6G6U

The dynamic nature of the VDAC1 channels in bilayers: human VDAC1 at 2.7 Angstrom resolution

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0001662	biological_process	behavioral fear response
A	0005244	molecular_function	voltage-gated monoatomic ion channel activity
A	0005515	molecular_function	protein binding
A	0005524	molecular_function	ATP binding
A	0005634	cellular_component	nucleus
A	0005739	cellular_component	mitochondrion
A	0005741	cellular_component	mitochondrial outer membrane
A	0005757	cellular_component	mitochondrial permeability transition pore complex
A	0005886	cellular_component	plasma membrane
A	0006811	biological_process	monoatomic ion transport
A	0006820	biological_process	monoatomic anion transport
A	0006869	biological_process	lipid transport
A	0006915	biological_process	apoptotic process
A	0007268	biological_process	chemical synaptic transmission
A	0007270	biological_process	neuron-neuron synaptic transmission
A	0007612	biological_process	learning
A	0008142	molecular_function	oxysterol binding
A	0008289	molecular_function	lipid binding
A	0008308	molecular_function	voltage-gated monoatomic anion channel activity
A	0015288	molecular_function	porin activity
A	0015485	molecular_function	cholesterol binding
A	0016020	cellular_component	membrane
A	0019901	molecular_function	protein kinase binding
A	0030855	biological_process	epithelial cell differentiation
A	0031210	molecular_function	phosphatidylcholine binding
A	0031966	cellular_component	mitochondrial membrane
A	0036444	biological_process	calcium import into the mitochondrion
A	0042645	cellular_component	mitochondrial nucleoid
A	0042802	molecular_function	identical protein binding
A	0042866	biological_process	pyruvate biosynthetic process
A	0043065	biological_process	positive regulation of apoptotic process
A	0043066	biological_process	negative regulation of apoptotic process
A	0044325	molecular_function	transmembrane transporter binding
A	0045121	cellular_component	membrane raft
A	0045202	cellular_component	synapse
A	0046930	cellular_component	pore complex
A	0055085	biological_process	transmembrane transport
A	0070062	cellular_component	extracellular exosome
A	0097001	molecular_function	ceramide binding
A	0098656	biological_process	monoatomic anion transmembrane transport
A	0110099	biological_process	negative regulation of calcium import into the mitochondrion
A	1901524	biological_process	regulation of mitophagy
A	1901526	biological_process	positive regulation of mitophagy
A	1903146	biological_process	regulation of autophagy of mitochondrion
A	1905091	biological_process	positive regulation of type 2 mitophagy
A	1990542	biological_process	mitochondrial transmembrane transport
A	2000378	biological_process	negative regulation of reactive oxygen species metabolic process
B	0000166	molecular_function	nucleotide binding
B	0001662	biological_process	behavioral fear response
B	0005244	molecular_function	voltage-gated monoatomic ion channel activity
B	0005515	molecular_function	protein binding
B	0005524	molecular_function	ATP binding
B	0005634	cellular_component	nucleus
B	0005739	cellular_component	mitochondrion
B	0005741	cellular_component	mitochondrial outer membrane
B	0005757	cellular_component	mitochondrial permeability transition pore complex
B	0005886	cellular_component	plasma membrane
B	0006811	biological_process	monoatomic ion transport
B	0006820	biological_process	monoatomic anion transport
B	0006869	biological_process	lipid transport
B	0006915	biological_process	apoptotic process
B	0007268	biological_process	chemical synaptic transmission
B	0007270	biological_process	neuron-neuron synaptic transmission
B	0007612	biological_process	learning
B	0008142	molecular_function	oxysterol binding
B	0008289	molecular_function	lipid binding
B	0008308	molecular_function	voltage-gated monoatomic anion channel activity
B	0015288	molecular_function	porin activity
B	0015485	molecular_function	cholesterol binding
B	0016020	cellular_component	membrane
B	0019901	molecular_function	protein kinase binding
B	0030855	biological_process	epithelial cell differentiation
B	0031210	molecular_function	phosphatidylcholine binding
B	0031966	cellular_component	mitochondrial membrane
B	0036444	biological_process	calcium import into the mitochondrion
B	0042645	cellular_component	mitochondrial nucleoid
B	0042802	molecular_function	identical protein binding
B	0042866	biological_process	pyruvate biosynthetic process
B	0043065	biological_process	positive regulation of apoptotic process
B	0043066	biological_process	negative regulation of apoptotic process
B	0044325	molecular_function	transmembrane transporter binding
B	0045121	cellular_component	membrane raft
B	0045202	cellular_component	synapse
B	0046930	cellular_component	pore complex
B	0055085	biological_process	transmembrane transport
B	0070062	cellular_component	extracellular exosome
B	0097001	molecular_function	ceramide binding
B	0098656	biological_process	monoatomic anion transmembrane transport
B	0110099	biological_process	negative regulation of calcium import into the mitochondrion
B	1901524	biological_process	regulation of mitophagy
B	1901526	biological_process	positive regulation of mitophagy
B	1903146	biological_process	regulation of autophagy of mitochondrion
B	1905091	biological_process	positive regulation of type 2 mitophagy
B	1990542	biological_process	mitochondrial transmembrane transport
B	2000378	biological_process	negative regulation of reactive oxygen species metabolic process

Functional Information from PDB Data

site_id	AC1
Number of Residues	3
Details	binding site for residue MC3 A 301

Chain	Residue
A	PHE190
A	GLY192
A	TRP210

---

site_id	AC2
Number of Residues	5
Details	binding site for residue NO3 A 302

Chain	Residue
A	ALA2
A	HIS122
A	GLY145
A	GLU147
A	GLY148

---

site_id	AC3
Number of Residues	6
Details	binding site for residue MC3 B 301

Chain	Residue
B	PHE190
B	GLY192
B	SER193
B	LEU208
B	TRP210
B	LEU180

---

site_id	AC4
Number of Residues	2
Details	binding site for residue MC3 B 302

Chain	Residue
B	TYR153
B	PHE169

---

site_id	AC5
Number of Residues	5
Details	binding site for residue NO3 B 303

Chain	Residue
B	ALA2
B	HIS122
B	GLY145
B	GLU147
B	GLY148

---

Functional Information from PROSITE/UniProt

site_id	PS00558
Number of Residues	23
Details	EUKARYOTIC_PORIN Eukaryotic mitochondrial porin signature. YqiDPdAcfsAKVNNssliGLgY

Chain	Residue	Details
A	TYR225-TYR247

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	328
Details	Transmembrane: {"description":"Beta stranded","evidences":[{"source":"PubMed","id":"18755977","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18832158","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"UniProtKB","id":"Q60932","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	12
Details	Binding site: {"evidences":[{"source":"PubMed","id":"18755977","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	2
Details	Site: {"description":"Involved in ceramide and phosphatidylcholine binding. Critical for channel structural stability and gating","evidences":[{"source":"PubMed","id":"31015432","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18832158","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	2
Details	Modified residue: {"description":"N-acetylalanine","evidences":[{"source":"PubMed","id":"2559745","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"MAR-2005","submissionDatabase":"UniProtKB","authors":["Bienvenut W.V."]}},{"source":"PubMed","id":"19413330","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"22223895","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"22814378","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"25944712","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"Q9Z2L0","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	2
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"UniProtKB","id":"Q60932","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	2
Details	Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"Q60932","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	2
Details	Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"Q60932","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI10
Number of Residues	2
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI11
Number of Residues	2
Details	Modified residue: {"description":"N6-acetyllysine; alternate","evidences":[{"source":"UniProtKB","id":"Q60932","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI12
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine; by NEK1","evidences":[{"source":"PubMed","id":"20230784","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI13
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI14
Number of Residues	2
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"Q60932","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI15
Number of Residues	2
Details	Modified residue: {"description":"N6-acetyllysine; alternate","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI16
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"32047033","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI17
Number of Residues	8
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"25621951","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"32047033","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI18
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate","evidences":[{"source":"PubMed","id":"32047033","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI19
Number of Residues	4
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"25621951","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI20
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate","evidences":[{"source":"PubMed","id":"25621951","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"32047033","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI21
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate","evidences":[{"source":"PubMed","id":"25621951","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---