2XTM - JenaLib

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Title :   CRYSTAL STRUCTURE OF GDP-BOUND HUMAN GIMAP2, AMINO ACID RESIDUES 1-234

Authors :   D. Schwefel, C. Froehlich, O. Daumke

Date :   11 Oct 10 (Deposition) - 20 Oct 10 (Release) - 08 Dec 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Immune System, G Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Schwefel, C. Froehlich, J. Eichhorst, B. Wiesner, J. Behlke, L. Aravind, O. Daumke
Structural Basis Of Oligomerization In Septin-Like Gtpase Of Immunity-Associated Protein 2 (Gimap2)
Proc. Natl. Acad. Sci. Usa V. 107 20299 2010
PubMed-ID: 21059949 | Reference-DOI: 10.1073/PNAS.1010322107
(for further references see the PDB file header)

Molecule 1 - GTPASE IMAP FAMILY MEMBER 2
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX6P1
	Expression System Strain	:	ROSETTA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 1-234
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	GIMAP2, IMMUNITY-ASSOCIATED PROTEIN 2, HIMAP2

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 7)

No.	Name	Count	Type	Full Name
1	GDP	2	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
2	GOL	3	Ligand/Ion	GLYCEROL
3	MG	2	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
2	GOL	3	Ligand/Ion	GLYCEROL
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
2	GOL	-1	Ligand/Ion	GLYCEROL
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:32 , THR A:33 , GLY A:34 , LYS A:35 , SER A:36 , ALA A:37 , SER A:50 , LYS A:51 , LEU A:52 , HIS A:147 , GLU A:149 , ASN A:184 , ARG A:185 , MG A:1229 , HOH A:2114 , HOH A:2188 , HOH A:2189 , HOH A:2191 , HOH A:2193 , HOH A:2194	BINDING SITE FOR RESIDUE GDP A1228
2	AC2	SOFTWARE	SER A:36 , GDP A:1228 , HOH A:2011 , HOH A:2059 , HOH A:2189 , HOH A:2191	BINDING SITE FOR RESIDUE MG A1229
3	AC3	SOFTWARE	GLU A:131 , ILE A:132 , GLY A:134 , ASN A:216 , GLY A:217 , LEU A:218 , GOL A:1231 , HOH A:2195 , HOH A:2196	BINDING SITE FOR RESIDUE GOL A1230
4	AC4	SOFTWARE	GLY A:217 , GOL A:1230 , HOH A:2197 , HOH A:2198 , GLU B:131 , ILE B:132 , GLY B:134 , ASN B:216 , GLY B:217 , LEU B:218	BINDING SITE FOR RESIDUE GOL A1231
5	AC5	SOFTWARE	SER A:62 , LYS A:63 , ARG A:97 , LEU A:101 , HOH A:2199 , HOH A:2200 , GLU B:208 , LYS B:209 , HOH B:2079	BINDING SITE FOR RESIDUE GOL A1232
6	AC6	SOFTWARE	GLY B:32 , THR B:33 , GLY B:34 , LYS B:35 , SER B:36 , ALA B:37 , SER B:50 , HIS B:147 , GLU B:149 , ASN B:183 , ASN B:184 , MG B:1228 , HOH B:2019	BINDING SITE FOR RESIDUE GDP B1227
7	AC7	SOFTWARE	SER B:36 , THR B:58 , GDP B:1227 , HOH B:2015 , HOH B:2019	BINDING SITE FOR RESIDUE MG B1228

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

Asymmetric Unit

No.	Residues
1	Ala A:103	-	Pro A:104
2	Ala B:103	-	Pro B:104

Asymmetric Unit (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	A/B	V	74	F
2	UniProt	VAR_049532	N	152	S	GIMA2_HUMAN	Polymorphism	17173567	A/B	N	152	S
3	UniProt	VAR_017305	H	161	R	GIMA2_HUMAN	Polymorphism	2075078	A/B	H	161	R

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

Biological Unit 1 (3, 3)

								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	V	74	F
2	UniProt	VAR_049532	N	152	S	GIMA2_HUMAN	Polymorphism	17173567	A	N	152	S
3	UniProt	VAR_017305	H	161	R	GIMA2_HUMAN	Polymorphism	2075078	A	H	161	R

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

Biological Unit 2 (3, 3)

								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	V	74	F
2	UniProt	VAR_049532	N	152	S	GIMA2_HUMAN	Polymorphism	17173567	B	N	152	S
3	UniProt	VAR_017305	H	161	R	GIMA2_HUMAN	Polymorphism	2075078	B	H	161	R

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

(no "PROSITE Motif" information available for 2XTM)

(no "Exon" information available for 2XTM)

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:207
 aligned with GIMA2_HUMAN | Q9UG22 from UniProtKB/Swiss-Prot  Length:337

    Alignment length:207
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       
          GIMA2_HUMAN    21 SELRIILVGKTGTGKSAAGNSILRKQAFESKLGSQTLTKTCSKSQGSWGNREIVIIDTPDMFSWKDHCEALYKEVQRCYLLSAPGPHVLLLVTQLGRYTSQDQQAAQRVKEIFGEDAMGHTIVLFTHKEDLNGGSLMDYMHDSDNKALSKLVAACGGRICAFNNRAEGSNQDDQVKELMDCIEDLLMEKNGDHYTNGLYSLIQRSKC 227
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhh.................eeeeeee..eeeeeee.hhhhhh.....hhhhhhhhhhhhhh....eeeeeee....hhhhhhhhhhhhhhhh.hhhh.eeeeeehhhhhh..hhhhhhhhh.hhhhhhhhhhh...eee.....hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------F-----------------------------------------------------------------------------S--------R------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xtm A  21 SELRIILVGKTGTGKSAAGNSILRKQAFESKLGSQTLTKTCSKSQGSWGNREIVIIDTPDMFSWKDHCEALYKEVQRCYLLSAPGPHVLLLVTQLGRYTSQDQQAAQRVKEIFGEDAMGHTIVLFTHKEDLNGGSLMDYMHDSDNKALSKLVAACGGRICAFNNRAEGSNQDDQVKELMDCIEDLLMEKNGDHYTNGLYSLIQRSKC 227
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

Chain B from PDB  Type:PROTEIN  Length:199
 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 (1) --AIG1-2xtmB01 B:23-226                                                                                                                                                                                        Pfam domains (1)
           Pfam domains (2) --AIG1-2xtmB02 B:23-226                                                                                                                                                                                        Pfam domains (2)
         Sec.struct. author .eeeeeee.....hhhhhhhhhhh......-------....eeeeeee..eeeeeee.hhhhhh.....hhhhhhhhhhhhhh....eeeeeee....hhhhhhhhhhhhhhhh.hhhh.eeeeeehhhhhh..hhhhhhhhh.hhhhhhhhhhh...eee.....hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------F-----------------------------------------------------------------------------S--------R----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xtm B  21 SELRIILVGKTGTGKSAAGNSILRKQAFES-------TKTCSKSQGSWGNREIVIIDTPDMFSWKDHCEALYKEVQRCYLLSAPGPHVLLLVTQLGRYTSQDQQAAQRVKEIFGEDAMGHTIVLFTHKEDLNGGSLMDYMHDSDNKALSKLVAACGGRICAFNNRAEGSNQDDQVKELMDCIEDLLMEKNGDHYTNGLYSLIQRSK 226
                                    30        40        50       |60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220      
                                                        50      58

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 2XTM)

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: AIG1 (6)

Homo sapiens (Human) (6)

1a	AIG1-2xtmB01	B:23-226
1b	AIG1-2xtmB02	B:23-226

Asymmetric Unit(hide GO term definitions)

Chain A,B (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.

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

Biological Units
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		Biological Unit 2	[ Jena3D ]

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	GIMA2_HUMAN \| Q9UG22	:	2xtn 2xto 2xtp 3p1j

2xtn	CRYSTAL STRUCTURE OF GTP-BOUND HUMAN GIMAP2 , AMINO ACID RESIDUES 1-234
2xto	CRYSTAL STRUCTURE OF GDP-BOUND HUMAN GIMAP2 , AMINO ACID RESIDUES 21-260
2xtp	CRYSTAL STRUCTURE OF NUCLEOTIDE-FREE HUMAN GIMAP2, AMINO ACID RESIDUES 1-260

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 6)

PROSITE Motifs (0, 0)

Exons (0, 0)

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SCOP Domains (0, 0)

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Pfam Domains (1, 2)

Gene Ontology (6, 6)

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