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Title :   ARFGAP DOMAIN OF HIV-1 REV BINDING PROTEIN

Authors :   Y. Tong, W. Tempel, L. Shen, S. Dimov, R. Landry, C. H. Arrowsmith, A. M. E M. Sundstrom, J. Weigelt, A. Bochkarev, H. Park, Structural Genomic Consortium (Sgc)

Date :   19 Jan 07 (Deposition) - 30 Jan 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.48

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Arfgap, Gtpase-Activating Protein, Rev-Interacting Protein, Hiv, Human Immunodeficiency Virus, Aids, Nucleoporin, Structural Genomics, Structural Genomics Consortium, Sgc, Hydrolase Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Tong, W. Tempel, L. Shen, S. Dimov, R. Landry, C. H. Arrowsmith, A. M. Edwards, M. Sundstrom, J. Weigelt, A. Bochkarev, H. Park, Structural Genomics Consortium (Sgc)
Arfgap Domain Of Hiv-1 Rev Binding Protein
To Be Published
PubMed: search

Molecule 1 - NUCLEOPORIN-LIKE PROTEIN RIP
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A-LIC
	Expression System Strain	:	BL21-CODONPLUS(DE3)-RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	ARFGAP DOMAIN: RESIDUES 4-141
	Gene	:	HRB, RAB, RIP
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	HIV-1 REV-BINDING PROTEIN, REV-INTERACTING PROTEIN, REV/REX ACTIVATION DOMAIN-BINDING PROTEIN

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 14)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	SO4	2	Ligand/Ion	SULFATE ION
3	UNL	1	Ligand/Ion	UNKNOWN LIGAND
4	UNX	9	Ligand/Ion	UNKNOWN ATOM OR ION
5	ZN	1	Ligand/Ion	ZINC ION

Biological Unit 1 (4, 26)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	SO4	4	Ligand/Ion	SULFATE ION
3	UNL	2	Ligand/Ion	UNKNOWN LIGAND
4	UNX	18	Ligand/Ion	UNKNOWN ATOM OR ION
5	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	CYS A:29 , CYS A:32 , CYS A:49 , CYS A:52	BINDING SITE FOR RESIDUE ZN A 201
02	AC2	SOFTWARE	ARG A:64 , THR A:71 , SER A:102 , ALA A:103 , ARG A:125 , TRP A:126 , UNX A:1007 , HOH A:2025 , HOH A:2060	BINDING SITE FOR RESIDUE SO4 A 2001
03	AC3	SOFTWARE	LYS A:8 , PRO A:24 , ARG A:27	BINDING SITE FOR RESIDUE SO4 A 2002
04	AC4	SOFTWARE	THR A:43 , PRO A:61 , PRO A:62	BINDING SITE FOR RESIDUE UNL A 202
05	AC5	SOFTWARE	THR A:72	BINDING SITE FOR RESIDUE UNX A 1001
06	AC6	SOFTWARE	HIS A:13 , THR A:74 , GLN A:75	BINDING SITE FOR RESIDUE UNX A 1002
07	AC7	SOFTWARE	TYR A:127	BINDING SITE FOR RESIDUE UNX A 1003
08	AC8	SOFTWARE	SER A:101	BINDING SITE FOR RESIDUE UNX A 1004
09	AC9	SOFTWARE	VAL A:44 , TRP A:93	BINDING SITE FOR RESIDUE UNX A 1005
10	BC1	SOFTWARE	TRP A:93 , LYS A:120 , LYS A:124 , ARG A:125 , TRP A:126 , TYR A:127	BINDING SITE FOR RESIDUE UNX A 1006
11	BC2	SOFTWARE	LYS A:66 , SO4 A:2001	BINDING SITE FOR RESIDUE UNX A 1007
12	BC3	SOFTWARE	GLU A:11 , LYS A:12 , ARG A:18 , HOH A:2034	BINDING SITE FOR RESIDUE UNX A 1008
13	BC4	SOFTWARE	ARG A:18 , HOH A:2067	BINDING SITE FOR RESIDUE UNX A 1009
14	BC5	SOFTWARE	ARG A:57 , PRO A:62 , PHE A:80 , PHE A:97 , ASP A:98 , ASP A:99 , HOH A:2069 , HOH A:2077	BINDING SITE FOR RESIDUE GOL A 203

(no "SS Bond" information available for 2OLM)

Asymmetric Unit

No.	Residues
1	Asn A:60	-	Pro A:61

(no "SAP(SNP)/Variant" information available for 2OLM)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ARFGAP	PS50115	ARF GTPase-activating proteins domain profile.	AGFG1_HUMAN	11-135	1	A:11-135

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ARFGAP	PS50115	ARF GTPase-activating proteins domain profile.	AGFG1_HUMAN	11-135	2	A:11-135

Asymmetric Unit (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000310078	1b	ENSE00001855491	chr2:228336878-228337304	427	AGFG1_HUMAN	1-56	56	1	A:3-56	54
1.2	ENST00000310078	2	ENSE00001183976	chr2:228356263-228356356	94	AGFG1_HUMAN	56-87	32	1	A:56-87	32
1.5	ENST00000310078	5	ENSE00001183971	chr2:228384664-228384779	116	AGFG1_HUMAN	88-126	39	1	A:88-126	39
1.6	ENST00000310078	6	ENSE00001183968	chr2:228388479-228388641	163	AGFG1_HUMAN	126-180	55	1	A:126-135	10
1.7b	ENST00000310078	7b	ENSE00001183965	chr2:228389478-228389631	154	AGFG1_HUMAN	181-232	52	0	-	-
1.8	ENST00000310078	8	ENSE00001183964	chr2:228395807-228395926	120	AGFG1_HUMAN	232-272	41	0	-	-
1.10b	ENST00000310078	10b	ENSE00001183961	chr2:228398265-228398474	210	AGFG1_HUMAN	272-342	71	0	-	-
1.11a	ENST00000310078	11a	ENSE00001183955	chr2:228399561-228399741	181	AGFG1_HUMAN	342-402	61	0	-	-
1.12	ENST00000310078	12	ENSE00001183952	chr2:228401341-228401420	80	AGFG1_HUMAN	402-429	28	0	-	-
1.13a	ENST00000310078	13a	ENSE00001183950	chr2:228401617-228401709	93	AGFG1_HUMAN	429-460	32	0	-	-
1.15	ENST00000310078	15	ENSE00001183947	chr2:228416675-228416833	159	AGFG1_HUMAN	460-513	54	0	-	-
1.16a	ENST00000310078	16a	ENSE00001183943	chr2:228418420-228418511	92	AGFG1_HUMAN	513-543	31	0	-	-
1.17e	ENST00000310078	17e	ENSE00001882126	chr2:228419152-228421384	2233	AGFG1_HUMAN	544-562	19	0	-	-

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:133
 aligned with AGFG1_HUMAN | P52594 from UniProtKB/Swiss-Prot  Length:562

    Alignment length:133
                                    12        22        32        42        52        62        72        82        92       102       112       122       132   
          AGFG1_HUMAN     3 ASAKRKQEEKHLKMLRDMTGLPHNRKCFDCDQRGPTYVNMTVGSFVCTSCSGSLRGLNPPHRVKSISMTTFTQQEIEFLQKHGNEVCKQIWLGLFDDRSSAIPDFRDPQKVKEFLQEKYEKKRWYVPPEQAKV 135
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------ArfGap-2olmA01 A:14-130                                                                                              ----- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhh..........eee....eeehhhhhhhhh.......eee......hhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhh......hhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------ARFGAP  PDB: A:11-135 UniProt: 11-135                                                                                         PROSITE
           Transcript 1 (1) Exon 1.1b  PDB: A:3-56 UniProt: 1-56 [INCOMPLETE]     -------------------------------Exon 1.5  PDB: A:88-126 UniProt: 88-126--------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------Exon 1.2  PDB: A:56-87          --------------------------------------Exon 1.6   Transcript 1 (2)
                 2olm A   3 SSAKRKQEEKHLKMLRDMTGLPHNRKCFDCDQRGPTYVNMTVGSFVCTSCSGSLRGLNPPHRVKSISMTTFTQQEIEFLQKHGNEVCKQIWLGLFDDRSSAIPDFRDPQKVKEFLQEKYEKKRWYVPPEQAKV 135
                                    12        22        32        42        52        62        72        82        92       102       112       122       132

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 2OLM)

(no "CATH Domain" information available for 2OLM)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: ArfGap] (6)

Family: ArfGap (6)

Homo sapiens (Human) (6)

ArfGap-2olmA01

A:14-130

Asymmetric Unit(hide GO term definitions)

Chain A (AGFG1_HUMAN | P52594)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0005096	GTPase activator activity	Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0001675	acrosome assembly	The formation of the acrosome from the spermatid Golgi.
	GO:0030154	cell differentiation	The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
	GO:0045109	intermediate filament organization	Control of the spatial distribution of intermediate filaments; includes organizing filaments into meshworks, bundles, or other structures, as by cross-linking.
	GO:0006406	mRNA export from nucleus	The directed movement of mRNA from the nucleus to the cytoplasm.
	GO:0051028	mRNA transport	The directed movement of mRNA, messenger ribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0007275	multicellular organism development	The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
	GO:0043547	positive regulation of GTPase activity	Any process that activates or increases the activity of a GTPase.
	GO:0007289	spermatid nucleus differentiation	The specialization of the spermatid nucleus during the development of a spermatid into a mature male gamete competent for fertilization.
	GO:0007283	spermatogenesis	The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0042995	cell projection	A prolongation or process extending from a cell, e.g. a flagellum or axon.
	GO:0031410	cytoplasmic vesicle	A vesicle found in the cytoplasm of a cell.
	GO:0043231	intracellular membrane-bounded organelle	Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
	GO:0043025	neuronal cell body	The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
	GO:0005643	nuclear pore	Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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		Asn A:60 - Pro A:61	[ RasMol ]

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	AGFG1_HUMAN \| P52594	:	2d9l 2vx8

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Description

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Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 14)

Sites (14, 14)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

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Exons (4, 4)

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