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 9X4P | pdb_00009x4p

photosystem I with six LHCIfrom a green alga as lichen phycobiont

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history. 

Literature

Structural insights into assembly and environmental adaptation of photosystem I from a lichen green alga

Su, X., Shi, L., Liu, Z., Zhao, X., Wei, X., Li, M.

(2026) Nat Commun 17: 10679

Macromolecule Content 

  • Total Structure Weight: 640.44 kDa 
  • Atom Count: 35,440 
  • Modeled Residue Count: 3,458 
  • Deposited Residue Count: 4,283 
  • Unique protein chains: 17

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Lhca1A [auth 1]248Diplosphaera chodatiiMutation(s): 0 
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Lhca3B [auth 3]308Diplosphaera chodatiiMutation(s): 0 
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Lhca5C [auth 5]271Diplosphaera chodatiiMutation(s): 0 
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Lhca5D [auth 6]266Diplosphaera chodatiiMutation(s): 0 
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Lhca7E [auth 7]279Diplosphaera chodatiiMutation(s): 0 
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Lhca8F [auth 8]263Diplosphaera chodatiiMutation(s): 0 
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaAG [auth A]751Diplosphaera chodatiiMutation(s): 0 
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaBH [auth B]734Diplosphaera chodatiiMutation(s): 0 
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerI [auth C]81Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.97.1.12
UniProt
Find proteins for Q00914 (Chlamydomonas reinhardtii)
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaDJ [auth D]239Diplosphaera chodatiiMutation(s): 0 
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaEK [auth E]111Diplosphaera chodatiiMutation(s): 0 
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaFL [auth F]251Diplosphaera chodatiiMutation(s): 0 
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIM [auth I]106Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A8IFG7 (Chlamydomonas reinhardtii)
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXN [auth J]41Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for P59777 (Chlamydomonas reinhardtii)
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaKO [auth K]126Diplosphaera chodatiiMutation(s): 0 
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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaLP [auth L]176Diplosphaera chodatiiMutation(s): 0 
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Reference Sequence
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIQ [auth M]32Bryopsis plumosaMutation(s): 0 
UniProt
Find proteins for A0A0D6E2L8 (Bryopsis plumosa)
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Reference Sequence

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA
(Subject of Investigation/LOI)

Query on CLA


Download:Ideal Coordinates CCD File
AA [auth 1]
AB [auth 5]
AC [auth 6]
AD [auth 8]
AE [auth A]
AA [auth 1],
AB [auth 5],
AC [auth 6],
AD [auth 8],
AE [auth A],
AF [auth A],
AG [auth B],
BA [auth 1],
BB [auth 5],
BC [auth 6],
BD [auth 8],
BE [auth A],
BF [auth A],
BG [auth B],
CA [auth 1],
CB [auth 5],
CC [auth 6],
CD [auth 8],
CE [auth A],
CF [auth A],
CG [auth B],
DA [auth 1],
DB [auth 5],
DC [auth 6],
DD [auth 8],
DE [auth A],
DG [auth B],
EA [auth 1],
EB [auth 5],
EC [auth 6],
ED [auth 8],
EE [auth A],
EF [auth A],
EG [auth B],
EH [auth F],
FA [auth 3],
FB [auth 5],
FC [auth 6],
FD [auth 8],
FE [auth A],
FG [auth B],
FH [auth F],
GA [auth 3],
GB [auth 5],
GC [auth 6],
GD [auth 8],
GE [auth A],
GG [auth B],
GH [auth F],
HA [auth 3],
HB [auth 5],
HD [auth 8],
HE [auth A],
HG [auth B],
IA [auth 3],
IB [auth 5],
IC [auth 7],
ID [auth 8],
IE [auth A],
IG [auth B],
IH [auth J],
JA [auth 3],
JB [auth 5],
JC [auth 7],
JD [auth 8],
JE [auth A],
JF [auth B],
JG [auth B],
JH [auth K],
KA [auth 3],
KB [auth 5],
KC [auth 7],
KD [auth 8],
KE [auth A],
KF [auth B],
KG [auth B],
KH [auth K],
LA [auth 3],
LB [auth 5],
LC [auth 7],
LD [auth 8],
LE [auth A],
LF [auth B],
LG [auth B],
LH [auth K],
MA [auth 3],
MB [auth 5],
MC [auth 7],
MD [auth 8],
ME [auth A],
MF [auth B],
MG [auth B],
MH [auth L],
NA [auth 3],
NB [auth 5],
NC [auth 7],
NE [auth A],
NF [auth B],
NG [auth B],
OA [auth 3],
OC [auth 7],
OD [auth A],
OE [auth A],
OF [auth B],
OG [auth B],
PA [auth 3],
PC [auth 7],
PD [auth A],
PE [auth A],
PF [auth B],
PG [auth B],
QA [auth 3],
QC [auth 7],
QD [auth A],
QE [auth A],
QF [auth B],
QG [auth B],
R [auth 1],
RA [auth 3],
RB [auth 6],
RC [auth 7],
RD [auth A],
RE [auth A],
RF [auth B],
RG [auth B],
S [auth 1],
SA [auth 3],
SB [auth 6],
SC [auth 7],
SD [auth A],
SE [auth A],
SF [auth B],
SG [auth B],
T [auth 1],
TB [auth 6],
TC [auth 7],
TD [auth A],
TE [auth A],
TF [auth B],
TG [auth B],
U [auth 1],
UB [auth 6],
UC [auth 7],
UD [auth A],
UE [auth A],
UF [auth B],
UG [auth B],
V [auth 1],
VB [auth 6],
VC [auth 7],
VD [auth A],
VE [auth A],
VF [auth B],
VG [auth B],
W [auth 1],
WA [auth 5],
WB [auth 6],
WD [auth A],
WE [auth A],
WF [auth B],
WG [auth B],
X [auth 1],
XA [auth 5],
XB [auth 6],
XD [auth A],
XE [auth A],
XF [auth B],
XG [auth B],
Y [auth 1],
YA [auth 5],
YB [auth 6],
YC [auth 8],
YD [auth A],
YE [auth A],
YF [auth B],
YG [auth B],
Z [auth 1],
ZA [auth 5],
ZB [auth 6],
ZC [auth 8],
ZD [auth A],
ZE [auth A],
ZF [auth B],
ZG [auth B]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
NEX

Query on NEX


Download:Ideal Coordinates CCD File
QB [auth 5](1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL
C40 H56 O4
PGYAYSRVSAJXTE-OQASCVKESA-N
XAT

Query on XAT


Download:Ideal Coordinates CCD File
HC [auth 6],
ND [auth 8],
PB [auth 5],
UA [auth 3],
XC [auth 7]		(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O4
SZCBXWMUOPQSOX-WVJDLNGLSA-N
LUT

Query on LUT


Download:Ideal Coordinates CCD File
OB [auth 5],
TA [auth 3],
WC [auth 7]		(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O2
KBPHJBAIARWVSC-NSIPBSJQSA-N
BCR

Query on BCR


Download:Ideal Coordinates CCD File
DH [auth F]
FF [auth A]
GF [auth A]
HH [auth J]
IF [auth A]
DH [auth F],
FF [auth A],
GF [auth A],
HH [auth J],
IF [auth A],
VA [auth 3]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
PQN

Query on PQN


Download:Ideal Coordinates CCD File
AH [auth B],
DF [auth A]		PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4

Query on SF4


Download:Ideal Coordinates CCD File
BH [auth C],
CH [auth C],
HF [auth A]		IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONRELION3.1.2

Structure Validation

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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32171183
Chinese Academy of SciencesChinaYSBR-015
Chinese Academy of SciencesChinaY2022038
National Natural Science Foundation of China (NSFC)China31930064
Chinese Academy of SciencesChinaXDB37020101

Revision History  (Full details and data files)

  • Version 1.0: 2026-10-21
    Type: Initial release