6D84

Structure of the cargo bound AP-1:Arf1:tetherin-Nef (L164A, L165A) dileucine mutant dimer

Functional Information from GO Data

Chain	GOid	namespace	contents
B	0006886	biological_process	intracellular protein transport
B	0015031	biological_process	protein transport
B	0016192	biological_process	vesicle-mediated transport
B	0030117	cellular_component	membrane coat
B	0030276	molecular_function	clathrin binding
C	0000139	cellular_component	Golgi membrane
C	0000166	molecular_function	nucleotide binding
C	0000287	molecular_function	magnesium ion binding
C	0002090	biological_process	regulation of receptor internalization
C	0003723	molecular_function	RNA binding
C	0003924	molecular_function	GTPase activity
C	0003925	molecular_function	G protein activity
C	0005515	molecular_function	protein binding
C	0005525	molecular_function	GTP binding
C	0005737	cellular_component	cytoplasm
C	0005794	cellular_component	Golgi apparatus
C	0005829	cellular_component	cytosol
C	0005886	cellular_component	plasma membrane
C	0005925	cellular_component	focal adhesion
C	0006878	biological_process	intracellular copper ion homeostasis
C	0006886	biological_process	intracellular protein transport
C	0012505	cellular_component	endomembrane system
C	0014069	cellular_component	postsynaptic density
C	0015031	biological_process	protein transport
C	0016192	biological_process	vesicle-mediated transport
C	0016787	molecular_function	hydrolase activity
C	0019904	molecular_function	protein domain specific binding
C	0030017	cellular_component	sarcomere
C	0031252	cellular_component	cell leading edge
C	0032991	cellular_component	protein-containing complex
C	0034315	biological_process	regulation of Arp2/3 complex-mediated actin nucleation
C	0043005	cellular_component	neuron projection
C	0045202	cellular_component	synapse
C	0060292	biological_process	long-term synaptic depression
C	0070062	cellular_component	extracellular exosome
C	0097061	biological_process	dendritic spine organization
C	0098586	biological_process	cellular response to virus
C	1990386	biological_process	mitotic cleavage furrow ingression
F	0006886	biological_process	intracellular protein transport
F	0015031	biological_process	protein transport
F	0016192	biological_process	vesicle-mediated transport
F	0030117	cellular_component	membrane coat
F	0030276	molecular_function	clathrin binding
G	0006886	biological_process	intracellular protein transport
G	0016192	biological_process	vesicle-mediated transport
G	0030117	cellular_component	membrane coat
H	0000139	cellular_component	Golgi membrane
H	0000166	molecular_function	nucleotide binding
H	0000287	molecular_function	magnesium ion binding
H	0002090	biological_process	regulation of receptor internalization
H	0003723	molecular_function	RNA binding
H	0003924	molecular_function	GTPase activity
H	0003925	molecular_function	G protein activity
H	0005515	molecular_function	protein binding
H	0005525	molecular_function	GTP binding
H	0005737	cellular_component	cytoplasm
H	0005794	cellular_component	Golgi apparatus
H	0005829	cellular_component	cytosol
H	0005886	cellular_component	plasma membrane
H	0005925	cellular_component	focal adhesion
H	0006878	biological_process	intracellular copper ion homeostasis
H	0006886	biological_process	intracellular protein transport
H	0012505	cellular_component	endomembrane system
H	0014069	cellular_component	postsynaptic density
H	0015031	biological_process	protein transport
H	0016192	biological_process	vesicle-mediated transport
H	0016787	molecular_function	hydrolase activity
H	0019904	molecular_function	protein domain specific binding
H	0030017	cellular_component	sarcomere
H	0031252	cellular_component	cell leading edge
H	0032991	cellular_component	protein-containing complex
H	0034315	biological_process	regulation of Arp2/3 complex-mediated actin nucleation
H	0043005	cellular_component	neuron projection
H	0045202	cellular_component	synapse
H	0060292	biological_process	long-term synaptic depression
H	0070062	cellular_component	extracellular exosome
H	0097061	biological_process	dendritic spine organization
H	0098586	biological_process	cellular response to virus
H	1990386	biological_process	mitotic cleavage furrow ingression
I	0000139	cellular_component	Golgi membrane
I	0000166	molecular_function	nucleotide binding
I	0000287	molecular_function	magnesium ion binding
I	0002090	biological_process	regulation of receptor internalization
I	0003723	molecular_function	RNA binding
I	0003924	molecular_function	GTPase activity
I	0003925	molecular_function	G protein activity
I	0005515	molecular_function	protein binding
I	0005525	molecular_function	GTP binding
I	0005737	cellular_component	cytoplasm
I	0005794	cellular_component	Golgi apparatus
I	0005829	cellular_component	cytosol
I	0005886	cellular_component	plasma membrane
I	0005925	cellular_component	focal adhesion
I	0006878	biological_process	intracellular copper ion homeostasis
I	0006886	biological_process	intracellular protein transport
I	0012505	cellular_component	endomembrane system
I	0014069	cellular_component	postsynaptic density
I	0015031	biological_process	protein transport
I	0016192	biological_process	vesicle-mediated transport
I	0016787	molecular_function	hydrolase activity
I	0019904	molecular_function	protein domain specific binding
I	0030017	cellular_component	sarcomere
I	0031252	cellular_component	cell leading edge
I	0032991	cellular_component	protein-containing complex
I	0034315	biological_process	regulation of Arp2/3 complex-mediated actin nucleation
I	0043005	cellular_component	neuron projection
I	0045202	cellular_component	synapse
I	0060292	biological_process	long-term synaptic depression
I	0070062	cellular_component	extracellular exosome
I	0097061	biological_process	dendritic spine organization
I	0098586	biological_process	cellular response to virus
I	1990386	biological_process	mitotic cleavage furrow ingression
K	0006886	biological_process	intracellular protein transport
K	0016192	biological_process	vesicle-mediated transport
K	0030117	cellular_component	membrane coat
L	0005102	molecular_function	signaling receptor binding
L	0005515	molecular_function	protein binding
L	0005525	molecular_function	GTP binding
L	0005576	cellular_component	extracellular region
L	0010561	biological_process	negative regulation of glycoprotein biosynthetic process
L	0016020	cellular_component	membrane
L	0017124	molecular_function	SH3 domain binding
L	0019058	biological_process	viral life cycle
L	0019901	molecular_function	protein kinase binding
L	0020002	cellular_component	host cell plasma membrane
L	0031996	molecular_function	thioesterase binding
L	0033668	biological_process	symbiont-mediated suppression of host apoptosis
L	0039504	biological_process	symbiont-mediated suppression of host adaptive immune response
L	0039505	biological_process	symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II
L	0042288	molecular_function	MHC class I protein binding
L	0042609	molecular_function	CD4 receptor binding
L	0044178	cellular_component	host cell Golgi membrane
L	0044423	cellular_component	virion component
L	0046776	biological_process	symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I
L	0050848	biological_process	regulation of calcium-mediated signaling
L	0051117	molecular_function	ATPase binding
L	0051246	biological_process	regulation of protein metabolic process
L	0051701	biological_process	biological process involved in interaction with host
L	0052031	biological_process	symbiont-mediated perturbation of host defense response
L	0052170	biological_process	symbiont-mediated suppression of host innate immune response
L	0070206	biological_process	protein trimerization
L	0140321	biological_process	symbiont-mediated suppression of host autophagy
M	0005515	molecular_function	protein binding
M	0005765	cellular_component	lysosomal membrane
M	0005769	cellular_component	early endosome
M	0005794	cellular_component	Golgi apparatus
M	0005802	cellular_component	trans-Golgi network
M	0005829	cellular_component	cytosol
M	0006886	biological_process	intracellular protein transport
M	0006896	biological_process	Golgi to vacuole transport
M	0015031	biological_process	protein transport
M	0016192	biological_process	vesicle-mediated transport
M	0030121	cellular_component	AP-1 adaptor complex
M	0030131	cellular_component	clathrin adaptor complex
M	0030665	cellular_component	clathrin-coated vesicle membrane
M	0031410	cellular_component	cytoplasmic vesicle
M	0032438	biological_process	melanosome organization
M	0032588	cellular_component	trans-Golgi network membrane
M	0035615	molecular_function	clathrin adaptor activity
M	0035646	biological_process	endosome to melanosome transport
M	0045202	cellular_component	synapse
M	0060155	biological_process	platelet dense granule organization
M	1903232	biological_process	melanosome assembly
N	0000139	cellular_component	Golgi membrane
N	0000166	molecular_function	nucleotide binding
N	0000287	molecular_function	magnesium ion binding
N	0002090	biological_process	regulation of receptor internalization
N	0003723	molecular_function	RNA binding
N	0003924	molecular_function	GTPase activity
N	0003925	molecular_function	G protein activity
N	0005515	molecular_function	protein binding
N	0005525	molecular_function	GTP binding
N	0005737	cellular_component	cytoplasm
N	0005794	cellular_component	Golgi apparatus
N	0005829	cellular_component	cytosol
N	0005886	cellular_component	plasma membrane
N	0005925	cellular_component	focal adhesion
N	0006878	biological_process	intracellular copper ion homeostasis
N	0006886	biological_process	intracellular protein transport
N	0012505	cellular_component	endomembrane system
N	0014069	cellular_component	postsynaptic density
N	0015031	biological_process	protein transport
N	0016192	biological_process	vesicle-mediated transport
N	0016787	molecular_function	hydrolase activity
N	0019904	molecular_function	protein domain specific binding
N	0030017	cellular_component	sarcomere
N	0031252	cellular_component	cell leading edge
N	0032991	cellular_component	protein-containing complex
N	0034315	biological_process	regulation of Arp2/3 complex-mediated actin nucleation
N	0043005	cellular_component	neuron projection
N	0045202	cellular_component	synapse
N	0060292	biological_process	long-term synaptic depression
N	0070062	cellular_component	extracellular exosome
N	0097061	biological_process	dendritic spine organization
N	0098586	biological_process	cellular response to virus
N	1990386	biological_process	mitotic cleavage furrow ingression
O	0005102	molecular_function	signaling receptor binding
O	0005515	molecular_function	protein binding
O	0005525	molecular_function	GTP binding
O	0005576	cellular_component	extracellular region
O	0010561	biological_process	negative regulation of glycoprotein biosynthetic process
O	0016020	cellular_component	membrane
O	0017124	molecular_function	SH3 domain binding
O	0019058	biological_process	viral life cycle
O	0019901	molecular_function	protein kinase binding
O	0020002	cellular_component	host cell plasma membrane
O	0031996	molecular_function	thioesterase binding
O	0033668	biological_process	symbiont-mediated suppression of host apoptosis
O	0039504	biological_process	symbiont-mediated suppression of host adaptive immune response
O	0039505	biological_process	symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II
O	0042288	molecular_function	MHC class I protein binding
O	0042609	molecular_function	CD4 receptor binding
O	0044178	cellular_component	host cell Golgi membrane
O	0044423	cellular_component	virion component
O	0046776	biological_process	symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I
O	0050848	biological_process	regulation of calcium-mediated signaling
O	0051117	molecular_function	ATPase binding
O	0051246	biological_process	regulation of protein metabolic process
O	0051701	biological_process	biological process involved in interaction with host
O	0052031	biological_process	symbiont-mediated perturbation of host defense response
O	0052170	biological_process	symbiont-mediated suppression of host innate immune response
O	0070206	biological_process	protein trimerization
O	0140321	biological_process	symbiont-mediated suppression of host autophagy
P	0005515	molecular_function	protein binding
P	0005765	cellular_component	lysosomal membrane
P	0005769	cellular_component	early endosome
P	0005794	cellular_component	Golgi apparatus
P	0005802	cellular_component	trans-Golgi network
P	0005829	cellular_component	cytosol
P	0006886	biological_process	intracellular protein transport
P	0006896	biological_process	Golgi to vacuole transport
P	0015031	biological_process	protein transport
P	0016192	biological_process	vesicle-mediated transport
P	0030121	cellular_component	AP-1 adaptor complex
P	0030131	cellular_component	clathrin adaptor complex
P	0030665	cellular_component	clathrin-coated vesicle membrane
P	0031410	cellular_component	cytoplasmic vesicle
P	0032438	biological_process	melanosome organization
P	0032588	cellular_component	trans-Golgi network membrane
P	0035615	molecular_function	clathrin adaptor activity
P	0035646	biological_process	endosome to melanosome transport
P	0045202	cellular_component	synapse
P	0060155	biological_process	platelet dense granule organization
P	1903232	biological_process	melanosome assembly
Q	0000139	cellular_component	Golgi membrane
Q	0005515	molecular_function	protein binding
Q	0005765	cellular_component	lysosomal membrane
Q	0005769	cellular_component	early endosome
Q	0005794	cellular_component	Golgi apparatus
Q	0005829	cellular_component	cytosol
Q	0005905	cellular_component	clathrin-coated pit
Q	0006605	biological_process	protein targeting
Q	0006886	biological_process	intracellular protein transport
Q	0015031	biological_process	protein transport
Q	0016192	biological_process	vesicle-mediated transport
Q	0030117	cellular_component	membrane coat
Q	0030121	cellular_component	AP-1 adaptor complex
Q	0030659	cellular_component	cytoplasmic vesicle membrane
Q	0031410	cellular_component	cytoplasmic vesicle
Q	0032588	cellular_component	trans-Golgi network membrane
Q	0035615	molecular_function	clathrin adaptor activity
Q	0060155	biological_process	platelet dense granule organization
Q	1903232	biological_process	melanosome assembly
R	0005102	molecular_function	signaling receptor binding
R	0005515	molecular_function	protein binding
R	0005525	molecular_function	GTP binding
R	0005576	cellular_component	extracellular region
R	0010561	biological_process	negative regulation of glycoprotein biosynthetic process
R	0016020	cellular_component	membrane
R	0017124	molecular_function	SH3 domain binding
R	0019058	biological_process	viral life cycle
R	0019901	molecular_function	protein kinase binding
R	0020002	cellular_component	host cell plasma membrane
R	0031996	molecular_function	thioesterase binding
R	0033668	biological_process	symbiont-mediated suppression of host apoptosis
R	0039504	biological_process	symbiont-mediated suppression of host adaptive immune response
R	0039505	biological_process	symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II
R	0042288	molecular_function	MHC class I protein binding
R	0042609	molecular_function	CD4 receptor binding
R	0044178	cellular_component	host cell Golgi membrane
R	0044423	cellular_component	virion component
R	0046776	biological_process	symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I
R	0050848	biological_process	regulation of calcium-mediated signaling
R	0051117	molecular_function	ATPase binding
R	0051246	biological_process	regulation of protein metabolic process
R	0051701	biological_process	biological process involved in interaction with host
R	0052031	biological_process	symbiont-mediated perturbation of host defense response
R	0052170	biological_process	symbiont-mediated suppression of host innate immune response
R	0070206	biological_process	protein trimerization
R	0140321	biological_process	symbiont-mediated suppression of host autophagy
S	0000139	cellular_component	Golgi membrane
S	0005515	molecular_function	protein binding
S	0005765	cellular_component	lysosomal membrane
S	0005769	cellular_component	early endosome
S	0005794	cellular_component	Golgi apparatus
S	0005829	cellular_component	cytosol
S	0005905	cellular_component	clathrin-coated pit
S	0006605	biological_process	protein targeting
S	0006886	biological_process	intracellular protein transport
S	0015031	biological_process	protein transport
S	0016192	biological_process	vesicle-mediated transport
S	0030117	cellular_component	membrane coat
S	0030121	cellular_component	AP-1 adaptor complex
S	0030659	cellular_component	cytoplasmic vesicle membrane
S	0031410	cellular_component	cytoplasmic vesicle
S	0032588	cellular_component	trans-Golgi network membrane
S	0035615	molecular_function	clathrin adaptor activity
S	0060155	biological_process	platelet dense granule organization
S	1903232	biological_process	melanosome assembly
T	0005102	molecular_function	signaling receptor binding
T	0005515	molecular_function	protein binding
T	0005525	molecular_function	GTP binding
T	0005576	cellular_component	extracellular region
T	0010561	biological_process	negative regulation of glycoprotein biosynthetic process
T	0016020	cellular_component	membrane
T	0017124	molecular_function	SH3 domain binding
T	0019058	biological_process	viral life cycle
T	0019901	molecular_function	protein kinase binding
T	0020002	cellular_component	host cell plasma membrane
T	0031996	molecular_function	thioesterase binding
T	0033668	biological_process	symbiont-mediated suppression of host apoptosis
T	0039504	biological_process	symbiont-mediated suppression of host adaptive immune response
T	0039505	biological_process	symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II
T	0042288	molecular_function	MHC class I protein binding
T	0042609	molecular_function	CD4 receptor binding
T	0044178	cellular_component	host cell Golgi membrane
T	0044423	cellular_component	virion component
T	0046776	biological_process	symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I
T	0050848	biological_process	regulation of calcium-mediated signaling
T	0051117	molecular_function	ATPase binding
T	0051246	biological_process	regulation of protein metabolic process
T	0051701	biological_process	biological process involved in interaction with host
T	0052031	biological_process	symbiont-mediated perturbation of host defense response
T	0052170	biological_process	symbiont-mediated suppression of host innate immune response
T	0070206	biological_process	protein trimerization
T	0140321	biological_process	symbiont-mediated suppression of host autophagy

Functional Information from PDB Data

site_id	AC1
Number of Residues	18
Details	binding site for residue GTP C 1001

Chain	Residue
C	ASP26
C	PRO47
C	THR48
C	GLY69
C	GLY70
C	LYS127
C	ASP129
C	CYS159
C	ALA160
C	MG1002
C	ALA27
C	ALA28
C	GLY29
C	LYS30
C	THR31
C	THR32
C	THR45
C	ILE46

---

site_id	AC2
Number of Residues	3
Details	binding site for residue MG C 1002

Chain	Residue
C	THR31
C	THR48
C	GTP1001

---

site_id	AC3
Number of Residues	18
Details	binding site for residue GTP H 1001

Chain	Residue
H	ALA27
H	ALA28
H	GLY29
H	LYS30
H	THR31
H	THR32
H	THR45
H	ILE46
H	PRO47
H	THR48
H	LEU71
H	ASN126
H	LYS127
H	ASP129
H	CYS159
H	ALA160
H	THR161
H	MG1002

---

site_id	AC4
Number of Residues	3
Details	binding site for residue MG H 1002

Chain	Residue
H	THR31
H	THR48
H	GTP1001

---

site_id	AC5
Number of Residues	18
Details	binding site for residue GTP I 1001

Chain	Residue
I	ASP26
I	ALA27
I	ALA28
I	GLY29
I	LYS30
I	THR31
I	THR32
I	THR45
I	ILE46
I	PRO47
I	THR48
I	GLY69
I	LEU71
I	LYS127
I	ASP129
I	CYS159
I	ALA160
I	MG1002

---

site_id	AC6
Number of Residues	3
Details	binding site for residue MG I 1002

Chain	Residue
I	THR31
I	THR48
I	GTP1001

---

site_id	AC7
Number of Residues	17
Details	binding site for residue GTP N 1001

Chain	Residue
N	ALA27
N	ALA28
N	GLY29
N	LYS30
N	THR31
N	THR32
N	THR45
N	ILE46
N	PRO47
N	THR48
N	LEU71
N	ASN126
N	LYS127
N	ASP129
N	ALA160
N	THR161
N	MG1002

---

site_id	AC8
Number of Residues	3
Details	binding site for residue MG N 1002

Chain	Residue
N	THR31
N	THR48
N	GTP1001

---

Functional Information from PROSITE/UniProt

site_id	PS00989
Number of Residues	11
Details	CLAT_ADAPTOR_S Clathrin adaptor complexes small chain signature. LVYKryasLYF

Chain	Residue	Details
S	LEU57-PHE67

---

site_id	PS00990
Number of Residues	21
Details	CLAT_ADAPTOR_M_1 Clathrin adaptor complexes medium chain signature 1. VSWRse.GikYrkNeVFLDVIE

Chain	Residue	Details
M	VAL157-GLU177

---

site_id	PS00991
Number of Residues	15
Details	CLAT_ADAPTOR_M_2 Clathrin adaptor complexes medium chain signature 2. IsFIPPdGeFeLmsY

Chain	Residue	Details
M	ILE253-TYR267

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI2
Number of Residues	2
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	2
Details	Modified residue: {"description":"3'-nitrotyrosine","evidences":[{"source":"UniProtKB","id":"O35643","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	32
Details	Binding site: {"evidences":[{"source":"PubMed","id":"7990966","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1HUR","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	12
Details	Binding site: {"evidences":[{"source":"PubMed","id":"14690595","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15308674","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"7990966","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"JUL-2010","submissionDatabase":"PDB data bank","title":"Crystal structure of ARFGAP1-ARF1 fusion protein.","authoringGroup":["Structural genomics consortium (SGC)."]}},{"source":"PDB","id":"1HUR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1RE0","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1U81","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3O47","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"15308674","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"7990966","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"JUL-2010","submissionDatabase":"PDB data bank","title":"Crystal structure of ARFGAP1-ARF1 fusion protein.","authoringGroup":["Structural genomics consortium (SGC)."]}},{"source":"PDB","id":"1HUR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1RE0","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3O47","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	506
Details	Domain: {"description":"MHD","evidences":[{"source":"PROSITE-ProRule","id":"PRU00404","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	2
Details	Modified residue: {"description":"N-acetylserine","evidences":[{"source":"UniProtKB","id":"Q9BXS5","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	4
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"17242355","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"21183079","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI10
Number of Residues	2
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"UniProtKB","id":"Q32Q06","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---