8B6H | pdb_00008b6h

Cryo-EM structure of cytochrome c oxidase dimer (complex IV) from respiratory supercomplex of Tetrahymena thermophila

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: mpstruc
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
XC [auth Ey]	F_UNCLASSIFIED	e8b6hEy1	A: few secondary structure elements	X: Tim10/DDP (From Topology)	H: Tim10/DDP (From Topology)	T: Tim10/DDP	F: F_UNCLASSIFIED	ECOD (1.6)
XA [auth EY]	F_UNCLASSIFIED	e8b6hEY1	A: few secondary structure elements	X: Tim10/DDP (From Topology)	H: Tim10/DDP (From Topology)	T: Tim10/DDP	F: F_UNCLASSIFIED	ECOD (1.6)
WA [auth EX]	F_UNCLASSIFIED	e8b6hEX1	A: few secondary structure elements	X: Tim10/DDP (From Topology)	H: Tim10/DDP (From Topology)	T: Tim10/DDP	F: F_UNCLASSIFIED	ECOD (1.6)
WC [auth Ex]	F_UNCLASSIFIED	e8b6hEx1	A: few secondary structure elements	X: Tim10/DDP (From Topology)	H: Tim10/DDP (From Topology)	T: Tim10/DDP	F: F_UNCLASSIFIED	ECOD (1.6)
SA [auth ET]	F_UNCLASSIFIED	e8b6hET1	A: few secondary structure elements	X: Tim10/DDP (From Topology)	H: Tim10/DDP (From Topology)	T: Tim10/DDP	F: F_UNCLASSIFIED	ECOD (1.6)
SC [auth Et]	F_UNCLASSIFIED	e8b6hEt1	A: few secondary structure elements	X: Tim10/DDP (From Topology)	H: Tim10/DDP (From Topology)	T: Tim10/DDP	F: F_UNCLASSIFIED	ECOD (1.6)
OA [auth EP]	F_UNCLASSIFIED	e8b6hEP1	A: alpha bundles	X: ACP-like	H: Acyl-carrier protein (ACP) (From Topology)	T: Acyl-carrier protein (ACP)	F: F_UNCLASSIFIED	ECOD (1.6)
OC [auth Ep]	F_UNCLASSIFIED	e8b6hEp1	A: alpha bundles	X: ACP-like	H: Acyl-carrier protein (ACP) (From Topology)	T: Acyl-carrier protein (ACP)	F: F_UNCLASSIFIED	ECOD (1.6)
U [auth DV]	F_UNCLASSIFIED	e8b6hDV1	A: alpha complex topology	X: Mitochondrial ADP/ATP carrier-like	H: Mitochondrial ADP/ATP carrier (From Topology)	T: Mitochondrial ADP/ATP carrier	F: F_UNCLASSIFIED	ECOD (1.6)
UB [auth Dv]	F_UNCLASSIFIED	e8b6hDv1	A: alpha complex topology	X: Mitochondrial ADP/ATP carrier-like	H: Mitochondrial ADP/ATP carrier (From Topology)	T: Mitochondrial ADP/ATP carrier	F: F_UNCLASSIFIED	ECOD (1.6)
R [auth DS]	F_UNCLASSIFIED	e8b6hDS1	A: alpha complex topology	X: Mitochondrial ADP/ATP carrier-like	H: Mitochondrial ADP/ATP carrier (From Topology)	T: Mitochondrial ADP/ATP carrier	F: F_UNCLASSIFIED	ECOD (1.6)
RB [auth Ds]	F_UNCLASSIFIED	e8b6hDs1	A: alpha complex topology	X: Mitochondrial ADP/ATP carrier-like	H: Mitochondrial ADP/ATP carrier (From Topology)	T: Mitochondrial ADP/ATP carrier	F: F_UNCLASSIFIED	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
AD [auth Dl], BD [auth DL]	PF00415	Regulator of chromosome condensation (RCC1) repeat (RCC1)	Regulator of chromosome condensation (RCC1) repeat	-	Repeat
ZA [auth FA], ZC [auth Fa]	PF02953	Tim10/DDP family zinc finger (zf-Tim10_DDP)	Tim10/DDP family zinc finger	Putative zinc binding domain with four conserved cysteine residues. This domain is found in the human disease protein Swiss:O60220. Members of this family such as Tim9 and Tim10 are involved in mitochondrial protein import [1]. Members of thi ...	Putative zinc binding domain with four conserved cysteine residues. This domain is found in the human disease protein Swiss:O60220. Members of this family such as Tim9 and Tim10 are involved in mitochondrial protein import [1]. Members of this family seem to be localised to the mitochondrial intermembrane space [2].	Domain
D [auth DD], DB [auth Dd]	PF01215	Cytochrome c oxidase subunit Vb (COX5B)	Cytochrome c oxidase subunit Vb		Domain
V [auth DW], VB [auth Dw]	PF02104	SURF1 family (SURF1)	SURF1 family	-	Family
U [auth DV], UB [auth Dv]	PF00153	Mitochondrial carrier protein (Mito_carr)	Mitochondrial carrier protein	-	Repeat
T [auth DU], TB [auth Du]	PF00153	Mitochondrial carrier protein (Mito_carr)	Mitochondrial carrier protein	-	Repeat
R [auth DS], RB [auth Ds]	PF00153	Mitochondrial carrier protein (Mito_carr)	Mitochondrial carrier protein	-	Repeat
O [auth DP], OB [auth Dp]	PF02104	SURF1 family (SURF1)	SURF1 family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
I [auth DI], IB [auth Di]	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial	-	-	-
H [auth DH], HB [auth Dh]	Transmembrane protein, putative	-	-	-
G [auth DG], GB [auth Dg]	Transmembrane protein, putative	-	-	-
F [auth DF], FB [auth Df]	Structural protein	-	-	-
AD [auth Dl], BD [auth DL]	COXBP,Chromosome condensation regulator RCC1 repeat protein,Chromosome condensation regulator RCC1 repeat protein	-	-	-
ZA [auth FA], ZC [auth Fa]	Tim10/DDP family zinc finger protein	-	localization establishment of protein localization protein transport transport macromolecule localization intracellular protein localization establishment of localization	membrane-bounded organelle mitochondrial membrane intracellular anatomical structure organelle inner membrane mitochondrion membrane intracellular membrane-bounded organelle mitochondrial inner membrane intracellular organelle organelle envelope cellular anatomical structure organelle mitochondrial envelope cytoplasm membrane-bounded organelle mitochondrial membrane intracellular anatomical structure organelle inner membrane mitochondrion membrane intracellular membrane-bounded organelle mitochondrial inner membrane intracellular organelle organelle envelope cellular anatomical structure organelle mitochondrial envelope cytoplasm organelle membrane
YA [auth EZ], YC [auth Ez]	Transposase	-	-	-
XA [auth EY], XC [auth Ey]	Annexin	-	-	-
E [auth DE], EB [auth De]	Transmembrane protein, putative	-	-	-
WA [auth EX], WC [auth Ex]	Zf-Tim10_DDP domain-containing protein	-	-	-
VA [auth EW], VC [auth Ew]	Cullin domain-containing protein	-	-	-
UA [auth EJ], UC [auth Ej]	YflT domain-containing protein	-	-	-
TA [auth EU], TC [auth Eu]	ABC transporter	-	-	-
SA [auth ET], SC [auth Et]	Zf-Tim10_DDP domain-containing protein	-	-	-
RA [auth ES], RC [auth Es]	Ymf70	-	-	-
QA [auth ER], QC [auth Er]	Lysozyme	-	-	-
PA [auth EQ], PC [auth Eq]	Transmembrane protein, putative	-	-	-
OA [auth EP], OC [auth Ep]	Phage protein	-	-	-
NA [auth EO], NC [auth Eo]	Transmembrane protein, putative	-	-	-
D [auth DD], DB [auth Dd]	Cytochrome C oxidase subunit Vb protein	cation binding ion binding binding metal ion binding small molecule binding	aerobic respiration cellular respiration aerobic electron transport chain oxidative phosphorylation energy derivation by oxidation of organic compounds ATP synthesis coupled electron transport electron transport chain generation of precursor metabolites and energy mitochondrial electron transport, cytochrome c to oxygen respiratory electron transport chain metabolic process cellular process mitochondrial ATP synthesis coupled electron transport	membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure intracellular anatomical structure mitochondrion mitochondrial envelope organelle cytoplasm intracellular membrane-bounded organelle respiratory chain complex protein-containing complex cytochrome complex catalytic complex membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure intracellular anatomical structure mitochondrion mitochondrial envelope organelle cytoplasm intracellular membrane-bounded organelle respiratory chain complex protein-containing complex cytochrome complex catalytic complex transmembrane transporter complex membrane membrane protein complex respiratory chain complex IV transporter complex
MA [auth EN], MC [auth En]	COXTT22	-	-	-
LA [auth EM], LC [auth Em]	Transmembrane protein, putative	-	-	-
KA [auth EL], KC [auth El]	Transmembrane protein, putative	-	-	-
JA [auth EK], JC [auth Ek]	Complex III subunit VII	-	-	-
IA [auth EV], IC [auth Ev]	Decapping nuclease	-	-	-
HA [auth EI], HC [auth Ei]	Transmembrane protein	-	-	-
GA [auth EH], GC [auth Eh]	Transmembrane protein, putative	-	-	-
FA [auth EG], FC [auth Eg]	COXTT28	-	-	-
EA [auth EF], EC [auth Ef]	Iron-binding zinc finger CDGSH type protein	iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding cation binding ion binding metal ion binding	-	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle
DA [auth EE], DC [auth Ee]	Mobilization protein	-	-	-
C [auth DC], CB [auth Dc]	Ymf68	-	-	-
CA [auth ED], CC [auth Ed]	Ymf75	-	-	-
BA [auth EC], BC [auth Ec]	COXTT27	-	-	-
AA [auth EB], AC [auth Eb]	Transmembrane protein, putative	-	-	-
Z [auth EA], ZB [auth Ea]	COXTT12,Transmembrane protein,Transmembrane protein	-	-	-
Y [auth DZ], YB [auth Dz]	39S ribosomal protein L9, mitochondrial	-	-	-
X [auth DY], XB [auth Dy]	COXTT10	-	-	-
W [auth DX], WB [auth Dx]	COXTT9	-	-	-
V [auth DW], VB [auth Dw]	SURF1-like protein	-	-	membrane-bounded organelle mitochondrial membrane intracellular anatomical structure organelle inner membrane mitochondrion membrane intracellular membrane-bounded organelle mitochondrial inner membrane intracellular organelle organelle envelope cellular anatomical structure organelle mitochondrial envelope cytoplasm membrane-bounded organelle mitochondrial membrane intracellular anatomical structure organelle inner membrane mitochondrion membrane intracellular membrane-bounded organelle mitochondrial inner membrane intracellular organelle organelle envelope cellular anatomical structure organelle mitochondrial envelope cytoplasm organelle membrane
U [auth DV], UB [auth Dv]	2-oxoglutarate/malate carrier protein	-	-	cellular anatomical structure membrane
T [auth DU], TB [auth Du]	Carrier protein	-	-	cellular anatomical structure membrane
B [auth DB], BB [auth Db]	Cytochrome c oxidase subunit 2	oxidoreductase activity catalytic activity cation binding transition metal ion binding copper ion binding ion binding binding metal ion binding small molecule binding monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity cytochrome-c oxidase activity electron transfer activity oxidoreductase activity catalytic activity cation binding transition metal ion binding copper ion binding ion binding binding metal ion binding small molecule binding monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity cytochrome-c oxidase activity electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity	aerobic respiration cellular respiration oxidative phosphorylation energy derivation by oxidation of organic compounds respiratory electron transport chain ATP synthesis coupled electron transport electron transport chain metabolic process cellular process generation of precursor metabolites and energy	cellular anatomical structure membrane
S [auth DT], SB [auth Dt]	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8, mitochondrial	-	-	-
R [auth DS], RB [auth Ds]	Oxoglutarate/malate translocator protein, putative	-	-	cellular anatomical structure membrane
Q [auth DR], QB [auth Dr]	Transmembrane protein, putative	-	-	-
P [auth DQ], PB [auth Dq]	TraB family protein	-	-	-
O [auth DP], OB [auth Dp]	SURF1-like protein	-	-	membrane-bounded organelle mitochondrial membrane intracellular anatomical structure organelle inner membrane mitochondrion membrane intracellular membrane-bounded organelle mitochondrial inner membrane intracellular organelle organelle envelope cellular anatomical structure organelle mitochondrial envelope cytoplasm membrane-bounded organelle mitochondrial membrane intracellular anatomical structure organelle inner membrane mitochondrion membrane intracellular membrane-bounded organelle mitochondrial inner membrane intracellular organelle organelle envelope cellular anatomical structure organelle mitochondrial envelope cytoplasm organelle membrane
N [auth DO], NB [auth Do]	Protein phosphatase 2C, putative	-	-	-
M [auth DN], MB [auth Dn]	Ymf67	-	-	-
L [auth DM], LB [auth Dm]	Transmembrane protein, putative	-	-	-
K [auth DK], KB [auth Dk]	CTF/NF-I domain-containing protein	transcription regulator activity DNA-binding transcription factor activity	-	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle
J [auth DJ], JB [auth Dj]	Transmembrane protein, putative	-	-	-
A [auth DA], AB [auth Da]	Cytochrome c oxidase subunit 1	oxidoreductase activity catalytic activity monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity cytochrome-c oxidase activity electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity binding oxidoreductase activity catalytic activity monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity cytochrome-c oxidase activity electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity binding tetrapyrrole binding heme binding cation binding ion binding metal ion binding small molecule binding	aerobic respiration cellular respiration aerobic electron transport chain oxidative phosphorylation energy derivation by oxidation of organic compounds ATP synthesis coupled electron transport electron transport chain generation of precursor metabolites and energy mitochondrial electron transport, cytochrome c to oxygen respiratory electron transport chain metabolic process cellular process mitochondrial ATP synthesis coupled electron transport electron transport coupled proton transport aerobic respiration cellular respiration aerobic electron transport chain oxidative phosphorylation energy derivation by oxidation of organic compounds ATP synthesis coupled electron transport electron transport chain generation of precursor metabolites and energy mitochondrial electron transport, cytochrome c to oxygen respiratory electron transport chain metabolic process cellular process mitochondrial ATP synthesis coupled electron transport electron transport coupled proton transport transport proton transmembrane transport monoatomic ion transmembrane transport establishment of localization monoatomic cation transmembrane transport transmembrane transport localization energy coupled proton transmembrane transport, against electrochemical gradient monoatomic ion transport monoatomic cation transport	membrane-bounded organelle mitochondrial membrane intracellular anatomical structure organelle inner membrane mitochondrion membrane intracellular membrane-bounded organelle mitochondrial inner membrane intracellular organelle organelle envelope cellular anatomical structure organelle mitochondrial envelope cytoplasm membrane-bounded organelle mitochondrial membrane intracellular anatomical structure organelle inner membrane mitochondrion membrane intracellular membrane-bounded organelle mitochondrial inner membrane intracellular organelle organelle envelope cellular anatomical structure organelle mitochondrial envelope cytoplasm organelle membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
AD [auth Dl], BD [auth DL]	IPR000408	Regulator of chromosome condensation, RCC1	Repeat
AD [auth Dl], BD [auth DL]	IPR051210	Ubiquitin ligases and GEF domain-containing protein	Family
AD [auth Dl], BD [auth DL]	IPR009091	Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II	Homologous Superfamily
ZA [auth FA], ZC [auth Fa]	IPR004217	Tim10-like	Domain
ZA [auth FA], ZC [auth Fa]	IPR035427	Tim10-like domain superfamily	Homologous Superfamily
WA [auth EX], WC [auth Ex]	IPR035427	Tim10-like domain superfamily	Homologous Superfamily
SA [auth ET], SC [auth Et]	IPR035427	Tim10-like domain superfamily	Homologous Superfamily
D [auth DD], DB [auth Dd]	IPR002124	Cytochrome c oxidase, subunit Vb	Family
D [auth DD], DB [auth Dd]	IPR036972	Cytochrome c oxidase, subunit Vb superfamily	Homologous Superfamily
EA [auth EF], EC [auth Ef]	IPR018967	Iron-binding zinc finger, CDGSH type	Domain
EA [auth EF], EC [auth Ef]	IPR042216	MitoNEET, CDGSH iron-sulfur domain	Homologous Superfamily
EA [auth EF], EC [auth Ef]	IPR052950	CDGSH iron-sulfur domain-containing protein	Family
V [auth DW], VB [auth Dw]	IPR002994	Surfeit locus 1/Shy1	Family
V [auth DW], VB [auth Dw]	IPR045214	Surfeit locus 1/4	Family
U [auth DV], UB [auth Dv]	IPR023395	Mitochondrial carrier protein domain superfamily	Homologous Superfamily
U [auth DV], UB [auth Dv]	IPR018108	Mitochondrial carrier protein, transmembrane region	Repeat
U [auth DV], UB [auth Dv]	IPR050391	Mitochondrial Metabolite Transporter	Family
T [auth DU], TB [auth Du]	IPR023395	Mitochondrial carrier protein domain superfamily	Homologous Superfamily
T [auth DU], TB [auth Du]	IPR018108	Mitochondrial carrier protein, transmembrane region	Repeat
B [auth DB], BB [auth Db]	IPR002429	Cytochrome c oxidase subunit II-like C-terminal	Domain
B [auth DB], BB [auth Db]	IPR008972	Cupredoxin	Homologous Superfamily
B [auth DB], BB [auth Db]	IPR045187	Cytochrome c/quinol oxidase subunit II	Family
R [auth DS], RB [auth Ds]	IPR023395	Mitochondrial carrier protein domain superfamily	Homologous Superfamily
R [auth DS], RB [auth Ds]	IPR018108	Mitochondrial carrier protein, transmembrane region	Repeat
R [auth DS], RB [auth Ds]	IPR050391	Mitochondrial Metabolite Transporter	Family
P [auth DQ], PB [auth Dq]	IPR046345	TraB/PryY-like	Family
O [auth DP], OB [auth Dp]	IPR002994	Surfeit locus 1/Shy1	Family
O [auth DP], OB [auth Dp]	IPR045214	Surfeit locus 1/4	Family
K [auth DK], KB [auth Dk]	IPR020604	CTF transcription factor/nuclear factor 1, DNA-binding domain	Domain
K [auth DK], KB [auth Dk]	IPR011990	Tetratricopeptide-like helical domain superfamily	Homologous Superfamily
A [auth DA], AB [auth Da]	IPR036927	Cytochrome c oxidase-like, subunit I superfamily	Homologous Superfamily
A [auth DA], AB [auth Da]	IPR000883	Cytochrome c oxidase subunit I	Family
A [auth DA], AB [auth Da]	IPR023615	Cytochrome c oxidase, subunit I, copper-binding site	Binding Site
A [auth DA], AB [auth Da]	IPR023616	Cytochrome c oxidase-like, subunit I domain	Domain

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A [auth DA], AA [auth EB], AB [auth Da], AC [auth Eb], AD [auth Dl] A [auth DA], AA [auth EB], AB [auth Da], AC [auth Eb], AD [auth Dl], B [auth DB], BB [auth Db], BD [auth DL], C [auth DC], CA [auth ED], CB [auth Dc], CC [auth Ed], E [auth DE], EA [auth EF], EB [auth De], EC [auth Ef], G [auth DG], GA [auth EH], GB [auth Dg], GC [auth Eh], H [auth DH], HB [auth Dh], J [auth DJ], JB [auth Dj], KA [auth EL], KC [auth El], L [auth DM], LA [auth EM], LB [auth Dm], LC [auth Em], M [auth DN], MB [auth Dn], NA [auth EO], NC [auth Eo], O [auth DP], OB [auth Dp], PA [auth EQ], PC [auth Eq], Q [auth DR], QB [auth Dr], R [auth DS], RA [auth ES], RB [auth Ds], RC [auth Es], T [auth DU], TB [auth Du], U [auth DV], UB [auth Dv], V [auth DW], VB [auth Dw], ZA [auth FA], ZC [auth Fa]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Electron Transport Chain Supercomplexes (Respirasome)	Respiratory chain super-complex, I-II-III₂-IV₂

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
I [auth DI], IB [auth Di]	SEP	Parent Component: SER RESID: AA0037 PSI-MOD : O-phospho-L-serine MOD:00046
H [auth DH], HB [auth Dh]	AME	Parent Component: MET RESID: AA0037
PA [auth EQ], PC [auth Eq]	AME	Parent Component: MET RESID: AA0037
D [auth DD], DB [auth Dd]	SEP	Parent Component: SER RESID: AA0037 , AA0037 PSI-MOD : O-phospho-L-serine MOD:00046 , O-phospho-L-serine MOD:00046
D [auth DD], DB [auth Dd]	TPO	Parent Component: THR RESID: AA0037 , AA0037 , AA0038 PSI-MOD : O-phospho-L-serine MOD:00046 , O-phospho-L-serine MOD:00046 , O-phospho-L-threonine MOD:00047
IA [auth EV], IC [auth Ev]	AME	Parent Component: MET RESID: AA0037 , AA0037 , AA0038
GA [auth EH], GC [auth Eh]	AME	Parent Component: MET RESID: AA0037 , AA0037 , AA0038
U [auth DV], UB [auth Dv]	AME	Parent Component: MET RESID: AA0037 , AA0037 , AA0038
R [auth DS], RB [auth Ds]	AME	Parent Component: MET RESID: AA0037 , AA0037 , AA0038
P [auth DQ], PB [auth Dq]	AME	Parent Component: MET RESID: AA0037 , AA0037 , AA0038