7PQD

Cryo-EM structure of the dimeric Rhodobacter sphaeroides RC-LH1 core complex at 2.9 A: the structural basis for dimerisation

  • Classification: PHOTOSYNTHESIS
  • Organism(s): Cereibacter sphaeroides 2.4.1
  • Mutation(s): No 

  • Deposited: 2021-09-17 Released: 2021-11-24 
  • Deposition Author(s): Qian, P., Hunter, C.N.
  • Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC), European Research Council (ERC), Wellcome Trust

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Cryo-EM structure of dimeric RC-LH1-PufXYZ complex from Rba. sphaeroides

Qian, P.Hunter, C.N.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LH1-alpha58Cereibacter sphaeroides 2.4.1Mutation(s): 0 
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Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
LH1-beta49Cereibacter sphaeroides 2.4.1Mutation(s): 0 
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Protein Feature View
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
RC-HCA [auth H],
LB [auth h]
246Cereibacter sphaeroides 2.4.1Mutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
RC-LDA [auth L],
MB [auth l]
281Cereibacter sphaeroides 2.4.1Mutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Reaction center protein M chainEA [auth M],
NB [auth m]
307Cereibacter sphaeroides 2.4.1Mutation(s): 0 
Gene Names: pufMRHOS4_18600RSP_0256
UniProt
Find proteins for Q3J1A6 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.))
Explore Q3J1A6 
Go to UniProtKB:  Q3J1A6
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UniProt GroupQ3J1A6
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
PufZFA [auth UA],
GA [auth UB],
OB [auth ua],
PB [auth ub]
31Cereibacter sphaeroides 2.4.1Mutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
PufYHA [auth UU],
QB [auth uu]
49Cereibacter sphaeroides 2.4.1Mutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
PufXIA [auth X],
RB [auth x]
55Cereibacter sphaeroides 2.4.1Mutation(s): 0 
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Small Molecules
Ligands 10 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CD4
Query on CD4

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GE [auth M],
PG [auth h],
WD [auth H],
ZG [auth m]
(2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate
C65 H126 O17 P2
SDCJNZZAOLRVCP-GTOSQJSUSA-N
 Ligand Interaction
BCL (Subject of Investigation/LOI)
Query on BCL

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AD [auth BB],
AE [auth L],
AG [auth bf],
AH [auth m],
BD [auth BC],
AD [auth BB],
AE [auth L],
AG [auth bf],
AH [auth m],
BD [auth BC],
CC [auth AD],
CG [auth bg],
DD [auth BD],
DF [auth ag],
EC [auth AE],
ED [auth BE],
EE [auth M],
EF [auth ah],
EG [auth bh],
FG [auth bi],
GC [auth AF],
GD [auth BF],
HF [auth ai],
HG [auth bj],
ID [auth BG],
IG [auth bk],
JC [auth AG],
JF [auth aj],
KC [auth AH],
KD [auth BH],
KE [auth M],
KG [auth bl],
LD [auth BI],
LE [auth aa],
MF [auth ak],
MG [auth bm],
NC [auth AI],
ND [auth BJ],
NE [auth ab],
NG [auth bn],
OD [auth BK],
OF [auth al],
PC [auth AJ],
QG [auth l],
RD [auth BL],
RE [auth ac],
RF [auth am],
SB [auth AA],
SC [auth AK],
SF [auth an],
TD [auth BM],
UB [auth AB],
UC [auth AL],
UD [auth BN],
UE [auth ad],
UF [auth ba],
UG [auth l],
VF [auth bb],
WC [auth AM],
WE [auth ae],
XC [auth AN],
XD [auth L],
XF [auth bc],
YB [auth AC],
YF [auth bd],
YG [auth m],
ZC [auth BA],
ZE [auth af],
ZF [auth be]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-RUUWGSCADZ
 Ligand Interaction
BPH (Subject of Investigation/LOI)
Query on BPH

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BE [auth L],
FE [auth M],
RG [auth l],
WG [auth m]
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
 Ligand Interaction
U10 (Subject of Investigation/LOI)
Query on U10

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JE [auth M],
SG [auth l],
XG [auth m],
ZD [auth L]
UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
 Ligand Interaction
SQD (Subject of Investigation/LOI)
Query on SQD

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CE [auth L],
DH [auth x]
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
 Ligand Interaction
3PE
Query on 3PE

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OG [auth h],
QE [auth ac],
VD [auth H],
ZB [auth AC]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
 Ligand Interaction
SP2
Query on SP2

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AC,
AF [auth af],
BC [auth AC],
BF [auth af],
BG [auth bf],
AC,
AF [auth af],
BC [auth AC],
BF [auth af],
BG [auth bf],
BH [auth m],
CD [auth BC],
CF [auth af],
DC [auth AE],
DG [auth bh],
FC [auth AF],
FD [auth BE],
FF [auth ah],
GF [auth ai],
GG [auth bj],
HC [auth AF],
HD [auth BF],
HE [auth M],
IC [auth AG],
IF [auth ai],
JD [auth BH],
JG [auth bk],
KF [auth aj],
LC [auth AH],
LF [auth aj],
LG [auth bl],
MC [auth AI],
MD [auth BJ],
ME [auth ab],
NF [auth ak],
OC [auth AI],
OE [auth ab],
PD [auth BK],
PE [auth ab],
PF [auth al],
QC [auth AJ],
QD [auth BL],
QF [auth am],
RC [auth AJ],
SD [auth BL],
SE [auth ac],
TB [auth AA],
TC [auth AK],
TE [auth ac],
TF [auth ba],
VB [auth AB],
VC [auth AM],
VE [auth ad],
WB [auth AB],
WF [auth bb],
XB [auth AB],
XE [auth ae],
YC [auth BA],
YE [auth ae]
3,4-DIHYDROSPHEROIDENE
C41 H62 O
IUUXWKRRZDDNQG-DJSFQYKBSA-N
 Ligand Interaction
LMT
Query on LMT

Download Ideal Coordinates CCD File 
DE [auth M],
VG [auth m]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
UQ1
Query on UQ1

Download Ideal Coordinates CCD File 
TG [auth l],
YD [auth L]
UBIQUINONE-1
C14 H18 O4
SOECUQMRSRVZQQ-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download Ideal Coordinates CCD File 
CH [auth m],
IE [auth M]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
A [auth AA],
B [auth AB],
C [auth AC],
D [auth AD],
E [auth AE],
A [auth AA],
B [auth AB],
C [auth AC],
D [auth AD],
E [auth AE],
F [auth AF],
G [auth AG],
H [auth AH],
I [auth AI],
J [auth AJ],
JA [auth aa],
K [auth AK],
KA [auth ab],
L [auth AL],
LA [auth ac],
M [auth AM],
MA [auth ad],
N [auth AN],
NA [auth ae],
OA [auth af],
PA [auth ag],
QA [auth ah],
RA [auth ai],
SA [auth aj],
TA [auth ak],
UA [auth al],
VA [auth am],
WA [auth an]
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data

  • Deposited Date: 2021-09-17 
  • Released Date: 2021-11-24 
  • Deposition Author(s): Qian, P., Hunter, C.N.

Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/M000265/1
European Research Council (ERC)United Kingdom845126
Wellcome TrustUnited Kingdom209407/Z/17/Z

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-24
    Type: Initial release