3P1J - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN GTPASE IMAP FAMILY MEMBER 2 IN THE NUCLEOTIDE-FREE STATE

Authors :   L. Shen, W. Tempel, Y. Tong, X. Guan, L. Nedyalkova, A. K. Wernimont, F. M C. H. Arrowsmith, A. M. Edwards, C. Bountra, J. Weigelt, A. Bochkarev, D. W. Andrews, H. Park, Structural Genomics Consortium (Sgc)

Date :   30 Sep 10 (Deposition) - 13 Oct 10 (Release) - 13 Oct 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.58

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,D  (1x)
Biol. Unit 2: B,C  (1x)

Keywords :   Immunity, Structural Genomics Consortium, Gtpase, Immunity-Associated Protein, Sgc, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Shen, W. Tempel, Y. Tong, X. Guan, L. Nedyalkova, A. K. Wernimont, F. Mackenzie, C. H. Arrowsmith, A. M. Edwards, C. Bountra, J. Weigelt, A. Bochkarev, D. W. Andrews, H. Park
Crystal Structure Of Human Gtpase Imap Family Member 2 In The Nucleotide-Free State
To Be Published
PubMed: search

Molecule 1 - GTPASE IMAP FAMILY MEMBER 2
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28-MHL
	Expression System Strain	:	BL21(DE3)-V2R-PRARE2
	Expression System Taxid	:	469008
	Gene	:	GIMAP2, IMAP2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	IMMUNITY-ASSOCIATED PROTEIN 2, HIMAP2

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A			D
Biological Unit 2 (1x)	:		B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 19)

No.	Name	Count	Type	Full Name
1	UNX	19	Ligand/Ion	UNKNOWN ATOM OR ION

Biological Unit 1 (1, 14)

No.	Name	Count	Type	Full Name
1	UNX	14	Ligand/Ion	UNKNOWN ATOM OR ION

Biological Unit 2 (1, 5)

No.	Name	Count	Type	Full Name
1	UNX	5	Ligand/Ion	UNKNOWN ATOM OR ION

(no "Site" information available for 3P1J)

(no "SS Bond" information available for 3P1J)

Asymmetric Unit

No.	Residues
1	Ala A:103	-	Pro A:104
2	Ala B:103	-	Pro B:104
3	Ala C:103	-	Pro C:104
4	Ala D:103	-	Pro D:104

Asymmetric Unit (3, 10)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_049531	V	74	F	GIMA2_HUMAN	Polymorphism	11558054	A/B/C/D	V	74	F
2	UniProt	VAR_049532	N	152	S	GIMA2_HUMAN	Polymorphism	17173567	B/C	N	152	S
3	UniProt	VAR_017305	H	161	R	GIMA2_HUMAN	Polymorphism	2075078	A/B/C/D	H	161	R

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_049531	V	74	F	GIMA2_HUMAN	Polymorphism	11558054	A/D	V	74	F
3	UniProt	VAR_017305	H	161	R	GIMA2_HUMAN	Polymorphism	2075078	A/D	H	161	R

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_049531	V	74	F	GIMA2_HUMAN	Polymorphism	11558054	B/C	V	74	F
2	UniProt	VAR_049532	N	152	S	GIMA2_HUMAN	Polymorphism	17173567	B/C	N	152	S
3	UniProt	VAR_017305	H	161	R	GIMA2_HUMAN	Polymorphism	2075078	B/C	H	161	R

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 3P1J)

(no "Exon" information available for 3P1J)

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:190
 aligned with GIMA2_HUMAN | Q9UG22 from UniProtKB/Swiss-Prot  Length:337

    Alignment length:205
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220     
          GIMA2_HUMAN    21 SELRIILVGKTGTGKSAAGNSILRKQAFESKLGSQTLTKTCSKSQGSWGNREIVIIDTPDMFSWKDHCEALYKEVQRCYLLSAPGPHVLLLVTQLGRYTSQDQQAAQRVKEIFGEDAMGHTIVLFTHKEDLNGGSLMDYMHDSDNKALSKLVAACGGRICAFNNRAEGSNQDDQVKELMDCIEDLLMEKNGDHYTNGLYSLIQRS 225
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhh....-------......eeeeeee..eeeeeee.hhhhhh...hhhhhhhhhhhhhhhh....eeeeeee....hhhhhhhhhhhhhhhhhhhhh.eeeeeee.-----hhhhhhhhhh.hhhhhhhhhhh...eeeee.---hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------F--------------------------------------------------------------------------------------R---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p1j A  21 SELRIILVGKTGTGKSAAGNSILRKQAF-------TLTKTCSKSQGSWGNREIVIIDTPDMFSWKDHCEALYKEVQRCYLLSAPGPHVLLLVTQLGRYTSQDQQAAQRVKEIFGEDAMGHTIVLFTHK-----GSLMDYMHDSDNKALSKLVAACGGRICAFNN---GSNQDDQVKELMDCIEDLLMEKNGDHYTNGLYSLIQRS 225
                                    30        40       | -     |  60        70        80        90       100       110       120       130       140       | -   |   160       170       180   |   190       200       210       220     
                                                      48      56                                                                                         148   154                           184 188

Chain B from PDB  Type:PROTEIN  Length:180
 aligned with GIMA2_HUMAN | Q9UG22 from UniProtKB/Swiss-Prot  Length:337

    Alignment length:204
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220    
          GIMA2_HUMAN    21 SELRIILVGKTGTGKSAAGNSILRKQAFESKLGSQTLTKTCSKSQGSWGNREIVIIDTPDMFSWKDHCEALYKEVQRCYLLSAPGPHVLLLVTQLGRYTSQDQQAAQRVKEIFGEDAMGHTIVLFTHKEDLNGGSLMDYMHDSDNKALSKLVAACGGRICAFNNRAEGSNQDDQVKELMDCIEDLLMEKNGDHYTNGLYSLIQR 224
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee.hhhhhhhhhhhhhh.----------......eeee.-----.eeeee.hhhhhh...hhhhhhhhhhhhhhhh....eeeeeee....hhhhhhhhhhhhhhhhhhhhh.eeeeeee----hhhhhhhhhhhh.hhhhhhhhhhh...eeeee.-----hhhhhhhhhhhhhhhhhhhh......hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------F-----------------------------------------------------------------------------S--------R--------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3p1j B  21 SELRIILVGKTGTGKSAAGNSILRK----------TLTKTCSKSQG-----EIVIIDTPDMFSWKDHCEALYKEVQRCYLLSAPGPHVLLLVTQLGRYTSQDQQAAQRVKEIFGEDAMGHTIVLFTH----NGGSLMDYMHDSDNKALSKLVAACGGRICAFNN-----NQDDQVKELMDCIEDLLMEKNGDHYTNGLYSLIQR 224
                                    30        40    |    -     |  60     |   - |      80        90       100       110       120       130       140      |  - |     160       170       180   |   190       200       210       220    
                                                   45         56        66    72                                                                        147  152                             184   190

Chain C from PDB  Type:PROTEIN  Length:186
 aligned with GIMA2_HUMAN | Q9UG22 from UniProtKB/Swiss-Prot  Length:337

    Alignment length:206
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220      
          GIMA2_HUMAN    21 SELRIILVGKTGTGKSAAGNSILRKQAFESKLGSQTLTKTCSKSQGSWGNREIVIIDTPDMFSWKDHCEALYKEVQRCYLLSAPGPHVLLLVTQLGRYTSQDQQAAQRVKEIFGEDAMGHTIVLFTHKEDLNGGSLMDYMHDSDNKALSKLVAACGGRICAFNNRAEGSNQDDQVKELMDCIEDLLMEKNGDHYTNGLYSLIQRSK 226
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhh---------------..eeeee..--.eeeeee.hhhhhh...hhhhhhhhhhhhhhhh....eeeeeee....hhhhhhhhhhhhhhhhhhhhh.eeeeeee.---hhhhhhhhhhhh.hhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------F-----------------------------------------------------------------------------S--------R----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p1j C  21 SELRIILVGKTGTGKSAAGNSILR---------------TCSKSQGSW--REIVIIDTPDMFSWKDHCEALYKEVQRCYLLSAPGPHVLLLVTQLGRYTSQDQQAAQRVKEIFGEDAMGHTIVLFTHK---NGGSLMDYMHDSDNKALSKLVAACGGRICAFNNRAEGSNQDDQVKELMDCIEDLLMEKNGDHYTNGLYSLIQRSK 226
                                    30        40   |     -        60       | -|       80        90       100       110       120       130       140       | - |     160       170       180       190       200       210       220      
                                                  44              60      68 71                                                                          148 152

Chain D from PDB  Type:PROTEIN  Length:193
 aligned with GIMA2_HUMAN | Q9UG22 from UniProtKB/Swiss-Prot  Length:337

    Alignment length:205
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220     
          GIMA2_HUMAN    21 SELRIILVGKTGTGKSAAGNSILRKQAFESKLGSQTLTKTCSKSQGSWGNREIVIIDTPDMFSWKDHCEALYKEVQRCYLLSAPGPHVLLLVTQLGRYTSQDQQAAQRVKEIFGEDAMGHTIVLFTHKEDLNGGSLMDYMHDSDNKALSKLVAACGGRICAFNNRAEGSNQDDQVKELMDCIEDLLMEKNGDHYTNGLYSLIQRS 225
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --AIG1-3p1jD01 D:23-225                                                                                                                                                                                       Pfam domains (1)
           Pfam domains (2) --AIG1-3p1jD02 D:23-225                                                                                                                                                                                       Pfam domains (2)
           Pfam domains (3) --AIG1-3p1jD03 D:23-225                                                                                                                                                                                       Pfam domains (3)
           Pfam domains (4) --AIG1-3p1jD04 D:23-225                                                                                                                                                                                       Pfam domains (4)
         Sec.struct. author ..eeeeee.....hhhhhhhhhhh......-----......eeeeeee..eeeeeee.hhhhhh...hhhhhhhhhhhhhhhh....eeeeeee....hhhhhhhhhhhhhhhhhhhhh.eeeeeee-------hhhhhhhhh.hhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------F--------------------------------------------------------------------------------------R---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p1j D  21 SELRIILVGKTGTGKSAAGNSILRKQAFES-----TLTKTCSKSQGSWGNREIVIIDTPDMFSWKDHCEALYKEVQRCYLLSAPGPHVLLLVTQLGRYTSQDQQAAQRVKEIFGEDAMGHTIVLFTH-------SLMDYMHDSDNKALSKLVAACGGRICAFNNRAEGSNQDDQVKELMDCIEDLLMEKNGDHYTNGLYSLIQRS 225
                                    30        40        50     |  60        70        80        90       100       110       120       130       140      |  -    |  160       170       180       190       200       210       220     
                                                        50    56                                                                                        147     155

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 3P1J)

(no "CATH Domain" information available for 3P1J)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: AIG1 (6)

Homo sapiens (Human) (6)

1a	AIG1-3p1jD01	D:23-225
1b	AIG1-3p1jD02	D:23-225
1c	AIG1-3p1jD03	D:23-225
1d	AIG1-3p1jD04	D:23-225

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (GIMA2_HUMAN | Q9UG22)

molecular function
	GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0005811	lipid droplet	An intracellular non-membrane-bounded organelle comprising a matrix of coalesced lipids surrounded by a phospholipid monolayer. May include associated proteins.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		UNX	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
(no "Sites" information available for 3p1j)

	Cis Peptide Bonds
		Ala A:103 - Pro A:104	[ RasMol ]
		Ala B:103 - Pro B:104	[ RasMol ]
		Ala C:103 - Pro C:104	[ RasMol ]
		Ala D:103 - Pro D:104	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	3p1j
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	GIMA2_HUMAN \| Q9UG22
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	GIMA2_HUMAN \| Q9UG22
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	GIMA2_HUMAN \| Q9UG22	:	2xtm 2xtn 2xto 2xtp

(no "Related Entries Specified in the PDB File" available for 3P1J)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 19)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 10)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (1, 4)

Gene Ontology (6, 6)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File