6Z5S

RC-LH1(14)-W complex from Rhodopseudomonas palustris


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.65 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

Structures of Rhodopseudomonas palustris RC-LH1 complexes with open or closed quinone channels.

Swainsbury, D.J.K.Qian, P.Jackson, P.J.Faries, K.M.Niedzwiedzki, D.M.Martin, E.C.Farmer, D.A.Malone, L.A.Thompson, R.F.Ranson, N.A.Canniffe, D.P.Dickman, M.J.Holten, D.Kirmaier, C.Hitchcock, A.Hunter, C.N.

(2021) Sci Adv 7

  • DOI: https://doi.org/10.1126/sciadv.abe2631
  • Primary Citation of Related Structures:  
    6Z5R, 6Z5S

  • PubMed Abstract: 

    The reaction-center light-harvesting complex 1 (RC-LH1) is the core photosynthetic component in purple phototrophic bacteria. We present two cryo-electron microscopy structures of RC-LH1 complexes from Rhodopseudomonas palustris A 2.65-Å resolution structure of the RC-LH1 14 -W complex consists of an open 14-subunit LH1 ring surrounding the RC interrupted by protein-W, whereas the complex without protein-W at 2.80-Å resolution comprises an RC completely encircled by a closed, 16-subunit LH1 ring. Comparison of these structures provides insights into quinone dynamics within RC-LH1 complexes, including a previously unidentified conformational change upon quinone binding at the RC Q B site, and the locations of accessory quinone binding sites that aid their delivery to the RC. The structurally unique protein-W prevents LH1 ring closure, creating a channel for accelerated quinone/quinol exchange.


  • Organizational Affiliation

    Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK. d.swainsbury@sheffield.ac.uk c.n.hunter@sheffield.ac.uk.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Light harvesting complex 1 Protein WA [auth W]102Rhodopseudomonas palustris CGA009Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q6N1K3 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009))
Explore Q6N1K3 
Go to UniProtKB:  Q6N1K3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6N1K3
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein M chainB [auth M]307Rhodopseudomonas palustris CGA009Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A4Z7 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009))
Explore A0A4Z7 
Go to UniProtKB:  A0A4Z7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4Z7
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein L chainC [auth L]277Rhodopseudomonas palustris CGA009Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for O83005 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009))
Explore O83005 
Go to UniProtKB:  O83005
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO83005
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
H subunit of photosynthetic reaction center complexD [auth H]255Rhodopseudomonas palustris CGA009Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A4Z9 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009))
Explore A0A4Z9 
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Entity Groups  
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UniProt GroupA0A4Z9
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Light-harvesting complex 1 alpha chain63Rhodopseudomonas palustris CGA009Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q6N9L4 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009))
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UniProt GroupQ6N9L4
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Light-harvesting complex 1 beta chain65Rhodopseudomonas palustris CGA009Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q6N9L5 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009))
Explore Q6N9L5 
Go to UniProtKB:  Q6N9L5
Entity Groups  
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UniProt GroupQ6N9L5
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  • Reference Sequence
Small Molecules
Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

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GD [auth G]
HB [auth 3]
JD [auth G]
LA [auth M]
SA [auth L]
GD [auth G],
HB [auth 3],
JD [auth G],
LA [auth M],
SA [auth L],
WA [auth H]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
BCL (Subject of Investigation/LOI)
Query on BCL

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BD [auth J]
CD [auth J]
DB [auth 5]
DC [auth C]
EB [auth 5]
BD [auth J],
CD [auth J],
DB [auth 5],
DC [auth C],
EB [auth 5],
GB [auth 3],
HA [auth M],
HC [auth D],
HD [auth G],
ID [auth G],
JB [auth 4],
LB [auth Y],
LC [auth R],
MA [auth M],
MB [auth Y],
MC [auth R],
OD [auth E],
PA [auth L],
PB [auth V],
PD [auth E],
QA [auth L],
QB [auth V],
QC [auth P],
SC [auth P],
UB [auth T],
VB [auth T],
WC [auth N],
XA [auth 1],
XC [auth N],
YB [auth A],
ZA [auth 2],
ZB [auth A]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
BPH (Subject of Investigation/LOI)
Query on BPH

Download Ideal Coordinates CCD File 
IA [auth M],
RA [auth L]
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
U10 (Subject of Investigation/LOI)
Query on U10

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JA [auth M],
UA [auth L],
YA [auth 1]
UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
6PL (Subject of Investigation/LOI)
Query on 6PL

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KA [auth M],
ND [auth E],
VA [auth H]
(4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE
C42 H85 N O8 P
PZNPLUBHRSSFHT-RRHRGVEJSA-O
PGT (Subject of Investigation/LOI)
Query on PGT

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RC [auth P](1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
C40 H79 O10 P
KBPVYRBBONZJHF-AMAPPZPBSA-N
CRT (Subject of Investigation/LOI)
Query on CRT

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AB [auth 2]
CC [auth B]
FD [auth K]
IB [auth 3]
IC [auth D]
AB [auth 2],
CC [auth B],
FD [auth K],
IB [auth 3],
IC [auth D],
JC [auth R],
MD [auth I],
NB [auth Z],
PC [auth S],
SB [auth X],
SD [auth F],
VC [auth Q],
ZC [auth O]
SPIRILLOXANTHIN
C42 H60 O2
VAZQBTJCYODOSV-RISZBRKMSA-N
QAK (Subject of Investigation/LOI)
Query on QAK

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GA [auth M](6~{R},10~{S},14~{R},19~{R},23~{S},24~{E},27~{S},28~{E})-2,6,10,14,19,23,27,31-octamethyldotriaconta-24,28-dien-2-ol
C40 H78 O
NKXXNXZGYNRQNV-BTRAWPHCSA-N
LMT (Subject of Investigation/LOI)
Query on LMT

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AC [auth B]
AD [auth J]
BB [auth 2]
BC [auth B]
CB [auth 2]
AC [auth B],
AD [auth J],
BB [auth 2],
BC [auth B],
CB [auth 2],
DD [auth K],
EC [auth D],
ED [auth K],
FB [auth 6],
FC [auth D],
GC [auth D],
KB [auth 4],
KC [auth R],
KD [auth I],
LD [auth I],
NC [auth S],
OA [auth M],
OB [auth Z],
OC [auth S],
QD [auth F],
RB [auth X],
RD [auth F],
TA [auth L],
TB [auth X],
TC [auth Q],
UC [auth Q],
WB [auth U],
XB [auth U],
YC [auth O]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
FE (Subject of Investigation/LOI)
Query on FE

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NA [auth M]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
AA [auth J]
CA [auth G]
E [auth 1]
EA [auth E]
G [auth 5]
AA [auth J],
CA [auth G],
E [auth 1],
EA [auth E],
G [auth 5],
I [auth 3],
K [auth Y],
M [auth V],
O [auth T],
Q [auth A],
S [auth C],
U [auth R],
W [auth P],
Y [auth N]
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.65 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0
MODEL REFINEMENTPHENIX1.16

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/M000265/1

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-13
    Type: Initial release
  • Version 1.1: 2021-02-10
    Changes: Database references