9H22 | pdb_00009h22

Cryo EM structure of RC-dLH complex model II from Gemmatimonas groenlandica


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Cryo EM structure of RC-dLH complex model II from Gemmatimonas groenlandica

Gardiner, A.T.Jing, Y.Bina, D.Mujakic, I.Gardian, Z.Kaftan, D.Joosten, M.Jakobi, A.Castro-Hartmann, P.Qian, P.Koblizek, M.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
reaction centre S sub unitA [auth S]204Gemmatimonas groenlandicaMutation(s): 0 
UniProt
Find proteins for A0A6M4IPJ3 (Gemmatimonas groenlandica)
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UniProt GroupA0A6M4IPJ3
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein L chainB [auth L]274Gemmatimonas groenlandicaMutation(s): 0 
UniProt
Find proteins for A0A6M4IPC7 (Gemmatimonas groenlandica)
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UniProt GroupA0A6M4IPC7
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein M chainC [auth M]392Gemmatimonas groenlandicaMutation(s): 0 
UniProt
Find proteins for A0A6M4ILR2 (Gemmatimonas groenlandica)
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UniProt GroupA0A6M4ILR2
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
reaction centre Ht su unitD [auth H]66Gemmatimonas groenlandicaMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
reaction centre Hc sub unitE [auth K]180Gemmatimonas groenlandicaMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic reaction center cytochrome c subunitF [auth C]373Gemmatimonas groenlandicaMutation(s): 0 
UniProt
Find proteins for A0A6M4ITL7 (Gemmatimonas groenlandica)
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UniProt GroupA0A6M4ITL7
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Light-harvesting protein56Gemmatimonas groenlandicaMutation(s): 0 
UniProt
Find proteins for A0A6M4IQ17 (Gemmatimonas groenlandica)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Light-harvesting protein44Gemmatimonas groenlandicaMutation(s): 0 
UniProt
Find proteins for A0A6M4IQ93 (Gemmatimonas groenlandica)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Light-harvesting protein71Gemmatimonas groenlandicaMutation(s): 0 
UniProt
Find proteins for A0A6M4INU2 (Gemmatimonas groenlandica)
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Small Molecules
Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CD4
Query on CD4

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TC [auth M],
ZH [auth Af]
(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
BCL (Subject of Investigation/LOI)
Query on BCL

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AE [auth AF]
AF [auth BL]
AI [auth Af]
AK [auth Bp]
BH [auth BX]
AE [auth AF],
AF [auth BL],
AI [auth Af],
AK [auth Bp],
BH [auth BX],
BI [auth Bf],
CF [auth AM],
CG [auth AR],
CJ [auth Bk],
DF [auth BM],
DG [auth BS],
DH [auth Aa],
DI [auth Bf],
EE [auth BG],
EJ [auth Al],
FD [auth BA],
FF [auth BN],
FH [auth Ba],
FI [auth Ag],
FJ [auth Bl],
GE [auth AH],
GG [auth BT],
HD [auth BB],
HJ [auth Bl],
IC [auth L],
IF [auth AN],
JC [auth L],
JE [auth BH],
JF [auth AO],
JG [auth AT],
JI [auth Bg],
KD [auth AB],
KH [auth Ac],
KJ [auth Am],
LE [auth AI],
MD [auth AC],
MF [auth BO],
MG [auth AT],
MI [auth Ah],
ND [auth BC],
NH [auth Bc],
NI [auth Bh],
NJ [auth Bm],
OE [auth BI],
OF [auth BP],
OG [auth AU],
OI [auth Bh],
PG [auth AU],
PI [auth Ai],
QD [auth BD],
QE [auth BJ],
QG [auth AV],
QJ [auth An],
RE [auth AK],
RF [auth BP],
RH [auth Bd],
SG [auth BV],
SI [auth Bi],
SJ [auth Bn],
TD [auth AD],
TF [auth AP],
TH [auth Bd],
UC [auth M],
UD [auth AE],
UE [auth BK],
UF [auth AQ],
UG [auth AW],
UI [auth Aj],
UJ [auth Ao],
VC [auth M],
VI [auth Bj],
WD [auth BE],
WF [auth AQ],
WG [auth BW],
WH [auth Ae],
WJ [auth Bo],
XE [auth AL],
XF [auth BQ],
XH [auth Be],
XJ [auth Bp],
YD [auth BF],
YG [auth AX],
ZF [auth BR],
ZI [auth Ak]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
BPH
Query on BPH

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KC [auth L],
WC [auth M]
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
MQ8
Query on MQ8

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AD [auth M],
PH [auth Ad],
RC [auth L]
MENAQUINONE 8
C51 H72 O2
LXKDFTDVRVLXFY-ACMRXAIVSA-N
HEC
Query on HEC

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BD [auth C],
CD [auth C],
DD [auth C],
ED [auth C]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
V7N
Query on V7N

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AH [auth BX]
BE [auth AF]
BG [auth BR]
BJ [auth Bk]
CI [auth Bf]
AH [auth BX],
BE [auth AF],
BG [auth BR],
BJ [auth Bk],
CI [auth Bf],
EH [auth Ba],
FG [auth BS],
GI [auth Ag],
GJ [auth Bl],
HE [auth AH],
HF [auth BN],
HG [auth BT],
ID [auth BB],
IH [auth Bb],
II [auth Bg],
KE [auth AI],
KG [auth AT],
LF [auth BO],
LJ [auth Am],
ME [auth AI],
MH [auth Bc],
MJ [auth Bm],
PD [auth BC],
QF [auth BP],
QH [auth Ad],
RG [auth BV],
RI [auth Bi],
RJ [auth An],
SD [auth BD],
SF [auth AP],
SH [auth Bd],
VD [auth BE],
VG [auth BW],
WE [auth BK],
XG [auth AX],
XI [auth Bj],
YE [auth AL],
ZD [auth BF],
ZE [auth BL],
ZJ [auth Bp]
(2~{E},4~{E},6~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{Z},24~{E},26~{E},28~{E})-23-methanoyl-31-methoxy-2,6,10,14,19,27,31-heptamethyl-dotriaconta-2,4,6,10,12,14,16,18,20,22,24,26,28-tridecaenoic acid
C41 H54 O4
XLPMAXZHNMJTID-YBNWOPDJSA-N
CRT
Query on CRT

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XC [auth M]SPIRILLOXANTHIN
C42 H60 O2
VAZQBTJCYODOSV-RISZBRKMSA-N
PEX
Query on PEX

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BK [auth Bp]
CE [auth AG]
DJ [auth Bk]
EI [auth Bf]
GH [auth Ba]
BK [auth Bp],
CE [auth AG],
DJ [auth Bk],
EI [auth Bf],
GH [auth Ba],
IJ [auth Bl],
JH [auth Bb],
KF [auth AO],
KI [auth Bg],
LG [auth AT],
OJ [auth Bm],
TI [auth Bi],
TJ [auth Bn],
UH [auth Bd],
YH [auth Be],
YI [auth Bj],
ZC [auth M]
1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
C25 H49 N O8 P
KKOSJVWUOHEQKA-HSZRJFAPSA-M
LMT
Query on LMT

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AG [auth BR]
AJ [auth Bk]
BF [auth BL]
CH [auth BX]
DE [auth BG]
AG [auth BR],
AJ [auth Bk],
BF [auth BL],
CH [auth BX],
DE [auth BG],
EF [auth BM],
EG [auth BS],
FE [auth BG],
GD [auth BA],
GF [auth BN],
HH [auth Ba],
HI [auth Bg],
IE [auth BH],
IG [auth BT],
JD [auth BB],
JJ [auth Bl],
LC [auth L],
LD [auth AB],
LH [auth Bc],
LI [auth Bg],
MC [auth L],
NC [auth L],
NE [auth BI],
NF [auth BO],
NG [auth BU],
OC [auth L],
OD [auth BC],
OH [auth Bc],
PC [auth L],
PE [auth BI],
PF [auth BP],
PJ [auth Bm],
QC [auth L],
QI [auth Bi],
RD [auth BD],
SE [auth AK],
TE [auth BK],
TG [auth BV],
VE [auth BK],
VF [auth AQ],
VH [auth Bd],
VJ [auth Bo],
WI [auth Bj],
XD [auth BF],
YC [auth M],
YF [auth BQ],
YJ [auth Bp],
ZG [auth BX]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
FE
Query on FE

Download Ideal Coordinates CCD File 
SC [auth M]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.2.1
MODEL REFINEMENTPHENIX1.20.1-4487

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Czech Academy of SciencesCzech Republic19-28778X

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-03
    Type: Initial release