8TOW

Structure of a mutated photosystem II complex reveals perturbation of the oxygen-evolving complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.14 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Mutation-induced shift of the photosystem II active site reveals insight into conserved water channels

Flesher, D.A.Brudvig, G.W.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein D1 2A,
V [auth a]
360Synechocystis sp. PCC 6803Mutation(s): 0 
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinB,
W [auth b]
507Synechocystis sp. PCC 6803Mutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinC,
X [auth c]
460Synechocystis sp. PCC 6803Mutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinD,
Y [auth d]
352Synechocystis sp. PCC 6803Mutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaE,
Z [auth e]
81Synechocystis sp. PCC 6803Mutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaAA [auth f],
F
44Synechocystis sp. PCC 6803Mutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HBA [auth h],
G [auth H]
64Synechocystis sp. PCC 6803Mutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ICA [auth i],
H [auth I]
38Synechocystis sp. PCC 6803Mutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein JDA [auth j],
I [auth J]
39Synechocystis sp. PCC 6803Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KEA [auth k],
J [auth K]
45Synechocystis sp. PCC 6803Mutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LFA [auth l],
K [auth L]
39Synechocystis sp. PCC 6803Mutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MGA [auth m],
L [auth M]
35Synechocystis sp. PCC 6803Mutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II manganese-stabilizing polypeptideHA [auth o],
M [auth O]
274Synechocystis sp. PCC 6803Mutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Sll1638 proteinIA [auth q],
N [auth Q]
149Synechocystis sp. PCC 6803Mutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein YJA [auth r],
O [auth R]
39Synechocystis sp. PCC 6803Mutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TKA [auth t],
P [auth T]
31Synechocystis sp. PCC 6803Mutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II 12 kDa extrinsic proteinLA [auth u],
Q [auth U]
131Synechocystis sp. PCC 6803Mutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c-550MA [auth v],
R [auth V]
160Synechocystis sp. PCC 6803Mutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center X proteinNA [auth x],
S [auth X]
39Synechocystis sp. PCC 6803Mutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12OA [auth y],
T [auth Y]
39Synechocystis sp. PCC 6803Mutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZPA [auth z],
U [auth Z]
62Synechocystis sp. PCC 6803Mutation(s): 0 
UniProt
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Small Molecules
Ligands 16 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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AD [auth C]
CE [auth H]
KH [auth c]
LH [auth c]
MH [auth c]
AD [auth C],
CE [auth H],
KH [auth c],
LH [auth c],
MH [auth c],
OI [auth h],
YC [auth C],
ZC [auth C]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA
Query on CLA

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AG [auth b]
AH [auth c]
BG [auth b]
BH [auth c]
CG [auth b]
AG [auth b],
AH [auth c],
BG [auth b],
BH [auth c],
CG [auth b],
CH [auth c],
DG [auth b],
DH [auth c],
EG [auth b],
EH [auth c],
FG [auth b],
FH [auth c],
GD [auth D],
GF [auth a],
GG [auth b],
GH [auth c],
HB [auth B],
HF [auth a],
HG [auth b],
HH [auth c],
IB [auth B],
ID [auth D],
IG [auth b],
IH [auth c],
JB [auth B],
JD [auth D],
JF [auth a],
KB [auth B],
KC [auth C],
LB [auth B],
LC [auth C],
MB [auth B],
MC [auth C],
NB [auth B],
NC [auth C],
OB [auth B],
OC [auth C],
PB [auth B],
PC [auth C],
QB [auth B],
QC [auth C],
RB [auth B],
RC [auth C],
SB [auth B],
SC [auth C],
SH [auth d],
TB [auth B],
TC [auth C],
TF [auth b],
UA [auth A],
UB [auth B],
UC [auth C],
UF [auth b],
UH [auth d],
VA [auth A],
VB [auth B],
VC [auth C],
VF [auth b],
VH [auth d],
WB [auth B],
WC [auth C],
WF [auth b],
WG [auth c],
XA [auth A],
XF [auth b],
XG [auth c],
YF [auth b],
YG [auth c],
ZF [auth b],
ZG [auth c]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO
Query on PHO

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HD [auth D],
IF [auth a],
TH [auth d],
WA [auth A]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD
Query on SQD

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AC [auth B]
BB [auth A]
BE [auth H]
CB [auth A]
JC [auth C]
AC [auth B],
BB [auth A],
BE [auth H],
CB [auth A],
JC [auth C],
JE [auth K],
JI [auth f],
MG [auth b],
NF [auth a],
NI [auth h],
OF [auth a],
VG [auth c],
VI [auth k],
XD [auth F]
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

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AI [auth d]
BC [auth B]
BD [auth C]
DB [auth A]
DD [auth C]
AI [auth d],
BC [auth B],
BD [auth C],
DB [auth A],
DD [auth C],
DE [auth H],
LF [auth a],
NG [auth b],
NH [auth c],
OD [auth D],
PF [auth a],
PH [auth c],
PI [auth h],
ZA [auth A]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9
Query on PL9

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AB [auth A],
KD [auth D],
MF [auth a],
WH [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

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BF [auth Z]
FI [auth e]
GC [auth B]
HC [auth B]
LD [auth D]
BF [auth Z],
FI [auth e],
GC [auth B],
HC [auth B],
LD [auth D],
MD [auth D],
ND [auth D],
NJ [auth z],
SG [auth b],
TD [auth E],
TG [auth b],
XH [auth d],
YH [auth d],
ZH [auth d]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEM
Query on HEM

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EJ [auth v],
HI [auth e],
SE [auth V],
VD [auth E]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
RRX
Query on RRX

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LI [auth h],
ZD [auth H]
(3R)-beta,beta-caroten-3-ol
C40 H56 O
DMASLKHVQRHNES-FKKUPVFPSA-N
BCR
Query on BCR

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AF [auth Z]
II [auth f]
JG [auth b]
JH [auth c]
KE [auth K]
AF [auth Z],
II [auth f],
JG [auth b],
JH [auth c],
KE [auth K],
KF [auth a],
KG [auth b],
LE [auth K],
LG [auth b],
MJ [auth z],
WD [auth F],
WI [auth k],
XB [auth B],
XC [auth C],
XI [auth k],
YA [auth A],
YB [auth B],
ZB [auth B]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT

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AE [auth H]
AJ [auth m]
BI [auth d]
BJ [auth m]
CC [auth B]
AE [auth H],
AJ [auth m],
BI [auth d],
BJ [auth m],
CC [auth B],
CD [auth C],
CI [auth d],
CJ [auth t],
DC [auth B],
DI [auth d],
EB [auth A],
EC [auth B],
ED [auth C],
EE [auth I],
EI [auth e],
FB [auth A],
FC [auth B],
FD [auth C],
FE [auth I],
GE [auth I],
GI [auth e],
GJ [auth x],
HE [auth I],
HJ [auth x],
IC [auth B],
IE [auth J],
IJ [auth x],
JJ [auth x],
KI [auth f],
KJ [auth x],
LJ [auth y],
MI [auth h],
NE [auth K],
OE [auth M],
OG [auth b],
OH [auth c],
PD [auth D],
PE [auth M],
PG [auth b],
QD [auth D],
QE [auth T],
QF [auth a],
QG [auth b],
QH [auth c],
QI [auth i],
RD [auth D],
RF [auth a],
RG [auth b],
RH [auth c],
RI [auth i],
SD [auth E],
SI [auth i],
TI [auth i],
UD [auth E],
UE [auth X],
UG [auth b],
UI [auth j],
VE [auth X],
WE [auth X],
XE [auth X],
YD [auth F],
YE [auth X],
ZE [auth Y],
ZI [auth k]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
OEX (Subject of Investigation/LOI)
Query on OEX

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CF [auth a],
QA [auth A]
CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
BCT
Query on BCT

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GB [auth A],
SF [auth a]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2
Query on FE2

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DF [auth a],
RA [auth A]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CA
Query on CA

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DJ [auth u]
FJ [auth v]
ME [auth K]
RE [auth U]
TE [auth V]
DJ [auth u],
FJ [auth v],
ME [auth K],
RE [auth U],
TE [auth V],
YI [auth k]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

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EF [auth a],
FF [auth a],
SA [auth A],
TA [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
CA [auth i],
H [auth I]
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.14 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-19
    Type: Initial release