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Description

Title :   CRYSTAL STRUCTURE OF THE VON WILLEBRAND FACTOR A DOMAIN OF HUMAN CAPILLARY MORPHOGENESIS PROTEIN 2: AN ANTHRAX TOXIN RECEPTOR

Authors :   D. B. Lacy, D. J. Wigelsworth, H. M. Scobie, J. A. T. Young, R. J. Collier

Date :   26 Feb 04 (Deposition) - 13 Apr 04 (Release) - 12 Nov 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.81

Chains :   Asym./Biol. Unit : X

Keywords :   Rossmann Fold, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. B. Lacy, D. J. Wigelsworth, H. M. Scobie, J. A. T. Young, R. J. Collier
Crystal Structure Of The Von Willebrand Factor A Domain Of Human Capillary Morphogenesis Protein 2: An Anthrax Toxin Receptor
Proc. Natl. Acad. Sci. Usa V. 101 6367 2004
PubMed-ID: 15079089 | Reference-DOI: 10.1073/PNAS.0401506101

Compounds

Molecule 1 - ANTHRAX TOXIN RECEPTOR 2
	Chains	:	X
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PGEX-4T-1
	Expression System Strain	:	BL21.DE3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	VWA DOMAIN
	Gene	:	ANTXR2, CMG2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CAPILLARY MORPHOGENESIS PROTEIN-2, CMG-2

Structural Features

Chains, Units

		1
Asymmetric/Biological Unit	:	X

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (2, 2)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	MG	1	Ligand/Ion	MAGNESIUM ION

Sites (2, 2)

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER X:52 , GLY X:53 , SER X:54 , GLY X:116 , GLU X:117 , THR X:118 , MG X:219 , HOH X:254 , HOH X:313	BINDING SITE FOR RESIDUE ACT X 218
2	AC2	SOFTWARE	SER X:52 , SER X:54 , THR X:118 , ACT X:218 , HOH X:313 , HOH X:314	BINDING SITE FOR RESIDUE MG X 219

SS Bonds (0, 0)

(no "SS Bond" information available for 1SHT)

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 1SHT)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 3)

Asymmetric/Biological Unit (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_022687	L	45	P	ANTR2_HUMAN	Disease (HFS)	---	X	L	45	P
2	UniProt	VAR_022688	G	105	D	ANTR2_HUMAN	Disease (HFS)	137852902	X	G	105	D
3	UniProt	VAR_022689	I	189	T	ANTR2_HUMAN	Disease (HFS)	137852905	X	I	189	T

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

PROSITE Motifs (1, 1)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	VWFA	PS50234	VWFA domain profile.	ANTR2_HUMAN	44-213	1	X:44-213

Exons (8, 8)

Asymmetric/Biological Unit (8, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.8d	ENST00000307333	8d	ENSE00001871464	chr4:80993717-80993563	155	ANTR2_HUMAN	1-51	51	1	X:41-51	11
1.9a	ENST00000307333	9a	ENSE00001761580	chr4:80992808-80992737	72	ANTR2_HUMAN	51-75	25	1	X:51-75	25
1.10	ENST00000307333	10	ENSE00001798474	chr4:80990661-80990590	72	ANTR2_HUMAN	75-99	25	1	X:75-99	25
1.11	ENST00000307333	11	ENSE00001123454	chr4:80977167-80977086	82	ANTR2_HUMAN	99-126	28	1	X:99-126	28
1.12	ENST00000307333	12	ENSE00001123446	chr4:80976621-80976514	108	ANTR2_HUMAN	127-162	36	1	X:127-162	36
1.13	ENST00000307333	13	ENSE00001123438	chr4:80976372-80976304	69	ANTR2_HUMAN	163-185	23	1	X:163-185	23
1.14b	ENST00000307333	14b	ENSE00001123430	chr4:80975506-80975426	81	ANTR2_HUMAN	186-212	27	1	X:186-212	27
1.15	ENST00000307333	15	ENSE00001123421	chr4:80957186-80957126	61	ANTR2_HUMAN	213-233	21	1	X:213-217	5
1.16	ENST00000307333	16	ENSE00001123410	chr4:80954724-80954626	99	ANTR2_HUMAN	233-266	34	0	-	-
1.17	ENST00000307333	17	ENSE00001123400	chr4:80952846-80952777	70	ANTR2_HUMAN	266-289	24	0	-	-
1.19	ENST00000307333	19	ENSE00001712373	chr4:80940130-80940052	79	ANTR2_HUMAN	289-315	27	0	-	-
1.20	ENST00000307333	20	ENSE00001665059	chr4:80929770-80929675	96	ANTR2_HUMAN	316-347	32	0	-	-
1.21	ENST00000307333	21	ENSE00001771910	chr4:80906017-80905973	45	ANTR2_HUMAN	348-362	15	0	-	-
1.22	ENST00000307333	22	ENSE00001710470	chr4:80905124-80905032	93	ANTR2_HUMAN	363-393	31	0	-	-
1.23	ENST00000307333	23	ENSE00001599114	chr4:80899328-80899161	168	ANTR2_HUMAN	394-449	56	0	-	-
1.24b	ENST00000307333	24b	ENSE00001257764	chr4:80898855-80898733	123	ANTR2_HUMAN	450-489	40	0	-	-

Sequences/Alignments

Asymmetric/Biological 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 X from PDB  Type:PROTEIN  Length:177
 aligned with ANTR2_HUMAN | P58335 from UniProtKB/Swiss-Prot  Length:489

    Alignment length:177
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       
          ANTR2_HUMAN    41 RAFDLYFVLDKSGSVANNWIEIYNFVQQLAERFVSPEMRLSFIVFSSQATIILPLTGDRGKISKGLEDLKRVSPVGETYIHEGLKLANEQIQKAGGLKTSSIIIALTDGKLDGLVPSYAEKEAKISRSLGASVYCVGVLDFEQAQLERIADSKEQVFPVKGGFQALKGIINSILAQS 217
               SCOP domains d1shtx_ X: Capillary morphogenesis protein 2 domain                                                                                                                               SCOP domains
               CATH domains 1shtX00 X:41-217  [code=3.40.50.410, no name defined]                                                                                                                             CATH domains
               Pfam domains ---VWA-1shtX02 X:44-213                                                                                                                                                      Anth Pfam domains
         Sec.struct. author ..eeeeeeee.hhhhhhhhhhhhhhhhhhhhhh.....eeeeeee...eeeeeeee.hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhheeeeeeee......hhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhh.hhh.eee.....hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----P-----------------------------------------------------------D-----------------------------------------------------------------------------------T---------------------------- SAPs(SNPs)
                    PROSITE ---VWFA  PDB: X:44-213 UniProt: 44-213                                                                                                                                       ---- PROSITE
           Transcript 1 (1) Exon 1.8d  -----------------------Exon 1.10  PDB: X:75-99  ---------------------------Exon 1.12  PDB: X:127-162           Exon 1.13              Exon 1.14b  PDB: X:186-212 1.15  Transcript 1 (1)
           Transcript 1 (2) ----------Exon 1.9a  PDB: X:51-75  -----------------------Exon 1.11  PDB: X:99-126    ------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1sht X  41 RAFDLYFVLDKSGSVANNWIEIYNFVQQLAERFVSPEMRLSFIVFSSQATIILPLTGDRGKISKGLEDLKRVSPVGETYIHEGLKLANEQIQKAGGLKTSSIIIALTDGKLDGLVPSYAEKEAKISRSLGASVYCVGVLDFEQAQLERIADSKEQVFPVKGGFQALKGIINSILAQS 217
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: vWA-like (111)

Superfamily: vWA-like (111)

Family: Integrin A (or I) domain (84)

Protein domain: Capillary morphogenesis protein 2 domain (3)

Human (Homo sapiens) [TaxId: 9606] (3)

d1shtx_

CATH Domains (1, 1)

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.410, no name defined] (87)

Human (Homo sapiens) (66)

1shtX00

X:41-217

Pfam Domains (2, 2)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Anth_Ig] (4)

Family: Anth_Ig (4)

Homo sapiens (Human) (4)

Anth_Ig-1shtX01

X:214-217

Clan: vWA-like (60)

Family: VWA (50)

Homo sapiens (Human) (47)

VWA-1shtX02

X:44-213

Gene Ontology (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

Chain X (ANTR2_HUMAN | P58335)

molecular function
	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).
	GO:0004872	receptor activity	Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
biological process
	GO:0022414	reproductive process	A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.
	GO:1901998	toxin transport	The directed movement of a toxin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
cellular component
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	GO:0010008	endosome membrane	The lipid bilayer surrounding an endosome.
	GO:0009897	external side of plasma membrane	The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	ANTR2_HUMAN \| P58335	:	1shu 1t6b 1tx5 1tzn

Related Entries Specified in the PDB File

1shv	CRYSTAL STRUCTURE OF THE VON WILLEBRAND FACTOR A DOMAIN OF HUMAN CAPILLARY MORPHOGENESIS PROTEIN 2