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5GTH

Native XFEL structure of photosystem II (dark dataset)

Functional Information from GO Data
ChainGOidnamespacecontents
A0005506molecular_functioniron ion binding
A0009055molecular_functionelectron transfer activity
A0009523cellular_componentphotosystem II
A0009579cellular_componentthylakoid
A0009635biological_processresponse to herbicide
A0009772biological_processphotosynthetic electron transport in photosystem II
A0010242molecular_functionoxygen evolving activity
A0015979biological_processphotosynthesis
A0016020cellular_componentmembrane
A0016168molecular_functionchlorophyll binding
A0016491molecular_functionoxidoreductase activity
A0016682molecular_functionoxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor
A0019684biological_processphotosynthesis, light reaction
A0031676cellular_componentplasma membrane-derived thylakoid membrane
A0042651cellular_componentthylakoid membrane
A0045156molecular_functionelectron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity
A0046872molecular_functionmetal ion binding
B0009521cellular_componentphotosystem
B0009523cellular_componentphotosystem II
B0009579cellular_componentthylakoid
B0009767biological_processphotosynthetic electron transport chain
B0009772biological_processphotosynthetic electron transport in photosystem II
B0015979biological_processphotosynthesis
B0016020cellular_componentmembrane
B0016168molecular_functionchlorophyll binding
B0019684biological_processphotosynthesis, light reaction
B0031676cellular_componentplasma membrane-derived thylakoid membrane
B0045156molecular_functionelectron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity
B0046872molecular_functionmetal ion binding
C0005737cellular_componentcytoplasm
C0009521cellular_componentphotosystem
C0009523cellular_componentphotosystem II
C0009579cellular_componentthylakoid
C0009767biological_processphotosynthetic electron transport chain
C0009772biological_processphotosynthetic electron transport in photosystem II
C0015979biological_processphotosynthesis
C0016020cellular_componentmembrane
C0016168molecular_functionchlorophyll binding
C0019684biological_processphotosynthesis, light reaction
C0031676cellular_componentplasma membrane-derived thylakoid membrane
C0043229cellular_componentintracellular organelle
C0045156molecular_functionelectron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity
C0046872molecular_functionmetal ion binding
D0009523cellular_componentphotosystem II
D0009579cellular_componentthylakoid
D0009772biological_processphotosynthetic electron transport in photosystem II
D0010242molecular_functionoxygen evolving activity
D0015979biological_processphotosynthesis
D0016020cellular_componentmembrane
D0016168molecular_functionchlorophyll binding
D0016491molecular_functionoxidoreductase activity
D0019684biological_processphotosynthesis, light reaction
D0031676cellular_componentplasma membrane-derived thylakoid membrane
D0045156molecular_functionelectron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity
D0046872molecular_functionmetal ion binding
E0005506molecular_functioniron ion binding
E0005737cellular_componentcytoplasm
E0009055molecular_functionelectron transfer activity
E0009523cellular_componentphotosystem II
E0009539cellular_componentphotosystem II reaction center
E0009579cellular_componentthylakoid
E0009767biological_processphotosynthetic electron transport chain
E0015979biological_processphotosynthesis
E0016020cellular_componentmembrane
E0019684biological_processphotosynthesis, light reaction
E0020037molecular_functionheme binding
E0031676cellular_componentplasma membrane-derived thylakoid membrane
E0042651cellular_componentthylakoid membrane
E0043229cellular_componentintracellular organelle
E0046872molecular_functionmetal ion binding
F0005506molecular_functioniron ion binding
F0005737cellular_componentcytoplasm
F0009055molecular_functionelectron transfer activity
F0009523cellular_componentphotosystem II
F0009539cellular_componentphotosystem II reaction center
F0009579cellular_componentthylakoid
F0009767biological_processphotosynthetic electron transport chain
F0015979biological_processphotosynthesis
F0016020cellular_componentmembrane
F0019684biological_processphotosynthesis, light reaction
F0020037molecular_functionheme binding
F0031676cellular_componentplasma membrane-derived thylakoid membrane
F0042651cellular_componentthylakoid membrane
F0043229cellular_componentintracellular organelle
F0046872molecular_functionmetal ion binding
H0009523cellular_componentphotosystem II
H0009579cellular_componentthylakoid
H0015979biological_processphotosynthesis
H0016020cellular_componentmembrane
H0031676cellular_componentplasma membrane-derived thylakoid membrane
H0042301molecular_functionphosphate ion binding
H0043229cellular_componentintracellular organelle
H0050821biological_processprotein stabilization
I0005737cellular_componentcytoplasm
I0009523cellular_componentphotosystem II
I0009539cellular_componentphotosystem II reaction center
I0009579cellular_componentthylakoid
I0015979biological_processphotosynthesis
I0016020cellular_componentmembrane
I0031676cellular_componentplasma membrane-derived thylakoid membrane
I0042651cellular_componentthylakoid membrane
I0043229cellular_componentintracellular organelle
J0009523cellular_componentphotosystem II
J0009539cellular_componentphotosystem II reaction center
J0009579cellular_componentthylakoid
J0015979biological_processphotosynthesis
J0016020cellular_componentmembrane
J0031676cellular_componentplasma membrane-derived thylakoid membrane
J0042651cellular_componentthylakoid membrane
K0005737cellular_componentcytoplasm
K0009523cellular_componentphotosystem II
K0009539cellular_componentphotosystem II reaction center
K0009579cellular_componentthylakoid
K0015979biological_processphotosynthesis
K0016020cellular_componentmembrane
K0031676cellular_componentplasma membrane-derived thylakoid membrane
K0043229cellular_componentintracellular organelle
L0005737cellular_componentcytoplasm
L0009523cellular_componentphotosystem II
L0009539cellular_componentphotosystem II reaction center
L0009579cellular_componentthylakoid
L0015979biological_processphotosynthesis
L0016020cellular_componentmembrane
L0031676cellular_componentplasma membrane-derived thylakoid membrane
L0042651cellular_componentthylakoid membrane
L0043229cellular_componentintracellular organelle
M0005737cellular_componentcytoplasm
M0009523cellular_componentphotosystem II
M0009579cellular_componentthylakoid
M0015979biological_processphotosynthesis
M0016020cellular_componentmembrane
M0019684biological_processphotosynthesis, light reaction
M0031676cellular_componentplasma membrane-derived thylakoid membrane
M0042651cellular_componentthylakoid membrane
M0043229cellular_componentintracellular organelle
O0009523cellular_componentphotosystem II
O0009579cellular_componentthylakoid
O0009654cellular_componentphotosystem II oxygen evolving complex
O0010207biological_processphotosystem II assembly
O0010242molecular_functionoxygen evolving activity
O0015979biological_processphotosynthesis
O0016020cellular_componentmembrane
O0031676cellular_componentplasma membrane-derived thylakoid membrane
O0042549biological_processphotosystem II stabilization
R0009523cellular_componentphotosystem II
R0009579cellular_componentthylakoid
R0015979biological_processphotosynthesis
R0016020cellular_componentmembrane
R0030145molecular_functionmanganese ion binding
R0031676cellular_componentplasma membrane-derived thylakoid membrane
T0009523cellular_componentphotosystem II
T0009539cellular_componentphotosystem II reaction center
T0009579cellular_componentthylakoid
T0015979biological_processphotosynthesis
T0016020cellular_componentmembrane
T0031676cellular_componentplasma membrane-derived thylakoid membrane
T0042651cellular_componentthylakoid membrane
U0009523cellular_componentphotosystem II
U0009579cellular_componentthylakoid
U0009654cellular_componentphotosystem II oxygen evolving complex
U0015979biological_processphotosynthesis
U0016020cellular_componentmembrane
U0019898cellular_componentextrinsic component of membrane
U0031676cellular_componentplasma membrane-derived thylakoid membrane
U0042549biological_processphotosystem II stabilization
V0005506molecular_functioniron ion binding
V0009055molecular_functionelectron transfer activity
V0009523cellular_componentphotosystem II
V0009579cellular_componentthylakoid
V0015979biological_processphotosynthesis
V0016020cellular_componentmembrane
V0019684biological_processphotosynthesis, light reaction
V0020037molecular_functionheme binding
V0022904biological_processrespiratory electron transport chain
V0031676cellular_componentplasma membrane-derived thylakoid membrane
V0042651cellular_componentthylakoid membrane
V0046872molecular_functionmetal ion binding
X0009523cellular_componentphotosystem II
X0009579cellular_componentthylakoid
X0015979biological_processphotosynthesis
X0016020cellular_componentmembrane
X0031676cellular_componentplasma membrane-derived thylakoid membrane
Y0009523cellular_componentphotosystem II
Y0009579cellular_componentthylakoid
Y0015979biological_processphotosynthesis
Y0016020cellular_componentmembrane
Y0031676cellular_componentplasma membrane-derived thylakoid membrane
Z0009523cellular_componentphotosystem II
Z0009539cellular_componentphotosystem II reaction center
Z0009579cellular_componentthylakoid
Z0015979biological_processphotosynthesis
Z0016020cellular_componentmembrane
Z0031676cellular_componentplasma membrane-derived thylakoid membrane
Z0042549biological_processphotosystem II stabilization
Z0042651cellular_componentthylakoid membrane
a0005506molecular_functioniron ion binding
a0009055molecular_functionelectron transfer activity
a0009523cellular_componentphotosystem II
a0009579cellular_componentthylakoid
a0009635biological_processresponse to herbicide
a0009772biological_processphotosynthetic electron transport in photosystem II
a0010242molecular_functionoxygen evolving activity
a0015979biological_processphotosynthesis
a0016020cellular_componentmembrane
a0016168molecular_functionchlorophyll binding
a0016491molecular_functionoxidoreductase activity
a0016682molecular_functionoxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor
a0019684biological_processphotosynthesis, light reaction
a0031676cellular_componentplasma membrane-derived thylakoid membrane
a0042651cellular_componentthylakoid membrane
a0045156molecular_functionelectron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity
a0046872molecular_functionmetal ion binding
b0009521cellular_componentphotosystem
b0009523cellular_componentphotosystem II
b0009579cellular_componentthylakoid
b0009767biological_processphotosynthetic electron transport chain
b0009772biological_processphotosynthetic electron transport in photosystem II
b0015979biological_processphotosynthesis
b0016020cellular_componentmembrane
b0016168molecular_functionchlorophyll binding
b0019684biological_processphotosynthesis, light reaction
b0031676cellular_componentplasma membrane-derived thylakoid membrane
b0045156molecular_functionelectron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity
b0046872molecular_functionmetal ion binding
c0005737cellular_componentcytoplasm
c0009521cellular_componentphotosystem
c0009523cellular_componentphotosystem II
c0009579cellular_componentthylakoid
c0009767biological_processphotosynthetic electron transport chain
c0009772biological_processphotosynthetic electron transport in photosystem II
c0015979biological_processphotosynthesis
c0016020cellular_componentmembrane
c0016168molecular_functionchlorophyll binding
c0019684biological_processphotosynthesis, light reaction
c0031676cellular_componentplasma membrane-derived thylakoid membrane
c0043229cellular_componentintracellular organelle
c0045156molecular_functionelectron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity
c0046872molecular_functionmetal ion binding
d0009523cellular_componentphotosystem II
d0009579cellular_componentthylakoid
d0009772biological_processphotosynthetic electron transport in photosystem II
d0010242molecular_functionoxygen evolving activity
d0015979biological_processphotosynthesis
d0016020cellular_componentmembrane
d0016168molecular_functionchlorophyll binding
d0016491molecular_functionoxidoreductase activity
d0019684biological_processphotosynthesis, light reaction
d0031676cellular_componentplasma membrane-derived thylakoid membrane
d0045156molecular_functionelectron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity
d0046872molecular_functionmetal ion binding
e0005506molecular_functioniron ion binding
e0005737cellular_componentcytoplasm
e0009055molecular_functionelectron transfer activity
e0009523cellular_componentphotosystem II
e0009539cellular_componentphotosystem II reaction center
e0009579cellular_componentthylakoid
e0009767biological_processphotosynthetic electron transport chain
e0015979biological_processphotosynthesis
e0016020cellular_componentmembrane
e0019684biological_processphotosynthesis, light reaction
e0020037molecular_functionheme binding
e0031676cellular_componentplasma membrane-derived thylakoid membrane
e0042651cellular_componentthylakoid membrane
e0043229cellular_componentintracellular organelle
e0046872molecular_functionmetal ion binding
f0005506molecular_functioniron ion binding
f0005737cellular_componentcytoplasm
f0009055molecular_functionelectron transfer activity
f0009523cellular_componentphotosystem II
f0009539cellular_componentphotosystem II reaction center
f0009579cellular_componentthylakoid
f0009767biological_processphotosynthetic electron transport chain
f0015979biological_processphotosynthesis
f0016020cellular_componentmembrane
f0019684biological_processphotosynthesis, light reaction
f0020037molecular_functionheme binding
f0031676cellular_componentplasma membrane-derived thylakoid membrane
f0042651cellular_componentthylakoid membrane
f0043229cellular_componentintracellular organelle
f0046872molecular_functionmetal ion binding
h0009523cellular_componentphotosystem II
h0009579cellular_componentthylakoid
h0015979biological_processphotosynthesis
h0016020cellular_componentmembrane
h0031676cellular_componentplasma membrane-derived thylakoid membrane
h0042301molecular_functionphosphate ion binding
h0043229cellular_componentintracellular organelle
h0050821biological_processprotein stabilization
i0005737cellular_componentcytoplasm
i0009523cellular_componentphotosystem II
i0009539cellular_componentphotosystem II reaction center
i0009579cellular_componentthylakoid
i0015979biological_processphotosynthesis
i0016020cellular_componentmembrane
i0031676cellular_componentplasma membrane-derived thylakoid membrane
i0042651cellular_componentthylakoid membrane
i0043229cellular_componentintracellular organelle
j0009523cellular_componentphotosystem II
j0009539cellular_componentphotosystem II reaction center
j0009579cellular_componentthylakoid
j0015979biological_processphotosynthesis
j0016020cellular_componentmembrane
j0031676cellular_componentplasma membrane-derived thylakoid membrane
j0042651cellular_componentthylakoid membrane
k0005737cellular_componentcytoplasm
k0009523cellular_componentphotosystem II
k0009539cellular_componentphotosystem II reaction center
k0009579cellular_componentthylakoid
k0015979biological_processphotosynthesis
k0016020cellular_componentmembrane
k0031676cellular_componentplasma membrane-derived thylakoid membrane
k0043229cellular_componentintracellular organelle
l0005737cellular_componentcytoplasm
l0009523cellular_componentphotosystem II
l0009539cellular_componentphotosystem II reaction center
l0009579cellular_componentthylakoid
l0015979biological_processphotosynthesis
l0016020cellular_componentmembrane
l0031676cellular_componentplasma membrane-derived thylakoid membrane
l0042651cellular_componentthylakoid membrane
l0043229cellular_componentintracellular organelle
m0005737cellular_componentcytoplasm
m0009523cellular_componentphotosystem II
m0009579cellular_componentthylakoid
m0015979biological_processphotosynthesis
m0016020cellular_componentmembrane
m0019684biological_processphotosynthesis, light reaction
m0031676cellular_componentplasma membrane-derived thylakoid membrane
m0042651cellular_componentthylakoid membrane
m0043229cellular_componentintracellular organelle
o0009523cellular_componentphotosystem II
o0009579cellular_componentthylakoid
o0009654cellular_componentphotosystem II oxygen evolving complex
o0010207biological_processphotosystem II assembly
o0010242molecular_functionoxygen evolving activity
o0015979biological_processphotosynthesis
o0016020cellular_componentmembrane
o0031676cellular_componentplasma membrane-derived thylakoid membrane
o0042549biological_processphotosystem II stabilization
t0009523cellular_componentphotosystem II
t0009539cellular_componentphotosystem II reaction center
t0009579cellular_componentthylakoid
t0015979biological_processphotosynthesis
t0016020cellular_componentmembrane
t0031676cellular_componentplasma membrane-derived thylakoid membrane
t0042651cellular_componentthylakoid membrane
u0009523cellular_componentphotosystem II
u0009579cellular_componentthylakoid
u0009654cellular_componentphotosystem II oxygen evolving complex
u0015979biological_processphotosynthesis
u0016020cellular_componentmembrane
u0019898cellular_componentextrinsic component of membrane
u0031676cellular_componentplasma membrane-derived thylakoid membrane
u0042549biological_processphotosystem II stabilization
v0005506molecular_functioniron ion binding
v0009055molecular_functionelectron transfer activity
v0009523cellular_componentphotosystem II
v0009579cellular_componentthylakoid
v0015979biological_processphotosynthesis
v0016020cellular_componentmembrane
v0019684biological_processphotosynthesis, light reaction
v0020037molecular_functionheme binding
v0022904biological_processrespiratory electron transport chain
v0031676cellular_componentplasma membrane-derived thylakoid membrane
v0042651cellular_componentthylakoid membrane
v0046872molecular_functionmetal ion binding
x0009523cellular_componentphotosystem II
x0009579cellular_componentthylakoid
x0015979biological_processphotosynthesis
x0016020cellular_componentmembrane
x0031676cellular_componentplasma membrane-derived thylakoid membrane
y0009523cellular_componentphotosystem II
y0009579cellular_componentthylakoid
y0015979biological_processphotosynthesis
y0016020cellular_componentmembrane
y0031676cellular_componentplasma membrane-derived thylakoid membrane
z0009523cellular_componentphotosystem II
z0009539cellular_componentphotosystem II reaction center
z0009579cellular_componentthylakoid
z0015979biological_processphotosynthesis
z0016020cellular_componentmembrane
z0031676cellular_componentplasma membrane-derived thylakoid membrane
z0042549biological_processphotosystem II stabilization
z0042651cellular_componentthylakoid membrane
Functional Information from PROSITE/UniProt
site_idPS00244
Number of Residues27
DetailsREACTION_CENTER Photosynthetic reaction center proteins signature. NwtlnPfHmmGvagvlggallcAiHGA
ChainResidueDetails
DASN190-ALA216
AASN191-SER217

site_idPS00537
Number of Residues15
DetailsCYTOCHROME_B559 Cytochrome b559 subunits heme-binding site signature. ItSVRYwvIHSITIP
ChainResidueDetails
EILE14-PRO28
FILE15-PRO29

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues20
DetailsTOPO_DOM: Lumenal => ECO:0000269|PubMed:21499260
ChainResidueDetails
mFME1-THR11
CLEU276-VAL290
CLEU472-ASP473
cALA23-THR68
cLYS156-ALA177
cLEU276-VAL290
cLEU472-ASP473
MFME1-THR11

site_idSWS_FT_FI2
Number of Residues30
DetailsTRANSMEM: Helical => ECO:0000269|PubMed:21499260
ChainResidueDetails
MALA12-VAL27
mALA12-VAL27
CLYS178-THR200
CTHR255-SER275
CTRP291-ALA312
CARG447-SER471
cLEU69-ALA93
cILE134-ASN155
cLYS178-THR200
cTHR255-SER275
cTRP291-ALA312
cARG447-SER471

site_idSWS_FT_FI3
Number of Residues16
DetailsTOPO_DOM: Cytoplasmic => ECO:0000269|PubMed:21499260
ChainResidueDetails
MGLN28-SER36
mGLN28-SER36
CGLN313-GLY446
cTHR94-ALA133
cASN201-THR254
cGLN313-GLY446

site_idSWS_FT_FI4
Number of Residues2
DetailsMOD_RES: Blocked amino end (Met) => ECO:0000269|PubMed:2503398
ChainResidueDetails
CALA52
CVAL114
CGLY128
CILE160
CVAL233
CGLY247
CLEU426
CPHE437
CGLY440
cTRP35
cLEU49
cALA52
cVAL114
cGLY128
cILE160
cVAL233
cGLY247
cLEU426
cPHE437
cGLY440
bHIS216
bHIS455
bHIS466
bHIS469
MFME1
mFME1

site_idSWS_FT_FI5
Number of Residues2
DetailsBINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_01496, ECO:0000269|PubMed:21499260, ECO:0000269|PubMed:23426624, ECO:0000303|PubMed:19433803
ChainResidueDetails
dGLN129
dPHE261
CGLU367
cGLU367

site_idSWS_FT_FI6
Number of Residues2
DetailsBINDING: BINDING => ECO:0000269|PubMed:21499260, ECO:0000269|PubMed:23426624, ECO:0000303|PubMed:19433803
ChainResidueDetails
dHIS214
dHIS268
AGLN130
aGLN130
DHIS268
dASN142

site_idSWS_FT_FI7
Number of Residues2
DetailsBINDING: BINDING => ECO:0000269|PubMed:19433803, ECO:0000269|PubMed:21499260, ECO:0000269|PubMed:23426624
ChainResidueDetails
ATYR147
aTYR147

site_idSWS_FT_FI8
Number of Residues4
DetailsBINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_01379, ECO:0000269|PubMed:21499260, ECO:0000269|PubMed:23426624, ECO:0000303|PubMed:12518057, ECO:0000303|PubMed:19433803
ChainResidueDetails
AASP170
AALA344
aASP170
aALA344

site_idSWS_FT_FI9
Number of Residues14
DetailsBINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_01379, ECO:0000269|PubMed:21499260, ECO:0000269|PubMed:23426624, ECO:0000303|PubMed:19433803
ChainResidueDetails
ASER264
AHIS272
AHIS332
AGLU333
AASP342
aGLU189
aHIS215
aSER264
aHIS272
aHIS332
aGLU333
aASP342
AGLU189
AHIS215

site_idSWS_FT_FI10
Number of Residues2
DetailsBINDING: axial binding residue => ECO:0000255|HAMAP-Rule:MF_01379, ECO:0000269|PubMed:21499260, ECO:0000269|PubMed:23426624
ChainResidueDetails
AHIS198
aHIS198

site_idSWS_FT_FI11
Number of Residues2
DetailsBINDING: BINDING => ECO:0000269|PubMed:19433803, ECO:0000269|PubMed:21499260
ChainResidueDetails
AMET214
aMET214

site_idSWS_FT_FI12
Number of Residues2
DetailsSITE: Tyrosine radical intermediate => ECO:0000255|HAMAP-Rule:MF_01379, ECO:0000269|PubMed:21499260, ECO:0000303|PubMed:12518057, ECO:0000303|PubMed:23426624
ChainResidueDetails
ATYR161
aTYR161

site_idSWS_FT_FI13
Number of Residues2
DetailsSITE: Stabilizes free radical intermediate => ECO:0000255|HAMAP-Rule:MF_01379
ChainResidueDetails
AHIS190
aHIS190

site_idSWS_FT_FI14
Number of Residues2
DetailsSITE: Cleavage; by CtpA => ECO:0000255|HAMAP-Rule:MF_01379
ChainResidueDetails
AALA344
aALA344

218500

PDB entries from 2024-04-17

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