S7	AG	178	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsG
Find proteins for P02359 (Escherichia coli (strain K12)) Go to UniProtKB:  P02359

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S8	AH	129	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsH
Find proteins for P0A7W7 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7W7

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S9	AI	129	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsI
Find proteins for P0A7X3 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7X3

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S10	AJ	103	Escherichia 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
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S11	AK	128	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsK
Find proteins for P0A7R9 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7R9

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S12	AL	123	Escherichia 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
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S13	AM	117	Escherichia 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
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S14	AN	100	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsN
Find proteins for P0AG59 (Escherichia coli (strain K12)) Go to UniProtKB:  P0AG59

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S15	AO	88	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S16	AP	82	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsP
Find proteins for P0A7T3 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7T3

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S17	AQ	83	Escherichia 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
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S18	AR	74	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsR
Find proteins for P0A7T7 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7T7

Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S19	AS	91	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsS
Find proteins for P0A7U3 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7U3

Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S20	AT	86	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsT
Find proteins for P0A7U7 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7U7

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S21	AU	70	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsU
Find proteins for P68679 (Escherichia coli (strain K12)) Go to UniProtKB:  P68679

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details
Preprotein translocase secY subunit	BA	435	Escherichia coli O6:K15:H31 (strain 536 / UPEC)	Mutation(s): 0  Gene Names: secY
Find proteins for A0A454A8B1 (Escherichia coli O6:K15:H31 (strain 536 / UPEC)) Go to UniProtKB:  A0A454A8B1

Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details
Preprotein translocase secE subunit	BB	116	Escherichia coli O6:K15:H31 (strain 536 / UPEC)	Mutation(s): 0  Gene Names: secE
Find proteins for A0A454AA55 (Escherichia coli O6:K15:H31 (strain 536 / UPEC)) Go to UniProtKB:  A0A454AA55

Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L1	B5	234	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplA
Find proteins for P0A7L0 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7L0

Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L2	B6	272	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplB
Find proteins for P60422 (Escherichia coli (strain K12)) Go to UniProtKB:  P60422

Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L3	BD	209	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplC
Find proteins for P60438 (Escherichia coli (strain K12)) Go to UniProtKB:  P60438

Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L4	BE	201	Escherichia 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
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L5	BF	178	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplE
Find proteins for P62399 (Escherichia coli (strain K12)) Go to UniProtKB:  P62399

Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L6	BG	176	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplF
Find proteins for P0AG55 (Escherichia coli (strain K12)) Go to UniProtKB:  P0AG55

Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L9	BH	149	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplI
Find proteins for P0A7R1 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7R1

Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L11	BI	141	Escherichia 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
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L13	BJ	142	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplM
Find proteins for P0AA10 (Escherichia coli (strain K12)) Go to UniProtKB:  P0AA10

Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L14	BK	123	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplN
Find proteins for P0ADY3 (Escherichia coli (strain K12)) Go to UniProtKB:  P0ADY3

Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L15	BL	144	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplO
Find proteins for P02413 (Escherichia coli (strain K12)) Go to UniProtKB:  P02413

Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L16	BM	136	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplP
Find proteins for P0ADY7 (Escherichia coli (strain K12)) Go to UniProtKB:  P0ADY7

Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L17	BN	127	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplQ
Find proteins for P0AG44 (Escherichia coli (strain K12)) Go to UniProtKB:  P0AG44

Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L18	BO	117	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplR
Find proteins for P0C018 (Escherichia coli (strain K12)) Go to UniProtKB:  P0C018

Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L19	BP	114	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplS
Find proteins for P0A7K6 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7K6

Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L20	BQ	117	Escherichia 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
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L21	BR	103	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplU
Find proteins for P0AG48 (Escherichia coli (strain K12)) Go to UniProtKB:  P0AG48

Entity ID: 47
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L22	BS	110	Escherichia 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
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L23	BT	100	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplW
Find proteins for P0ADZ0 (Escherichia coli (strain K12)) Go to UniProtKB:  P0ADZ0

Entity ID: 49
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L24	BU	103	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplX
Find proteins for P60624 (Escherichia coli (strain K12)) Go to UniProtKB:  P60624

Entity ID: 50
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L25	BV	94	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplY
Find proteins for P68919 (Escherichia coli (strain K12)) Go to UniProtKB:  P68919

Entity ID: 51
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L27	BW	84	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpmA
Find proteins for P0A7L8 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7L8

Entity ID: 52
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L28	BX	77	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpmB
Find proteins for P0A7M2 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7M2

Entity ID: 53
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L29	BY	63	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpmC
Find proteins for P0A7M6 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7M6

Entity ID: 54
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L30	BZ	58	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpmD
Find proteins for P0AG51 (Escherichia coli (strain K12)) Go to UniProtKB:  P0AG51

Entity ID: 55
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L32	B0	56	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpmF
Find proteins for P0A7N4 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7N4

Entity ID: 56
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L33	B1	54	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpmG
Find proteins for P0A7N9 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7N9

Entity ID: 57
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L34	B2	46	Escherichia 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
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L35	B3	64	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpmI
Find proteins for P0A7Q1 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7Q1

Entity ID: 59
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L36	B4	38	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpmJ
Find proteins for P0A7Q6 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7Q6

Entity ID: 1
Molecule	Chains	Length	Organism
16S RIBOSOMAL RNA	AA	1542	Escherichia coli

Entity ID: 2
Molecule	Chains	Length	Organism
mRNA	AX	11	Escherichia coli

Entity ID: 3
Molecule	Chains	Length	Organism
FtsQ nascent chain	AV	77	Escherichia coli DH1

Entity ID: 26
Molecule	Chains	Length	Organism
5S RIBOSOMAL RNA	B7	120	Escherichia coli DH1

Entity ID: 27
Molecule	Chains	Length	Organism
23S RIBOSOMAL RNA	B8	2904	Escherichia coli DH1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
PEV	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
PGV	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

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-02-08 
• Released Date: 2014-07-09 
• Deposition Author(s): Frauenfeld, J., Gumbart, J., van der Sluis, E.O., Funes, S., Gartmann, M., Beatrix, B., Mielke, T., Berninghausen, O., Becker, T., Schulten, K., Beckmann, R.
• This entry supersedes: 3J00 3J01

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