9YGV | pdb_00009ygv

Photosystem I FCP Supercomplex from Macrocystis pyrifera


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.47 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9YGV

This is version 1.0 of the entry. See complete history

Literature

Structure of a Photosystem-I-FCP supercomplex from brown alga Macrocystis pyrifera (giant kelp)

Weissman, J.D.Maturana, P.Riddle, R.Wyatt, G.Dubinin, V.G.T.Zerbe, P.Maldonado, M.

To be published.

Macromolecule Content 

  • Total Structure Weight: 855.59 kDa 
  • Atom Count: 52,767 
  • Modeled Residue Count: 5,060 
  • Deposited Residue Count: 5,759 
  • Unique protein chains: 27

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
FCP1A [auth 1]230Macrocystis pyriferaMutation(s): 0 
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
FCP3B [auth 3]191Macrocystis pyriferaMutation(s): 0 
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
FCP5C [auth 5]222Macrocystis pyriferaMutation(s): 0 
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
FCP7D [auth 7]169Macrocystis pyriferaMutation(s): 0 
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
FCP8E [auth 8]215Macrocystis pyriferaMutation(s): 0 
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1F [auth A]749Macrocystis pyriferaMutation(s): 0 
EC: 1.97.1.12
UniProt
Find proteins for A0A8F0JYL2 (Macrocystis pyrifera)
Explore A0A8F0JYL2 
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Entity Groups
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UniProt GroupA0A8F0JYL2
Sequence Annotations
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2G [auth B]734Macrocystis pyriferaMutation(s): 0 
EC: 1.97.1.12
UniProt
Find proteins for A0A8F0F8K8 (Macrocystis pyrifera)
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Entity Groups
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UniProt GroupA0A8F0F8K8
Sequence Annotations
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerH [auth C]81Macrocystis pyriferaMutation(s): 0 
EC: 1.97.1.12
UniProt
Find proteins for A0A8F0F8D0 (Macrocystis pyrifera)
Explore A0A8F0F8D0 
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Entity Groups
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UniProt GroupA0A8F0F8D0
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit III [auth D]132Macrocystis pyriferaMutation(s): 0 
UniProt
Find proteins for A0A8F0F8I9 (Macrocystis pyrifera)
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UniProt GroupA0A8F0F8I9
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IVJ [auth E]61Macrocystis pyriferaMutation(s): 0 
UniProt
Find proteins for A0A8F0F8D1 (Macrocystis pyrifera)
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UniProt GroupA0A8F0F8D1
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIIK [auth F]202Macrocystis pyriferaMutation(s): 0 
UniProt
Find proteins for A0A8F0JY91 (Macrocystis pyrifera)
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Entity Groups
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UniProt GroupA0A8F0JY91
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIL [auth I]36Macrocystis pyriferaMutation(s): 0 
UniProt
Find proteins for A0A8F0F8C2 (Macrocystis pyrifera)
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UniProt GroupA0A8F0F8C2
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXM [auth J]42Macrocystis pyriferaMutation(s): 0 
UniProt
Find proteins for A0A8F0F8B4 (Macrocystis pyrifera)
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Entity Groups
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UniProt GroupA0A8F0F8B4
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIN [auth M]30Macrocystis pyriferaMutation(s): 0 
UniProt
Find proteins for A0A8F0JYJ8 (Macrocystis pyrifera)
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UniProt GroupA0A8F0JYJ8
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaRO [auth R]132Macrocystis pyriferaMutation(s): 0 
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
FCPBP [auth b]141Macrocystis pyriferaMutation(s): 0 
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
FCP6 and FCP10Q [auth 6],
R [auth 10]
212Macrocystis pyriferaMutation(s): 0 
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
FCP11S [auth 11]213Macrocystis pyriferaMutation(s): 0 
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
FCP9 and FCP13AA [auth 9],
T [auth 13]
216Macrocystis pyriferaMutation(s): 0 
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
FCP15U [auth 15]155Macrocystis pyriferaMutation(s): 0 
EC: 1.97.1.12
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
FCP16V [auth 16]163Macrocystis pyriferaMutation(s): 0 
EC: 1.97.1.12
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
FCP17W [auth 17]218Macrocystis pyriferaMutation(s): 0 
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
FCP19X [auth 19]150Macrocystis pyriferaMutation(s): 0 
EC: 1.97.1.12
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
FCP2Y [auth 2]104Macrocystis pyriferaMutation(s): 0 
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
FCP4Z [auth 4]237Macrocystis pyriferaMutation(s): 0 
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIBA [auth L]145Macrocystis pyriferaMutation(s): 0 
UniProt
Find proteins for A0A8F0F8N6 (Macrocystis pyrifera)
Explore A0A8F0F8N6 
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Entity Groups
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UniProt GroupA0A8F0F8N6
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Reference Sequence
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
FCPACA [auth a]151Macrocystis pyriferaMutation(s): 0 

Small Molecules

Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD

Query on DGD



Download:Ideal Coordinates CCD File
AD [auth 8],
IL [auth 4],
SK [auth 4]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA

Query on CLA



Download:Ideal Coordinates CCD File
AC [auth 7]
AE [auth A]
AF [auth A]
AG [auth B]
AI [auth 6]
AC [auth 7],
AE [auth A],
AF [auth A],
AG [auth B],
AI [auth 6],
AK [auth 16],
AM [auth L],
BD [auth A],
BE [auth A],
BF [auth A],
BG [auth B],
BJ [auth 11],
BK [auth 16],
BL [auth 4],
BM [auth L],
CC [auth 7],
CD [auth A],
CE [auth A],
CF [auth B],
CG [auth B],
CJ [auth 11],
CK [auth 16],
DA [auth 1],
DD [auth A],
DE [auth A],
DF [auth B],
DG [auth B],
DJ [auth 11],
DK [auth 16],
DM [auth L],
EB [auth 3],
ED [auth A],
EE [auth A],
EF [auth B],
EG [auth B],
EH [auth F],
EI [auth 6],
EJ [auth 11],
EK [auth 17],
EM [auth a],
FA [auth 1],
FB [auth 5],
FC [auth 7],
FD [auth A],
FE [auth A],
FF [auth B],
FG [auth B],
FH [auth F],
FJ [auth 11],
FK [auth 17],
FM [auth a],
GA [auth 1],
GB [auth 5],
GC [auth 7],
GD [auth A],
GE [auth A],
GF [auth B],
GG [auth B],
GI [auth 6],
GJ [auth 11],
GK [auth 17],
GM [auth a],
HA [auth 1],
HB [auth 5],
HD [auth A],
HE [auth A],
HF [auth B],
HG [auth B],
HK [auth 17],
HL [auth 4],
HM [auth a],
IB [auth 5],
ID [auth A],
IE [auth A],
IF [auth B],
IG [auth B],
IK [auth 17],
JA [auth 1],
JB [auth 5],
JD [auth A],
JE [auth A],
JF [auth B],
JG [auth B],
JJ [auth 11],
KA [auth 1],
KB [auth 5],
KD [auth A],
KE [auth A],
KF [auth B],
KG [auth B],
KI [auth 10],
KJ [auth 11],
KK [auth 17],
LD [auth A],
LE [auth A],
LF [auth B],
LH [auth J],
LI [auth 10],
MA [auth 1],
MC [auth 7],
MD [auth A],
MF [auth B],
MH [auth J],
MI [auth 10],
MJ [auth 11],
MK [auth 17],
ML [auth 9],
NB [auth 5],
NC [auth 8],
ND [auth A],
NF [auth B],
NL [auth 9],
OC [auth 8],
OD [auth A],
OF [auth B],
OI [auth 10],
OJ [auth 11],
OL [auth 9],
PC [auth 8],
PD [auth A],
PF [auth B],
PI [auth 10],
PJ [auth 13],
QA [auth 1],
QC [auth 8],
QD [auth A],
QF [auth B],
QI [auth 10],
QJ [auth 13],
QK [auth 19],
QL [auth 9],
RA [auth 3],
RB [auth 5],
RC [auth 8],
RD [auth A],
RF [auth B],
RH [auth R],
RI [auth 10],
RJ [auth 13],
RK [auth 19],
RL [auth 9],
SD [auth A],
SF [auth B],
SG [auth B],
SI [auth 10],
TA [auth 3],
TD [auth A],
TE [auth A],
TF [auth B],
TH [auth R],
TJ [auth 13],
TL [auth 9],
UA [auth 3],
UD [auth A],
UE [auth A],
UF [auth B],
UG [auth B],
UH [auth 6],
UJ [auth 13],
UK [auth 4],
UL [auth 9],
VA [auth 3],
VB [auth 7],
VD [auth A],
VE [auth A],
VF [auth B],
VH [auth 6],
VJ [auth 13],
VK [auth 4],
WA [auth 3],
WB [auth 7],
WC [auth 8],
WD [auth A],
WF [auth B],
WG [auth B],
WH [auth 6],
WK [auth 4],
XA [auth 3],
XB [auth 7],
XD [auth A],
XE [auth A],
XF [auth B],
XG [auth B],
XH [auth 6],
XK [auth 4],
YB [auth 7],
YD [auth A],
YF [auth B],
YG [auth B],
YJ [auth 15],
YK [auth 4],
YL [auth L],
ZB [auth 7],
ZC [auth 8],
ZD [auth A],
ZF [auth B],
ZH [auth 6],
ZI [auth 10],
ZJ [auth 16]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
LMG

Query on LMG



Download:Ideal Coordinates CCD File
HH [auth F]1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG

Query on LHG



Download:Ideal Coordinates CCD File
EC [auth 7]
JH [auth I]
KL [auth 9]
LA [auth 1]
LJ [auth 11]
EC [auth 7],
JH [auth I],
KL [auth 9],
LA [auth 1],
LJ [auth 11],
LL [auth 9],
NE [auth A],
OE [auth A],
RG [auth B],
SB [auth 5],
TB [auth 5],
TG [auth B],
TK [auth 4],
XL [auth 9],
ZE [auth A]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
A86

Query on A86



Download:Ideal Coordinates CCD File
AB [auth 3]
AJ [auth 10]
BB [auth 3]
CB [auth 3]
EA [auth 1]
AB [auth 3],
AJ [auth 10],
BB [auth 3],
CB [auth 3],
EA [auth 1],
EL [auth 4],
FL [auth 4],
HI [auth 6],
IJ [auth 11],
KH [auth J],
LK [auth 17],
PA [auth 1],
QB [auth 5],
QH [auth R],
SH [auth R],
UC [auth 8],
VI [auth 10],
VL [auth 9]
(3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate
C42 H58 O6
SJWWTRQNNRNTPU-XJUZQKKNSA-N
KC1

Query on KC1



Download:Ideal Coordinates CCD File
AL [auth 4]
BC [auth 7]
BI [auth 6]
CI [auth 6]
CL [auth 4]
AL [auth 4],
BC [auth 7],
BI [auth 6],
CI [auth 6],
CL [auth 4],
DC [auth 7],
DI [auth 6],
DL [auth 4],
HJ [auth 11],
IA [auth 1],
IM [auth a],
JK [auth 17],
MB [auth 5],
NI [auth 10],
PK [auth 17],
PL [auth 9],
SA [auth 3],
SC [auth 8],
SJ [auth 13],
SL [auth 9],
TC [auth 8],
TI [auth 10],
UI [auth 10],
YA [auth 3],
YH [auth 6],
ZA [auth 3],
ZK [auth 4]
Chlorophyll c1
C35 H30 Mg N4 O5
DGNIJJSSARBJSH-QIEHNWLWSA-L
XAT

Query on XAT



Download:Ideal Coordinates CCD File
DB [auth 3]
FI [auth 6]
GL [auth 4]
HC [auth 7]
IC [auth 7]
DB [auth 3],
FI [auth 6],
GL [auth 4],
HC [auth 7],
IC [auth 7],
II [auth 6],
JC [auth 7],
JI [auth 6],
JL [auth 4],
KC [auth 7],
LB [auth 5],
LC [auth 7],
NA [auth 1],
NJ [auth 11],
OB [auth 5],
OH [auth J],
OK [auth 17],
PB [auth 5],
UB [auth 5],
WI [auth 10],
WJ [auth 13],
WL [auth 9],
XC [auth 8],
XI [auth 10],
XJ [auth 13],
YC [auth 8],
YI [auth 10]
(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
BCR

Query on BCR



Download:Ideal Coordinates CCD File
AH [auth B]
CM [auth L]
DH [auth F]
GH [auth F]
IH [auth I]
AH [auth B],
CM [auth L],
DH [auth F],
GH [auth F],
IH [auth I],
MG [auth B],
NG [auth B],
NH [auth J],
NK [auth 17],
OA [auth 1],
OG [auth B],
PE [auth A],
PG [auth B],
PH [auth M],
QE [auth A],
QG [auth B],
RE [auth A],
SE [auth A],
VC [auth 8],
VG [auth B],
YE [auth A],
ZG [auth B],
ZL [auth L]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
PQN

Query on PQN



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

Query on SF4



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

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.47 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONcryoSPARC4.7.1

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited StatesUCD Hellman Foundation
Other privateUnited StatesC-S2C-ST-CA237

Revision History  (Full details and data files)

  • Version 1.0: 2026-06-17
    Type: Initial release