4TNK | pdb_00004tnk

RT XFEL structure of Photosystem II 250 microsec after the third illumination at 5.2 A resolution

External Resource: Annotation


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
L [auth M]SCOP2B SuperfamilyPhotosystem II reaction center protein M, PsbM 8032762 3001573 SCOP2B (2022-06-29)
FA [auth m]SCOP2B SuperfamilyPhotosystem II reaction center protein M, PsbM 8032762 3001573 SCOP2B (2022-06-29)
I [auth J]SCOP2B SuperfamilyPhotosystem II reaction center protein J, PsbJ 8032755 3001534 SCOP2B (2022-06-29)
CA [auth j]SCOP2B SuperfamilyPhotosystem II reaction center protein J, PsbJ 8032755 3001534 SCOP2B (2022-06-29)
BA [auth i]SCOP2B SuperfamilyPhotosystem II reaction center protein I, PsbI 8032754 3001590 SCOP2B (2022-06-29)
H [auth I]SCOP2B SuperfamilyPhotosystem II reaction center protein I, PsbI 8032754 3001590 SCOP2B (2022-06-29)
G [auth H]SCOP2B SuperfamilyPhotosystem II 10 kDa phosphoprotein PsbH 8032753 3001547 SCOP2B (2022-06-29)
AA [auth h]SCOP2B SuperfamilyPhotosystem II 10 kDa phosphoprotein PsbH 8032753 3001547 SCOP2B (2022-06-29)
Z [auth f]SCOP2B SuperfamilyCytochrome b559 subunits 8032752 3001602 SCOP2B (2022-06-29)
FSCOP2B SuperfamilyCytochrome b559 subunits 8032752 3001602 SCOP2B (2022-06-29)
Y [auth e]SCOP2B SuperfamilyCytochrome b559 subunits 8032749 3001602 SCOP2B (2022-06-29)
ESCOP2B SuperfamilyCytochrome b559 subunits 8032749 3001602 SCOP2B (2022-06-29)
X [auth d]SCOP2B SuperfamilyBacterial photosystem II reaction centre, L and M subunits 8032750 3000736 SCOP2B (2022-06-29)
DSCOP2B SuperfamilyBacterial photosystem II reaction centre, L and M subunits 8032750 3000736 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyPhotosystem II antenna protein-like 8032746 3001674 SCOP2B (2022-06-29)
W [auth c]SCOP2B SuperfamilyPhotosystem II antenna protein-like 8032746 3001674 SCOP2B (2022-06-29)
T [auth Z]SCOP2B SuperfamilyPsbZ-like 8032770 3001624 SCOP2B (2022-06-29)
NA [auth z]SCOP2B SuperfamilyPsbZ-like 8032770 3001624 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyPhotosystem II antenna protein-like 8032743 3001674 SCOP2B (2022-06-29)
V [auth b]SCOP2B SuperfamilyPhotosystem II antenna protein-like 8032743 3001674 SCOP2B (2022-06-29)
KA [auth g]SCOP2B SuperfamilyPhotosystem II reaction center protein Ycf12 8093136 3002680 SCOP2B (2022-06-29)
Q [auth y]SCOP2B SuperfamilyPhotosystem II reaction center protein Ycf12 8093136 3002680 SCOP2B (2022-06-29)
JA [auth v]SCOP2B SuperfamilyCytochrome c 8036565 3000815 SCOP2B (2022-06-29)
P [auth V]SCOP2B SuperfamilyCytochrome c 8036565 3000815 SCOP2B (2022-06-29)
IA [auth u]SCOP2B SuperfamilyPsbU/PolX domain-like 8032768 3000893 SCOP2B (2022-06-29)
O [auth U]SCOP2B SuperfamilyPsbU/PolX domain-like 8032768 3000893 SCOP2B (2022-06-29)
HA [auth t]SCOP2B SuperfamilyPhotosystem II reaction center protein T, PsbT 8032769 3001561 SCOP2B (2022-06-29)
N [auth T]SCOP2B SuperfamilyPhotosystem II reaction center protein T, PsbT 8032769 3001561 SCOP2B (2022-06-29)
M [auth O]SCOP2B SuperfamilyOMPA barrel-like 8032765 3000208 SCOP2B (2022-06-29)
GA [auth o]SCOP2B SuperfamilyOMPA barrel-like 8032765 3000208 SCOP2B (2022-06-29)
EA [auth l]SCOP2B SuperfamilyPhotosystem II reaction center protein L, PsbL 8032759 3001523 SCOP2B (2022-06-29)
K [auth L]SCOP2B SuperfamilyPhotosystem II reaction center protein L, PsbL 8032759 3001523 SCOP2B (2022-06-29)
J [auth K]SCOP2B SuperfamilyPhotosystem II reaction center protein K, PsbK 8032757 3001585 SCOP2B (2022-06-29)
DA [auth k]SCOP2B SuperfamilyPhotosystem II reaction center protein K, PsbK 8032757 3001585 SCOP2B (2022-06-29)
U [auth a]SCOP2B SuperfamilyBacterial photosystem II reaction centre, L and M subunits 8032741 3000736 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyBacterial photosystem II reaction centre, L and M subunits 8032741 3000736 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
L [auth M]AP_endonuc_2e4tnkM1 A: alpha bundlesX: YrdC/RibBH: YrdC/RibBT: YrdC/RibBF: AP_endonuc_2ECOD (develop294)
FA [auth m]AP_endonuc_2e4tnkm1 A: alpha bundlesX: YrdC/RibBH: YrdC/RibBT: YrdC/RibBF: AP_endonuc_2ECOD (develop294)
I [auth J]AP_endonuc_2e4tnkJ1 A: alpha bundlesX: YrdC/RibBH: YrdC/RibBT: YrdC/RibBF: AP_endonuc_2ECOD (develop294)
CA [auth j]AP_endonuc_2e4tnkj1 A: alpha bundlesX: YrdC/RibBH: YrdC/RibBT: YrdC/RibBF: AP_endonuc_2ECOD (develop294)
BA [auth i]AP_endonuc_2e4tnki1 A: alpha bundlesX: YrdC/RibBH: YrdC/RibBT: YrdC/RibBF: AP_endonuc_2ECOD (develop294)
H [auth I]AP_endonuc_2e4tnkI1 A: alpha bundlesX: YrdC/RibBH: YrdC/RibBT: YrdC/RibBF: AP_endonuc_2ECOD (develop294)
G [auth H]AP_endonuc_2e4tnkH1 A: alpha bundlesX: YrdC/RibBH: YrdC/RibBT: YrdC/RibBF: AP_endonuc_2ECOD (develop294)
AA [auth h]AP_endonuc_2e4tnkh1 A: alpha bundlesX: YrdC/RibBH: YrdC/RibBT: YrdC/RibBF: AP_endonuc_2ECOD (develop294)
Z [auth f]AP_endonuc_2e4tnkf1 A: alpha bundlesX: YrdC/RibBH: YrdC/RibBT: YrdC/RibBF: AP_endonuc_2ECOD (develop294)
FAP_endonuc_2e4tnkF1 A: alpha bundlesX: YrdC/RibBH: YrdC/RibBT: YrdC/RibBF: AP_endonuc_2ECOD (develop294)
Y [auth e]AP_endonuc_2e4tnke1 A: alpha bundlesX: YrdC/RibBH: YrdC/RibBT: YrdC/RibBF: AP_endonuc_2ECOD (develop294)
EAP_endonuc_2e4tnkE1 A: alpha bundlesX: YrdC/RibBH: YrdC/RibBT: YrdC/RibBF: AP_endonuc_2ECOD (develop294)
X [auth d]AP_endonuc_2e4tnkd1 A: alpha bundlesX: YrdC/RibBH: YrdC/RibBT: YrdC/RibBF: AP_endonuc_2ECOD (develop294)
DAP_endonuc_2e4tnkD1 A: alpha bundlesX: YrdC/RibBH: YrdC/RibBT: YrdC/RibBF: AP_endonuc_2ECOD (develop294)
CAP_endonuc_2e4tnkC1 A: alpha bundlesX: YrdC/RibBH: YrdC/RibBT: YrdC/RibBF: AP_endonuc_2ECOD (develop294)
W [auth c]AP_endonuc_2e4tnkc1 A: alpha bundlesX: YrdC/RibBH: YrdC/RibBT: YrdC/RibBF: AP_endonuc_2ECOD (develop294)
T [auth Z]AP_endonuc_2e4tnkZ1 A: alpha bundlesX: YrdC/RibBH: YrdC/RibBT: YrdC/RibBF: AP_endonuc_2ECOD (develop294)
NA [auth z]AP_endonuc_2e4tnkz1 A: alpha bundlesX: YrdC/RibBH: YrdC/RibBT: YrdC/RibBF: AP_endonuc_2ECOD (develop294)
BAP_endonuc_2e4tnkB1 A: alpha bundlesX: YrdC/RibBH: YrdC/RibBT: YrdC/RibBF: AP_endonuc_2ECOD (develop294)
V [auth b]AP_endonuc_2e4tnkb1 A: alpha bundlesX: YrdC/RibBH: YrdC/RibBT: YrdC/RibBF: AP_endonuc_2ECOD (develop294)
LA [auth x]AP_endonuc_2e4tnkx1 A: alpha bundlesX: YrdC/RibBH: YrdC/RibBT: YrdC/RibBF: AP_endonuc_2ECOD (develop294)
R [auth X]AP_endonuc_2e4tnkX1 A: alpha bundlesX: YrdC/RibBH: YrdC/RibBT: YrdC/RibBF: AP_endonuc_2ECOD (develop294)
KA [auth g]AP_endonuc_2e4tnkg1 A: alpha bundlesX: YrdC/RibBH: YrdC/RibBT: YrdC/RibBF: AP_endonuc_2ECOD (develop294)
Q [auth y]AP_endonuc_2e4tnky1 A: alpha bundlesX: YrdC/RibBH: YrdC/RibBT: YrdC/RibBF: AP_endonuc_2ECOD (develop294)
JA [auth v]AP_endonuc_2e4tnkv1 A: alpha bundlesX: YrdC/RibBH: YrdC/RibBT: YrdC/RibBF: AP_endonuc_2ECOD (develop294)
P [auth V]AP_endonuc_2e4tnkV1 A: alpha bundlesX: YrdC/RibBH: YrdC/RibBT: YrdC/RibBF: AP_endonuc_2ECOD (develop294)
IA [auth u]AP_endonuc_2e4tnku1 A: alpha bundlesX: YrdC/RibBH: YrdC/RibBT: YrdC/RibBF: AP_endonuc_2ECOD (develop294)
O [auth U]AP_endonuc_2e4tnkU1 A: alpha bundlesX: YrdC/RibBH: YrdC/RibBT: YrdC/RibBF: AP_endonuc_2ECOD (develop294)
HA [auth t]AP_endonuc_2e4tnkt1 A: alpha bundlesX: YrdC/RibBH: YrdC/RibBT: YrdC/RibBF: AP_endonuc_2ECOD (develop294)
N [auth T]AP_endonuc_2e4tnkT1 A: alpha bundlesX: YrdC/RibBH: YrdC/RibBT: YrdC/RibBF: AP_endonuc_2ECOD (develop294)
M [auth O]AP_endonuc_2e4tnkO1 A: alpha bundlesX: YrdC/RibBH: YrdC/RibBT: YrdC/RibBF: AP_endonuc_2ECOD (develop294)
GA [auth o]AP_endonuc_2e4tnko1 A: alpha bundlesX: YrdC/RibBH: YrdC/RibBT: YrdC/RibBF: AP_endonuc_2ECOD (develop294)
EA [auth l]AP_endonuc_2e4tnkl1 A: alpha bundlesX: YrdC/RibBH: YrdC/RibBT: YrdC/RibBF: AP_endonuc_2ECOD (develop294)
K [auth L]AP_endonuc_2e4tnkL1 A: alpha bundlesX: YrdC/RibBH: YrdC/RibBT: YrdC/RibBF: AP_endonuc_2ECOD (develop294)
J [auth K]AP_endonuc_2e4tnkK1 A: alpha bundlesX: YrdC/RibBH: YrdC/RibBT: YrdC/RibBF: AP_endonuc_2ECOD (develop294)
DA [auth k]AP_endonuc_2e4tnkk1 A: alpha bundlesX: YrdC/RibBH: YrdC/RibBT: YrdC/RibBF: AP_endonuc_2ECOD (develop294)
U [auth a]AP_endonuc_2e4tnka1 A: alpha bundlesX: YrdC/RibBH: YrdC/RibBT: YrdC/RibBF: AP_endonuc_2ECOD (develop294)
AAP_endonuc_2e4tnkA1 A: alpha bundlesX: YrdC/RibBH: YrdC/RibBT: YrdC/RibBF: AP_endonuc_2ECOD (develop294)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
FA [auth m],
L [auth M]		PF05151Photosystem II reaction centre M protein (PsbM) (PsbM)Photosystem II reaction centre M protein (PsbM)- Family
BA [auth i],
H [auth I]		PF02532Photosystem II reaction centre I protein (PSII 4.8 kDa protein) (PsbI)Photosystem II reaction centre I protein (PSII 4.8 kDa protein)- Family
AA [auth h],
G [auth H]		PF00737Photosystem II 10 kDa phosphoprotein (PsbH)Photosystem II 10 kDa phosphoprotein- Family
E,
Y [auth e]		PF00283Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits (Cytochrom_B559)Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits- Family
E,
Y [auth e]		PF00284Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit (Cytochrom_B559a)Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit- Family
D,
X [auth d]		PF00124Photosynthetic reaction centre protein (Photo_RC)Photosynthetic reaction centre protein- Family
C,
W [auth c]		PF00421Photosystem II protein (PSII)Photosystem II protein- Family
NA [auth z],
T [auth Z]		PF01737YCF9 (Ycf9)YCF9- Family
LA [auth x],
R [auth X]		PF06596Photosystem II reaction centre X protein (PsbX) (PsbX)Photosystem II reaction centre X protein (PsbX)- Family
JA [auth v],
P [auth V]		PF14495Cytochrome c-550 domain (Cytochrom_C550)Cytochrome c-550 domainThis domain is a heme binding cytochrome known as cytochrome c550, or cytochrome c549, or PsbV [1]. Domain
IA [auth u],
O [auth U]		PF06514Photosystem II 12 kDa extrinsic protein (PsbU) (PsbU)Photosystem II 12 kDa extrinsic protein (PsbU)- Family
HA [auth t],
N [auth T]		PF01405Photosystem II reaction centre T protein (PsbT)Photosystem II reaction centre T proteinThe exact function of this protein is unknown. It probably consists of a single transmembrane spanning helix. The Swiss:P37256 protein, appears to be (i) a novel photosystem II subunit and (ii) required for maintaining optimal photosystem II activity ...The exact function of this protein is unknown. It probably consists of a single transmembrane spanning helix. The Swiss:P37256 protein, appears to be (i) a novel photosystem II subunit and (ii) required for maintaining optimal photosystem II activity under adverse growth conditions [1].
Domain
EA [auth l],
K [auth L]		PF02419PsbL protein (PsbL)PsbL protein- Family
A,
U [auth a]		PF00124Photosynthetic reaction centre protein (Photo_RC)Photosynthetic reaction centre protein- Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
FA [auth m],
L [auth M]		Photosystem II reaction center protein M-
CA [auth j],
I [auth J]		Photosystem II reaction center protein J-
BA [auth i],
H [auth I]		Photosystem II reaction center protein I-
AA [auth h],
G [auth H]		Photosystem II reaction center protein H
F,
Z [auth f]		Cytochrome b559 subunit beta
E,
Y [auth e]		Cytochrome b559 subunit alpha
D,
X [auth d]		Photosystem II D2 protein
C,
W [auth c]		Photosystem II CP43 protein
NA [auth z],
T [auth Z]		Photosystem II reaction center protein Z-
B,
V [auth b]		Photosystem II core light harvesting protein
MA [auth G],
S [auth Y]		Photosystem II reaction center protein Y---
LA [auth x],
R [auth X]		Photosystem II reaction center X protein-
KA [auth g],
Q [auth y]		Photosystem II reaction center protein Ycf12-
JA [auth v],
P [auth V]		Cytochrome c-550
IA [auth u],
O [auth U]		Photosystem II 12 kDa extrinsic protein-
HA [auth t],
N [auth T]		Photosystem II reaction center protein T-
GA [auth o],
M [auth O]		Photosystem II manganese-stabilizing polypeptide
EA [auth l],
K [auth L]		Photosystem II reaction center protein L-
DA [auth k],
J [auth K]		Photosystem II reaction center protein K-
A,
U [auth a]		Photosystem Q(B) protein 1

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
FA [auth m],
L [auth M]		IPR007826Photosystem II PsbMFamily
FA [auth m],
L [auth M]		IPR037269Photosystem II PsbM superfamilyHomologous Superfamily
CA [auth j],
I [auth J]		IPR002682Photosystem II PsbJFamily
CA [auth j],
I [auth J]		IPR037267Photosystem II PsbJ superfamilyHomologous Superfamily
BA [auth i],
H [auth I]		IPR037271Photosystem II PsbI superfamilyHomologous Superfamily
BA [auth i],
H [auth I]		IPR003686Photosystem II PsbIFamily
AA [auth h],
G [auth H]		IPR036863Photosystem II reaction centre protein H superfamilyHomologous Superfamily
AA [auth h],
G [auth H]		IPR001056Photosystem II reaction centre protein HFamily
F,
Z [auth f]		IPR006241Photosystem II cytochrome b559, beta subunitFamily
F,
Z [auth f]		IPR013081Photosystem II cytochrome b559, N-terminalDomain
F,
Z [auth f]		IPR006216Photosystem II cytochrome b559, conserved siteConserved Site
E,
Y [auth e]		IPR013081Photosystem II cytochrome b559, N-terminalDomain
E,
Y [auth e]		IPR006217Photosystem II cytochrome b559, alpha subunitFamily
E,
Y [auth e]		IPR013082Photosystem II cytochrome b559, alpha subunit, lumenal regionDomain
E,
Y [auth e]		IPR037025Photosystem II cytochrome b559, alpha subunit superfamilyHomologous Superfamily
E,
Y [auth e]		IPR006216Photosystem II cytochrome b559, conserved siteConserved Site
D,
X [auth d]		IPR005868Photosystem II D2Family
D,
X [auth d]		IPR036854Photosystem II protein D1/D2 superfamilyHomologous Superfamily
D,
X [auth d]		IPR000484Photosynthetic reaction centre, L/MFamily
D,
X [auth d]		IPR055265Photosynthetic reaction centre, L/M, conserved siteConserved Site
D,
X [auth d]		IPR055266Photosystem II protein D1/D2Family
C,
W [auth c]		IPR036001Photosystem antenna protein-like superfamilyHomologous Superfamily
C,
W [auth c]		IPR000932Photosystem antenna protein-likeFamily
C,
W [auth c]		IPR005869Photosystem II CP43 reaction centre proteinFamily
C,
W [auth c]		IPR044900Photosystem II CP43 reaction centre protein superfamilyHomologous Superfamily
NA [auth z],
T [auth Z]		IPR036512Photosystem II PsbZ superfamilyHomologous Superfamily
NA [auth z],
T [auth Z]		IPR002644Photosystem II PsbZ, reaction centreFamily
B,
V [auth b]		IPR036001Photosystem antenna protein-like superfamilyHomologous Superfamily
B,
V [auth b]		IPR000932Photosystem antenna protein-likeFamily
B,
V [auth b]		IPR017486Photosystem II CP47 reaction centre proteinFamily
LA [auth x],
R [auth X]		IPR009518Photosystem II PsbXFamily
LA [auth x],
R [auth X]		IPR023431Photosystem II PsbX, type 1 subfamilyFamily
KA [auth g],
Q [auth y]		IPR010284Photosystem II reaction center protein Ycf12Family
JA [auth v],
P [auth V]		IPR017851Photosystem II extrinsic protein V, cytochrome c-550 precursorFamily
JA [auth v],
P [auth V]		IPR016003Photosystem II extrinsic protein V, cytochrome c-550 precursor-likeFamily
JA [auth v],
P [auth V]		IPR036909Cytochrome c-like domain superfamilyHomologous Superfamily
JA [auth v],
P [auth V]		IPR009056Cytochrome c-like domainDomain
JA [auth v],
P [auth V]		IPR029490Cytochrome c-550 domainDomain
IA [auth u],
O [auth U]		IPR010527Photosystem II PsbU, oxygen evolving complexFamily
HA [auth t],
N [auth T]		IPR001743Photosystem II PsbTFamily
HA [auth t],
N [auth T]		IPR037268Photosystem II PsbT superfamilyHomologous Superfamily
GA [auth o],
M [auth O]		IPR011250Outer membrane protein/outer membrane enzyme PagP, beta-barrelHomologous Superfamily
GA [auth o],
M [auth O]		IPR002628Photosystem II extrinsic protein OFamily
EA [auth l],
K [auth L]		IPR003372Photosystem II PsbLFamily
EA [auth l],
K [auth L]		IPR037266Photosystem II PsbL superfamilyHomologous Superfamily
DA [auth k],
J [auth K]		IPR037270Photosystem II PsbK superfamilyHomologous Superfamily
DA [auth k],
J [auth K]		IPR003687Photosystem II PsbKFamily
A,
U [auth a]		IPR036854Photosystem II protein D1/D2 superfamilyHomologous Superfamily
A,
U [auth a]		IPR005867Photosystem II protein D1Family
A,
U [auth a]		IPR000484Photosynthetic reaction centre, L/MFamily
A,
U [auth a]		IPR055265Photosynthetic reaction centre, L/M, conserved siteConserved Site
A,
U [auth a]		IPR055266Photosystem II protein D1/D2Family

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

ChainsExternal LinkComment
PDBTMAnnotated as membrane protein by PDBTM