Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6CRI

Structure of the cargo bound AP-1:Arf1:tetherin-Nef stable closed trimer

Functional Information from GO Data

Chain	GOid	namespace	contents
a	0000139	cellular_component	Golgi membrane
a	0005515	molecular_function	protein binding
a	0005765	cellular_component	lysosomal membrane
a	0005769	cellular_component	early endosome
a	0005794	cellular_component	Golgi apparatus
a	0005829	cellular_component	cytosol
a	0005905	cellular_component	clathrin-coated pit
a	0006605	biological_process	protein targeting
a	0006886	biological_process	intracellular protein transport
a	0015031	biological_process	protein transport
a	0016192	biological_process	vesicle-mediated transport
a	0030117	cellular_component	membrane coat
a	0030121	cellular_component	AP-1 adaptor complex
a	0030659	cellular_component	cytoplasmic vesicle membrane
a	0031410	cellular_component	cytoplasmic vesicle
a	0032588	cellular_component	trans-Golgi network membrane
a	0035615	molecular_function	clathrin adaptor activity
a	0043231	cellular_component	intracellular membrane-bounded organelle
a	0060155	biological_process	platelet dense granule organization
a	1903232	biological_process	melanosome assembly
b	0000139	cellular_component	Golgi membrane
b	0005515	molecular_function	protein binding
b	0005765	cellular_component	lysosomal membrane
b	0005769	cellular_component	early endosome
b	0005794	cellular_component	Golgi apparatus
b	0005829	cellular_component	cytosol
b	0005905	cellular_component	clathrin-coated pit
b	0006605	biological_process	protein targeting
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	0030121	cellular_component	AP-1 adaptor complex
b	0030659	cellular_component	cytoplasmic vesicle membrane
b	0031410	cellular_component	cytoplasmic vesicle
b	0032588	cellular_component	trans-Golgi network membrane
b	0035615	molecular_function	clathrin adaptor activity
b	0043231	cellular_component	intracellular membrane-bounded organelle
b	0060155	biological_process	platelet dense granule organization
b	1903232	biological_process	melanosome assembly
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	0005525	molecular_function	GTP binding
C	0000139	cellular_component	Golgi membrane
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	0005515	molecular_function	protein binding
C	0005525	molecular_function	GTP binding
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	0016020	cellular_component	membrane
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
d	0005525	molecular_function	GTP 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	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	0005515	molecular_function	protein binding
H	0005525	molecular_function	GTP binding
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	0016020	cellular_component	membrane
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	0006886	biological_process	intracellular protein transport
I	0015031	biological_process	protein transport
I	0016192	biological_process	vesicle-mediated transport
I	0030117	cellular_component	membrane coat
I	0030276	molecular_function	clathrin binding
J	0006886	biological_process	intracellular protein transport
J	0015031	biological_process	protein transport
J	0016192	biological_process	vesicle-mediated transport
J	0030117	cellular_component	membrane coat
J	0030276	molecular_function	clathrin binding
K	0000139	cellular_component	Golgi membrane
K	0000287	molecular_function	magnesium ion binding
K	0002090	biological_process	regulation of receptor internalization
K	0003723	molecular_function	RNA binding
K	0003924	molecular_function	GTPase activity
K	0005515	molecular_function	protein binding
K	0005525	molecular_function	GTP binding
K	0005794	cellular_component	Golgi apparatus
K	0005829	cellular_component	cytosol
K	0005886	cellular_component	plasma membrane
K	0005925	cellular_component	focal adhesion
K	0006878	biological_process	intracellular copper ion homeostasis
K	0006886	biological_process	intracellular protein transport
K	0012505	cellular_component	endomembrane system
K	0014069	cellular_component	postsynaptic density
K	0015031	biological_process	protein transport
K	0016020	cellular_component	membrane
K	0016192	biological_process	vesicle-mediated transport
K	0016787	molecular_function	hydrolase activity
K	0019904	molecular_function	protein domain specific binding
K	0030017	cellular_component	sarcomere
K	0031252	cellular_component	cell leading edge
K	0032991	cellular_component	protein-containing complex
K	0034315	biological_process	regulation of Arp2/3 complex-mediated actin nucleation
K	0043005	cellular_component	neuron projection
K	0045202	cellular_component	synapse
K	0060292	biological_process	long-term synaptic depression
K	0070062	cellular_component	extracellular exosome
K	0097061	biological_process	dendritic spine organization
K	0098586	biological_process	cellular response to virus
K	1990386	biological_process	mitotic cleavage furrow ingression
L	0000139	cellular_component	Golgi membrane
L	0000287	molecular_function	magnesium ion binding
L	0002090	biological_process	regulation of receptor internalization
L	0003723	molecular_function	RNA binding
L	0003924	molecular_function	GTPase activity
L	0005515	molecular_function	protein binding
L	0005525	molecular_function	GTP binding
L	0005794	cellular_component	Golgi apparatus
L	0005829	cellular_component	cytosol
L	0005886	cellular_component	plasma membrane
L	0005925	cellular_component	focal adhesion
L	0006878	biological_process	intracellular copper ion homeostasis
L	0006886	biological_process	intracellular protein transport
L	0012505	cellular_component	endomembrane system
L	0014069	cellular_component	postsynaptic density
L	0015031	biological_process	protein transport
L	0016020	cellular_component	membrane
L	0016192	biological_process	vesicle-mediated transport
L	0016787	molecular_function	hydrolase activity
L	0019904	molecular_function	protein domain specific binding
L	0030017	cellular_component	sarcomere
L	0031252	cellular_component	cell leading edge
L	0032991	cellular_component	protein-containing complex
L	0034315	biological_process	regulation of Arp2/3 complex-mediated actin nucleation
L	0043005	cellular_component	neuron projection
L	0045202	cellular_component	synapse
L	0060292	biological_process	long-term synaptic depression
L	0070062	cellular_component	extracellular exosome
L	0097061	biological_process	dendritic spine organization
L	0098586	biological_process	cellular response to virus
L	1990386	biological_process	mitotic cleavage furrow ingression
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	0015031	biological_process	protein transport
M	0016020	cellular_component	membrane
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	0035646	biological_process	endosome to melanosome transport
M	0043231	cellular_component	intracellular membrane-bounded organelle
M	0045202	cellular_component	synapse
M	0060155	biological_process	platelet dense granule organization
M	1903232	biological_process	melanosome assembly
N	0005525	molecular_function	GTP binding
Q	0006886	biological_process	intracellular protein transport
Q	0016192	biological_process	vesicle-mediated transport
Q	0030117	cellular_component	membrane coat
R	0006886	biological_process	intracellular protein transport
R	0016192	biological_process	vesicle-mediated transport
R	0030117	cellular_component	membrane coat
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	0043231	cellular_component	intracellular membrane-bounded organelle
S	0060155	biological_process	platelet dense granule organization
S	1903232	biological_process	melanosome assembly
T	0005525	molecular_function	GTP binding
U	0000139	cellular_component	Golgi membrane
U	0000287	molecular_function	magnesium ion binding
U	0002090	biological_process	regulation of receptor internalization
U	0003723	molecular_function	RNA binding
U	0003924	molecular_function	GTPase activity
U	0005515	molecular_function	protein binding
U	0005525	molecular_function	GTP binding
U	0005794	cellular_component	Golgi apparatus
U	0005829	cellular_component	cytosol
U	0005886	cellular_component	plasma membrane
U	0005925	cellular_component	focal adhesion
U	0006878	biological_process	intracellular copper ion homeostasis
U	0006886	biological_process	intracellular protein transport
U	0012505	cellular_component	endomembrane system
U	0014069	cellular_component	postsynaptic density
U	0015031	biological_process	protein transport
U	0016020	cellular_component	membrane
U	0016192	biological_process	vesicle-mediated transport
U	0016787	molecular_function	hydrolase activity
U	0019904	molecular_function	protein domain specific binding
U	0030017	cellular_component	sarcomere
U	0031252	cellular_component	cell leading edge
U	0032991	cellular_component	protein-containing complex
U	0034315	biological_process	regulation of Arp2/3 complex-mediated actin nucleation
U	0043005	cellular_component	neuron projection
U	0045202	cellular_component	synapse
U	0060292	biological_process	long-term synaptic depression
U	0070062	cellular_component	extracellular exosome
U	0097061	biological_process	dendritic spine organization
U	0098586	biological_process	cellular response to virus
U	1990386	biological_process	mitotic cleavage furrow ingression
V	0000139	cellular_component	Golgi membrane
V	0000287	molecular_function	magnesium ion binding
V	0002090	biological_process	regulation of receptor internalization
V	0003723	molecular_function	RNA binding
V	0003924	molecular_function	GTPase activity
V	0005515	molecular_function	protein binding
V	0005525	molecular_function	GTP binding
V	0005794	cellular_component	Golgi apparatus
V	0005829	cellular_component	cytosol
V	0005886	cellular_component	plasma membrane
V	0005925	cellular_component	focal adhesion
V	0006878	biological_process	intracellular copper ion homeostasis
V	0006886	biological_process	intracellular protein transport
V	0012505	cellular_component	endomembrane system
V	0014069	cellular_component	postsynaptic density
V	0015031	biological_process	protein transport
V	0016020	cellular_component	membrane
V	0016192	biological_process	vesicle-mediated transport
V	0016787	molecular_function	hydrolase activity
V	0019904	molecular_function	protein domain specific binding
V	0030017	cellular_component	sarcomere
V	0031252	cellular_component	cell leading edge
V	0032991	cellular_component	protein-containing complex
V	0034315	biological_process	regulation of Arp2/3 complex-mediated actin nucleation
V	0043005	cellular_component	neuron projection
V	0045202	cellular_component	synapse
V	0060292	biological_process	long-term synaptic depression
V	0070062	cellular_component	extracellular exosome
V	0097061	biological_process	dendritic spine organization
V	0098586	biological_process	cellular response to virus
V	1990386	biological_process	mitotic cleavage furrow ingression
W	0005515	molecular_function	protein binding
W	0005765	cellular_component	lysosomal membrane
W	0005769	cellular_component	early endosome
W	0005794	cellular_component	Golgi apparatus
W	0005802	cellular_component	trans-Golgi network
W	0005829	cellular_component	cytosol
W	0006886	biological_process	intracellular protein transport
W	0015031	biological_process	protein transport
W	0016020	cellular_component	membrane
W	0016192	biological_process	vesicle-mediated transport
W	0030121	cellular_component	AP-1 adaptor complex
W	0030131	cellular_component	clathrin adaptor complex
W	0030665	cellular_component	clathrin-coated vesicle membrane
W	0031410	cellular_component	cytoplasmic vesicle
W	0032438	biological_process	melanosome organization
W	0032588	cellular_component	trans-Golgi network membrane
W	0035646	biological_process	endosome to melanosome transport
W	0043231	cellular_component	intracellular membrane-bounded organelle
W	0045202	cellular_component	synapse
W	0060155	biological_process	platelet dense granule organization
W	1903232	biological_process	melanosome assembly
X	0005515	molecular_function	protein binding
X	0005765	cellular_component	lysosomal membrane
X	0005769	cellular_component	early endosome
X	0005794	cellular_component	Golgi apparatus
X	0005802	cellular_component	trans-Golgi network
X	0005829	cellular_component	cytosol
X	0006886	biological_process	intracellular protein transport
X	0015031	biological_process	protein transport
X	0016020	cellular_component	membrane
X	0016192	biological_process	vesicle-mediated transport
X	0030121	cellular_component	AP-1 adaptor complex
X	0030131	cellular_component	clathrin adaptor complex
X	0030665	cellular_component	clathrin-coated vesicle membrane
X	0031410	cellular_component	cytoplasmic vesicle
X	0032438	biological_process	melanosome organization
X	0032588	cellular_component	trans-Golgi network membrane
X	0035646	biological_process	endosome to melanosome transport
X	0043231	cellular_component	intracellular membrane-bounded organelle
X	0045202	cellular_component	synapse
X	0060155	biological_process	platelet dense granule organization
X	1903232	biological_process	melanosome assembly
Y	0005525	molecular_function	GTP binding
Z	0005525	molecular_function	GTP binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	17
Details	binding site for residue GTP C 1001

Chain	Residue
C	ASP26
C	PRO47
C	THR48
C	GLY69
C	LYS127
C	ASP129
C	ALA160
C	THR161
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	GLY69
H	LEU71
H	ASN126
H	LYS127
H	ASP129
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	17
Details	binding site for residue GTP K 1001

Chain	Residue
K	ASP26
K	ALA27
K	ALA28
K	GLY29
K	LYS30
K	THR31
K	THR32
K	THR45
K	ILE46
K	PRO47
K	THR48
K	GLY69
K	LYS127
K	ASP129
K	ALA160
K	THR161
K	MG1002

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

Chain	Residue
K	THR31
K	THR48
K	GTP1001

site_id	AC7
Number of Residues	18
Details	binding site for residue GTP U 1001

Chain	Residue
U	ALA27
U	ALA28
U	GLY29
U	LYS30
U	THR31
U	THR32
U	THR45
U	ILE46
U	PRO47
U	THR48
U	GLY69
U	LEU71
U	ASN126
U	LYS127
U	ASP129
U	ALA160
U	THR161
U	MG1002

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

Chain	Residue
U	THR31
U	THR48
U	GTP1001

site_id	AC9
Number of Residues	17
Details	binding site for residue GTP L 1001

Chain	Residue
L	ASP26
L	ALA27
L	ALA28
L	GLY29
L	LYS30
L	THR31
L	THR32
L	THR45
L	ILE46
L	PRO47
L	THR48
L	GLY69
L	LYS127
L	ASP129
L	ALA160
L	THR161
L	MG1002

site_id	AD1
Number of Residues	3
Details	binding site for residue MG L 1002

Chain	Residue
L	THR31
L	THR48
L	GTP1001

site_id	AD2
Number of Residues	18
Details	binding site for residue GTP V 1001

Chain	Residue
V	ALA27
V	ALA28
V	GLY29
V	LYS30
V	THR31
V	THR32
V	THR45
V	ILE46
V	PRO47
V	THR48
V	GLY69
V	LEU71
V	ASN126
V	LYS127
V	ASP129
V	ALA160
V	THR161
V	MG1002

site_id	AD3
Number of Residues	3
Details	binding site for residue MG V 1002

Chain	Residue
V	THR31
V	THR48
V	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_FI1
Number of Residues	3
Details	MOD_RES: N-acetylserine => ECO:0000250\|UniProtKB:Q9BXS5

Chain	Residue	Details
M	SER2
Z	LYS-13
W	SER2
X	SER2
U	GLY24
L	GLY24
V	GLY24
Y	LYS-13
d	LYS18

site_id	SWS_FT_FI2
Number of Residues	6
Details	MOD_RES: Phosphothreonine => ECO:0007744\|PubMed:17242355, ECO:0007744\|PubMed:21183079

Chain	Residue	Details
M	THR152
M	THR154
W	THR152
W	THR154
X	THR152
X	THR154

site_id	SWS_FT_FI3
Number of Residues	3
Details	MOD_RES: Phosphothreonine => ECO:0000250\|UniProtKB:Q32Q06

Chain	Residue	Details
M	THR223
W	THR223
X	THR223
U	ALA160
L	ALA160
V	ALA160

site_id	SWS_FT_FI4
Number of Residues	6
Details	MOD_RES: Phosphoserine; by host => ECO:0000255\|HAMAP-Rule:MF_04078

Chain	Residue	Details
T	SER37
N	SER6
c	SER37
Y	SER6
d	SER37
Z	SER6

site_id	SWS_FT_FI5
Number of Residues	6
Details	LIPID: N-myristoyl glycine; by host => ECO:0000255\|HAMAP-Rule:MF_04078

Chain	Residue	Details
T	GLY33
N	GLY2
c	GLY33
Y	GLY2
d	GLY33
Z	GLY2

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)