6S0K

Ribosome nascent chain in complex with SecA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The molecular mechanism of cotranslational membrane protein recognition and targeting by SecA.

Wang, S.Jomaa, A.Jaskolowski, M.Yang, C.I.Ban, N.Shan, S.O.

(2019) Nat Struct Mol Biol 26: 919-929

  • DOI: 10.1038/s41594-019-0297-8
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Cotranslational protein targeting is a conserved process for membrane protein biogenesis. In Escherichia coli, the essential ATPase SecA was found to cotranslationally target a subset of nascent membrane proteins to the SecYEG translocase at the plas ...

    Cotranslational protein targeting is a conserved process for membrane protein biogenesis. In Escherichia coli, the essential ATPase SecA was found to cotranslationally target a subset of nascent membrane proteins to the SecYEG translocase at the plasma membrane. The molecular mechanism of this pathway remains unclear. Here we use biochemical and cryoelectron microscopy analyses to show that the amino-terminal amphipathic helix of SecA and the ribosomal protein uL23 form a composite binding site for the transmembrane domain (TMD) on the nascent protein. This binding mode further enables recognition of charged residues flanking the nascent TMD and thus explains the specificity of SecA recognition. Finally, we show that membrane-embedded SecYEG promotes handover of the translating ribosome from SecA to the translocase via a concerted mechanism. Our work provides a molecular description of the SecA-mediated cotranslational targeting pathway and demonstrates an unprecedented role of the ribosome in shielding nascent TMDs.


    Organizational Affiliation

    Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA. sshan@caltech.edu.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
C
273Escherichia coliMutation(s): 0 
Find proteins for P60422 (Escherichia coli (strain K12))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
D
209Escherichia coliMutation(s): 0 
Find proteins for P60438 (Escherichia coli (strain K12))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
E
201Escherichia coliMutation(s): 0 
Find proteins for P60723 (Escherichia coli (strain K12))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
F
179Escherichia coliMutation(s): 0 
Find proteins for P62399 (Escherichia coli (strain K12))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
G
177Escherichia coliMutation(s): 0 
Find proteins for P0AG55 (Escherichia coli (strain K12))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
H
149Escherichia coliMutation(s): 0 
Find proteins for P0A7R1 (Escherichia coli (strain K12))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10
I
165Escherichia coliMutation(s): 0 
Find proteins for A0A073UC57 (Escherichia coli 5-366-08_S1_C1)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
J
142Escherichia coliMutation(s): 0 
Find proteins for P0A7J7 (Escherichia coli (strain K12))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
K
142Escherichia coliMutation(s): 0 
Find proteins for P0AA10 (Escherichia coli (strain K12))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
L
123Escherichia coliMutation(s): 0 
Find proteins for P0ADY3 (Escherichia coli (strain K12))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
M
144Escherichia coliMutation(s): 0 
Find proteins for P02413 (Escherichia coli (strain K12))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
N
136Escherichia coliMutation(s): 0 
Find proteins for P0ADY7 (Escherichia coli (strain K12))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
O
127Escherichia coliMutation(s): 0 
Find proteins for P0AG44 (Escherichia coli (strain K12))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
P
117Escherichia coliMutation(s): 0 
Find proteins for P0C018 (Escherichia coli (strain K12))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
Q
115Escherichia coliMutation(s): 0 
Find proteins for P0A7K6 (Escherichia coli (strain K12))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
R
118Escherichia coliMutation(s): 0 
Find proteins for P0A7L3 (Escherichia coli (strain K12))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
S
103Escherichia coliMutation(s): 0 
Find proteins for P0AG48 (Escherichia coli (strain K12))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
T
110Escherichia coliMutation(s): 0 
Find proteins for P61175 (Escherichia coli (strain K12))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
U
100Escherichia coliMutation(s): 0 
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
V
104Escherichia coliMutation(s): 0 
Find proteins for P60624 (Escherichia coli (strain K12))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
X
85Escherichia coliMutation(s): 0 
Find proteins for P0A7L8 (Escherichia coli (strain K12))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
Y
78Escherichia coliMutation(s): 0 
Find proteins for P0A7M2 (Escherichia coli (strain K12))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
Z
63Escherichia coliMutation(s): 0 
Find proteins for P0A7M6 (Escherichia coli (strain K12))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
a
59Escherichia coliMutation(s): 0 
Find proteins for P0AG51 (Escherichia coli (strain K12))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
b
57Escherichia coliMutation(s): 0 
Find proteins for P0A7N4 (Escherichia coli (strain K12))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
c
55Escherichia coliMutation(s): 0 
Find proteins for P0A7N9 (Escherichia coli (strain K12))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
d
46Escherichia coliMutation(s): 0 
Find proteins for P0A7P5 (Escherichia coli (strain K12))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
e
65Escherichia coliMutation(s): 0 
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
f
38Escherichia coliMutation(s): 0 
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
Protein translocase subunit SecA
h
838Escherichia coliMutation(s): 0 
Gene Names: 
secAazidivA8C65_16295A9P13_21545ACN68_30130ACN81_28915ACU57_16035ACU90_26895AM270_12025AUQ13_07855AWB10_21395B9T59_07925BANRA_00479BANRA_00570BANRA_02341BANRA_03271BEN53_02700BK248_21050BK292_13315BK296_02885BMT91_01720BON63_04275BON71_00565BON86_13400BUE81_03750BvCms2454_01608BvCmsHHP001_03356BvCmsKSP026_04779BvCmsNSNP036_02420BvCmsOUP014_04165BvCmsSINP011_00780BvCmsSIP019_01094BvCmsSIP044_04874BVL39_02565BW690_21995BZL31_13370C5N07_08195C6669_04640C7235_20610C9098_16455C9Z37_13980C9Z39_04640CA593_03250CDL37_06840CF006_13815CG692_01215CIG45_07370CO706_22680COD46_06255CQP61_22465CRM83_15470CV83915_01479D0X26_09800D3821_05850D4V08_18855D6T60_04390D9H94_05480D9K48_09625DAH18_05665DAH34_04570DBQ99_21740DEO04_16725DJ503_00515DM129_16885DTL43_06305DWB25_20700DXT69_01850E0I42_17625E0K84_13195E2115_19590E2116_06575E2119_07760E2127_05565E2128_00995E2129_03210E2134_11625E4K55_07315E5S47_11980EAI52_02055EC1094V2_3755EC3234A_2c00820EC3426_00849ECTO6_03969EEP23_00520EHH55_17330EI021_04690EI028_09845EIZ93_07545EL75_3664EL79_3774EL80_3721ELT20_04120ELT49_10590ELT58_18630ELV08_09210EPT01_02945ExPECSC038_04062EXX24_10555EXX71_12680EXX78_15220EYD11_18890EYY78_10355F1E13_08205FORC82_3946FV293_03245FZ043_03670GJ11_00520HmCmsJML079_03645HW43_04220PGD_03739PU06_15055WQ89_09200

Find proteins for A0A037YQ84 (Escherichia coli)
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
Cytoskeleton protein RodZ
k
57Escherichia coliMutation(s): 0 
Gene Names: rodZSAMEA3472055_00952
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
W
94Escherichia coliMutation(s): 0 
Find proteins for P68919 (Escherichia coli (strain K12))
Go to UniProtKB:  P68919
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 1
MoleculeChainsLengthOrganism
tRNA-CCA23Escherichia coli

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Entity ID: 2
MoleculeChainsLengthOrganism
23S ribosomal RNAA2883Escherichia coli

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Entity ID: 3
MoleculeChainsLengthOrganism
5S ribosomal RNAB120Escherichia coli
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
f
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B, b
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland--
National Institutes of Health/National Center for Research ResourcesUnited States--

Revision History 

  • Version 1.0: 2019-10-09
    Type: Initial release
  • Version 1.1: 2019-11-27
    Changes: Database references