9GNW | pdb_00009gnw

Universal PSII assembly intermediate


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.93 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

Universal PSII assembly intermediate

Fadeeva, M.Klaiman, D.Nelson, N.

To be published.

Macromolecule Content 

  • Total Structure Weight: 345.8 kDa 
  • Atom Count: 24,204 
  • Modeled Residue Count: 2,619 
  • Deposited Residue Count: 2,619 
  • Unique protein chains: 20

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II protein D1336Dunaliella salinaMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
Find proteins for D0FY08 (Dunaliella salina)
Explore D0FY08 
Go to UniProtKB:  D0FY08
Entity Groups
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UniProt GroupD0FY08
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center protein484Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1C8XRM6 (Dunaliella salina)
Explore A0A1C8XRM6 
Go to UniProtKB:  A0A1C8XRM6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1C8XRM6
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Psb30C [auth V]33Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0FY13 (Dunaliella salina)
Explore D0FY13 
Go to UniProtKB:  D0FY13
Entity Groups
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UniProt GroupD0FY13
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinD [auth C]449Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0FXY3 (Dunaliella salina)
Explore D0FXY3 
Go to UniProtKB:  D0FXY3
Entity Groups
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UniProt GroupD0FXY3
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinE [auth D]348Dunaliella salinaMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
Find proteins for A0A1C8XRK9 (Dunaliella salina)
Explore A0A1C8XRK9 
Go to UniProtKB:  A0A1C8XRK9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1C8XRK9
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaF [auth E]76Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0FY01 (Dunaliella salina)
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Go to UniProtKB:  D0FY01
Entity Groups
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UniProt GroupD0FY01
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaG [auth F]31Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1C8XRP4 (Dunaliella salina)
Explore A0A1C8XRP4 
Go to UniProtKB:  A0A1C8XRP4
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UniProt GroupA0A1C8XRP4
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein H67Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1C8XRP3 (Dunaliella salina)
Explore A0A1C8XRP3 
Go to UniProtKB:  A0A1C8XRP3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1C8XRP3
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein I33Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0FXX5 (Dunaliella salina)
Explore D0FXX5 
Go to UniProtKB:  D0FXX5
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UniProt GroupD0FXX5
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein J36Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1C8XRM8 (Dunaliella salina)
Explore A0A1C8XRM8 
Go to UniProtKB:  A0A1C8XRM8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1C8XRM8
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein K37Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0FXX2 (Dunaliella salina)
Explore D0FXX2 
Go to UniProtKB:  D0FXX2
Entity Groups
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UniProt GroupD0FXX2
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein L36Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0FY19 (Dunaliella salina)
Explore D0FY19 
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Entity Groups
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UniProt GroupD0FY19
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein M31Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0FXZ3 (Dunaliella salina)
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Entity Groups
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UniProt GroupD0FXZ3
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
PsbON [auth O]238Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A7S3QTM3 (Dunaliella tertiolecta)
Explore A0A7S3QTM3 
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Entity Groups
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UniProt GroupA0A7S3QTM3
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
PsbPO [auth P]187Dunaliella salinaMutation(s): 0 
UniProt
Find proteins for A0A9J4RF14 (Dunaliella salina)
Explore A0A9J4RF14 
Go to UniProtKB:  A0A9J4RF14
Entity Groups
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UniProt GroupA0A9J4RF14
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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TP [auth T]30Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0FY04 (Dunaliella salina)
Explore D0FY04 
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Entity Groups
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UniProt GroupD0FY04
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Reference Sequence
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
PSII 6.1 kDa proteinQ [auth W]45Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A9J4RF15 (Dunaliella salina)
Explore A0A9J4RF15 
Go to UniProtKB:  A0A9J4RF15
Entity Groups
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UniProt GroupA0A9J4RF15
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Reference Sequence
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II PsbXR [auth X]33Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A7S3VKF3 (Dunaliella tertiolecta)
Explore A0A7S3VKF3 
Go to UniProtKB:  A0A7S3VKF3
Entity Groups
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UniProt GroupA0A7S3VKF3
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Reference Sequence
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZS [auth Z]61Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0FXZ2 (Dunaliella salina)
Explore D0FXZ2 
Go to UniProtKB:  D0FXZ2
Entity Groups
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UniProt GroupD0FXZ2
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Reference Sequence
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein U, PsbUT [auth U]28Dunaliella salinaMutation(s): 0 

Small Molecules

Ligands 19 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD

Query on DGD



Download:Ideal Coordinates CCD File
DB [auth B],
XB [auth C],
YB [auth C],
ZB [auth C]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA

Query on CLA



Download:Ideal Coordinates CCD File
BA [auth A]
CC [auth D]
EC [auth D]
FC [auth D]
HB [auth C]
BA [auth A],
CC [auth D],
EC [auth D],
FC [auth D],
HB [auth C],
IB [auth C],
JA [auth B],
JB [auth C],
KA [auth B],
KB [auth C],
LA [auth B],
LB [auth C],
MA [auth B],
MB [auth C],
NA [auth B],
NB [auth C],
OA [auth B],
OB [auth C],
PA [auth B],
PB [auth C],
QA [auth B],
QB [auth C],
RA [auth B],
RB [auth C],
SA [auth B],
SB [auth C],
TA [auth B],
TB [auth C],
UA [auth B],
VA [auth B],
WA [auth B],
XA [auth B],
Y [auth A],
YA [auth B],
Z [auth A]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO

Query on PHO



Download:Ideal Coordinates CCD File
AA [auth A],
DC [auth D]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD

Query on SQD



Download:Ideal Coordinates CCD File
DA [auth A],
SC [auth M]
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG

Query on LMG



Download:Ideal Coordinates CCD File
AC [auth C]
BC [auth C]
CB [auth B]
EA [auth A]
GB [auth C]
AC [auth C],
BC [auth C],
CB [auth B],
EA [auth A],
GB [auth C],
IA [auth A],
KC [auth D],
OC [auth H]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9

Query on PL9



Download:Ideal Coordinates CCD File
HC [auth D]2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE
C53 H80 O2
FKUYMLZIRPABFK-UHFFFAOYSA-N
LHG

Query on LHG



Download:Ideal Coordinates CCD File
HA [auth A],
IC [auth D],
JC [auth D],
LC [auth D],
RC [auth L]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
3PH

Query on 3PH



Download:Ideal Coordinates CCD File
EB [auth B]1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
C39 H77 O8 P
YFWHNAWEOZTIPI-DIPNUNPCSA-N
DGA

Query on DGA



Download:Ideal Coordinates CCD File
FB [auth B]DIACYL GLYCEROL
C39 H76 O5
UHUSDOQQWJGJQS-QNGWXLTQSA-N
HEM

Query on HEM



Download:Ideal Coordinates CCD File
MC [auth E]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
C7Z

Query on C7Z



Download:Ideal Coordinates CCD File
BB [auth B](1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol
C40 H56 O2
JKQXZKUSFCKOGQ-ANDPMPNWSA-N
RRX

Query on RRX



Download:Ideal Coordinates CCD File
NC [auth H](3R)-beta,beta-caroten-3-ol
C40 H56 O
DMASLKHVQRHNES-FKKUPVFPSA-N
BCR

Query on BCR



Download:Ideal Coordinates CCD File
AB [auth B]
CA [auth A]
GC [auth D]
PC [auth J]
UB [auth C]
AB [auth B],
CA [auth A],
GC [auth D],
PC [auth J],
UB [auth C],
VB [auth C],
WB [auth C],
ZA [auth B]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMU

Query on LMU



Download:Ideal Coordinates CCD File
QC [auth J]DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
OEX

Query on OEX



Download:Ideal Coordinates CCD File
U [auth A]CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
BCT

Query on BCT



Download:Ideal Coordinates CCD File
GA [auth A]BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2

Query on FE2



Download:Ideal Coordinates CCD File
V [auth A]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
W [auth A],
X [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
FA [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSD
Query on CSD
B
L-PEPTIDE LINKINGC3 H7 N O4 SCYS

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.93 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION4.0.0

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Israel Science FoundationIsrael199/21

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-17
    Type: Initial release