6Z5R

RC-LH1(16) complex from Rhodopseudomonas palustris


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Light-harvesting complex 1 alpha chain48Rhodopseudomonas palustris CGA009Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q6N9L4 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009))
Explore Q6N9L4 
Go to UniProtKB:  Q6N9L4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6N9L4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Light-harvesting complex 1 beta chain52Rhodopseudomonas 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  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6N9L5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
H subunit of photosynthetic reaction center complexK [auth H]255Rhodopseudomonas palustris CGA009Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A4Z9 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009))
Explore A0A4Z9 
Go to UniProtKB:  A0A4Z9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4Z9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein L chain277Rhodopseudomonas 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
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein M chain307Rhodopseudomonas 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
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

Download Ideal Coordinates CCD File 
EC [auth M]
FC [auth M]
PA [auth E]
TA [auth G]
WB [auth L]
EC [auth M],
FC [auth M],
PA [auth E],
TA [auth G],
WB [auth L],
XA [auth G]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
BCL (Subject of Investigation/LOI)
Query on BCL

Download Ideal Coordinates CCD File 
AC [auth M]
AD [auth Y]
AE [auth 7]
BB [auth J]
BD [auth Y]
AC [auth M],
AD [auth Y],
AE [auth 7],
BB [auth J],
BD [auth Y],
CE [auth 7],
DB [auth J],
FD [auth A],
GB [auth N],
GE [auth 9],
HB [auth N],
HC [auth R],
HD [auth B],
HE [auth 0],
JA [auth C],
JC [auth R],
KA [auth C],
KD [auth 1],
LD [auth 1],
MC [auth T],
NA [auth E],
NB [auth L],
NC [auth U],
PD [auth 3],
QC [auth V],
RA [auth F],
RC [auth V],
RD [auth 4],
UB [auth L],
UD [auth 5],
VA [auth G],
VC [auth P],
WA [auth G],
WD [auth 5],
XC [auth Q],
YB [auth M]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
BPH (Subject of Investigation/LOI)
Query on BPH

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

Download Ideal Coordinates CCD File 
CC [auth M],
GC [auth M],
PB [auth L],
TB [auth L],
VB [auth L]
UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
6PL (Subject of Investigation/LOI)
Query on 6PL

Download Ideal Coordinates CCD File 
AB [auth I]
ED [auth Z]
EE [auth 8]
FB [auth K]
JD [auth B]
AB [auth I],
ED [auth Z],
EE [auth 8],
FB [auth K],
JD [auth B],
JE [auth 0],
KB [auth O],
LB [auth H],
LC [auth S],
MA [auth D],
OA [auth E],
OD [auth 2],
PC [auth U],
QB [auth L],
RB [auth L],
SA [auth F],
TC [auth X],
TD [auth 4],
VD [auth 5],
WC [auth P],
XB [auth M],
YA [auth I],
YD [auth 6],
ZC [auth Q]
(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

Download Ideal Coordinates CCD File 
BE [auth 7],
FE [auth 9]
(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

Download Ideal Coordinates CCD File 
DD [auth Z]
DE [auth 8]
EB [auth K]
ID [auth B]
IE [auth 0]
DD [auth Z],
DE [auth 8],
EB [auth K],
ID [auth B],
IE [auth 0],
JB [auth O],
KC [auth S],
LA [auth D],
ND [auth 2],
OC [auth U],
SC [auth X],
SD [auth 4],
UA [auth G],
YC [auth Q],
ZA [auth I],
ZD [auth 7]
SPIRILLOXANTHIN
C42 H60 O2
VAZQBTJCYODOSV-RISZBRKMSA-N
QAK (Subject of Investigation/LOI)
Query on QAK

Download Ideal Coordinates CCD File 
DC [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

Download Ideal Coordinates CCD File 
CB [auth J]
CD [auth Z]
GD [auth B]
IB [auth O]
IC [auth R]
CB [auth J],
CD [auth Z],
GD [auth B],
IB [auth O],
IC [auth R],
MB [auth H],
MD [auth 2],
QA [auth F],
QD [auth 4],
SB [auth L],
UC [auth P],
XD [auth 6]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
FE (Subject of Investigation/LOI)
Query on FE

Download Ideal Coordinates CCD File 
ZB [auth M]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
A [auth C]
BA [auth 3]
C [auth E]
DA [auth 5]
E [auth G]
A [auth C],
BA [auth 3],
C [auth E],
DA [auth 5],
E [auth G],
FA [auth 7],
G [auth J],
HA [auth 9],
I [auth N],
N [auth R],
P [auth T],
R [auth V],
T [auth P],
V [auth Y],
X [auth A],
Z [auth 1]
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 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