9H19 | pdb_00009h19

Cryo-EM structure of RC-dLH complex model I from Gem. groenlandica strain TET16


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 I from Gem. groenlandica strain TET16

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

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Light-harvesting protein71Gemmatimonas groenlandicaMutation(s): 0 
UniProt
Find proteins for A0A6M4INU2 (Gemmatimonas groenlandica)
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UniProt GroupA0A6M4INU2
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Light-harvesting protein44Gemmatimonas groenlandicaMutation(s): 0 
UniProt
Find proteins for A0A6M4IQ93 (Gemmatimonas groenlandica)
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UniProt GroupA0A6M4IQ93
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
reaction centre S sub unitGA [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: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein L chainHA [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: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein M chainIA [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: 6
MoleculeChains Sequence LengthOrganismDetailsImage
reaction centre Ht sub unitJA [auth H]60Gemmatimonas groenlandicaMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
reaction centre Hc sub unitKA [auth K]179Gemmatimonas groenlandicaMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic reaction center cytochrome c subunitLA [auth C]373Gemmatimonas groenlandicaMutation(s): 0 
UniProt
Find proteins for A0A6M4ITL7 (Gemmatimonas groenlandica)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Light-harvesting protein56Gemmatimonas groenlandicaMutation(s): 0 
UniProt
Find proteins for A0A6M4IQ17 (Gemmatimonas groenlandica)
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UniProt GroupA0A6M4IQ17
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Small Molecules
Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CD4
Query on CD4

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KD [auth Af],
MF [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
BCL (Subject of Investigation/LOI)
Query on BCL

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AE [auth Bi]
AF [auth Bo]
AH [auth AG]
AI [auth BL]
AJ [auth BS]
AE [auth Bi],
AF [auth Bo],
AH [auth AG],
AI [auth BL],
AJ [auth BS],
BE [auth Aj],
BG [auth BA],
BK [auth BX],
CD [auth Bd],
CH [auth BG],
CI [auth AM],
DD [auth Ae],
DF [auth Bp],
DI [auth AM],
EF [auth Bp],
EG [auth BB],
EH [auth AH],
EJ [auth AS],
FF [auth L],
FI [auth BN],
GF [auth L],
HE [auth Bj],
HG [auth AB],
HI [auth AN],
HJ [auth AT],
ID [auth Be],
IE [auth Ak],
IG [auth AC],
IH [auth BH],
II [auth AO],
IJ [auth AT],
JC [auth Aa],
JD [auth Af],
JG [auth BC],
JH [auth AI],
KH [auth AI],
KJ [auth BU],
LE [auth Bk],
LI [auth BO],
MC [auth Ba],
ME [auth Al],
MG [auth BD],
MH [auth BI],
NF [auth M],
NI [auth BP],
NJ [auth AU],
OC [auth Ab],
OD [auth Bf],
OF [auth M],
OJ [auth AV],
PE [auth Bl],
PH [auth AJ],
QE [auth Am],
QG [auth AD],
QH [auth AJ],
QI [auth AP],
QJ [auth BV],
RC [auth Bb],
RD [auth Bg],
RI [auth AQ],
SC [auth Ac],
SD [auth Ah],
SG [auth AE],
SH [auth AK],
SI [auth AQ],
SJ [auth AW],
TE [auth Bm],
TG [auth BE],
TJ [auth AW],
UH [auth BK],
UJ [auth AW],
VG [auth BF],
WC [auth Bc],
WI [auth BR],
XC [auth Ad],
XD [auth Bh],
XE [auth Bn],
XH [auth AL],
YD [auth Ai],
YE [auth Ao],
ZF [auth BA],
ZG [auth AF],
ZI [auth AR],
ZJ [auth AX]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
BPH
Query on BPH

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

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JF [auth L],
RF [auth M],
ZC [auth Ad]
MENAQUINONE 8
C51 H72 O2
LXKDFTDVRVLXFY-ACMRXAIVSA-N
HEC
Query on HEC

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UF [auth C],
VF [auth C],
WF [auth C],
XF [auth C]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
V7N
Query on V7N

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AG [auth BA]
AK [auth BX]
BD [auth Bd]
BH [auth BG]
CF [auth Bp]
AG [auth BA],
AK [auth BX],
BD [auth Bd],
BH [auth BG],
CF [auth Bp],
CJ [auth BS],
FE [auth Bj],
FG [auth BB],
FJ [auth BT],
GD [auth Be],
GH [auth BH],
GI [auth BN],
IC [auth Aa],
JE [auth Bk],
KI [auth BO],
LG [auth BC],
LH [auth BI],
MD [auth Bf],
MJ [auth BU],
OE [auth Bl],
OG [auth BD],
OI [auth BP],
PD [auth Bg],
PJ [auth BV],
QC [auth Bb],
RE [auth Bm],
RH [auth BJ],
UC [auth Bc],
UD [auth Bh],
UE [auth An],
VE [auth Bn],
VI [auth BQ],
WH [auth BK],
WJ [auth BW],
XG [auth BF],
YG [auth AF],
YH [auth AL],
YI [auth BR],
ZD [auth Bi],
ZH [auth BL]
(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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QF [auth M]SPIRILLOXANTHIN
C42 H60 O2
VAZQBTJCYODOSV-RISZBRKMSA-N
PEX
Query on PEX

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DE [auth Aj]
DJ [auth AS]
ED [auth Be]
GJ [auth AT]
HD [auth Be]
DE [auth Aj],
DJ [auth AS],
ED [auth Be],
GJ [auth AT],
HD [auth Be],
KE [auth Bk],
LC [auth Ba],
OH [auth AJ],
PG [auth AD],
PI [auth AP],
QD [auth Bg],
RG [auth AE],
SE [auth Bm],
VC [auth Bc],
VD [auth Bh],
WE [auth Bn],
YF [auth AA]
1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
C25 H49 N O8 P
KKOSJVWUOHEQKA-HSZRJFAPSA-M
LMT
Query on LMT

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AD [auth Bd]
BF [auth Bp]
BI [auth BL]
BJ [auth BS]
CE [auth Aj]
AD [auth Bd],
BF [auth Bp],
BI [auth BL],
BJ [auth BS],
CE [auth Aj],
CG [auth BA],
DG [auth BA],
DH [auth BG],
EE [auth Bj],
EI [auth BM],
FD [auth Be],
FH [auth BH],
GE [auth Bj],
GG [auth BB],
HH [auth BH],
IF [auth L],
JI [auth BO],
JJ [auth BU],
KC [auth Aa],
KF [auth M],
KG [auth BC],
LD [auth Bf],
LJ [auth BU],
MI [auth BO],
NC [auth Ba],
ND [auth Bf],
NE [auth Bl],
NG [auth BD],
NH [auth BI],
PC [auth Bb],
RJ [auth AW],
SF [auth K],
TC [auth Bc],
TD [auth Bh],
TF [auth C],
TH [auth BK],
TI [auth BQ],
UG [auth BE],
UI [auth BQ],
VH [auth BK],
VJ [auth BW],
WD [auth Bh],
WG [auth BF],
XI [auth BR],
XJ [auth BW],
YC [auth Ad],
YJ [auth AX],
ZE [auth Bo]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
FE
Query on FE

Download Ideal Coordinates CCD File 
LF [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 Science FoundationCzech Republic19-28778X

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-29
    Type: Initial release