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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF ECTODOMAIN OF BST-2/TETHERIN/CD317 (P21)

Authors :   Y. Xiong, H. Yang, J. Wang, W. Meng

Date :   27 Apr 10 (Deposition) - 27 Oct 10 (Release) - 24 Nov 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Hiv, Antiviral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Yang, J. Wang, X. Jia, M. W. Mcnatt, T. Zang, B. Pan, W. Meng, H. W. Wang P. D. Bieniasz, Y. Xiong
Structural Insight Into The Mechanisms Of Enveloped Virus Tethering By Tetherin.
Proc. Natl. Acad. Sci. Usa V. 107 18428 2010
PubMed-ID: 20940320 | Reference-DOI: 10.1073/PNAS.1011485107

Molecule 1 - BONE MARROW STROMAL ANTIGEN 2
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMAT9S
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 47-161
	Gene	:	BST2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	BST-2, TETHERIN, HM1.24 ANTIGEN

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 12)

No.	Name	Count	Type	Full Name
1	MSE	12	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 12)

No.	Name	Count	Type	Full Name
1	MSE	12	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 6)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 3MQC)

Asymmetric Unit

No.	Residues
1	A:51	-	B:51
2	C:51	-	D:51

(no "Cis Peptide Bond" information available for 3MQC)

Asymmetric Unit (1, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_012067	V	143	F	BST2_HUMAN	Polymorphism	1804402	A/B/C/D	V	103	F

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

Biological Unit 1 (1, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_012067	V	143	F	BST2_HUMAN	Polymorphism	1804402	A/B/C/D	V	103	F

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

Biological Unit 2 (1, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_012067	V	143	F	BST2_HUMAN	Polymorphism	1804402	A/B/C/D	V	103	F

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

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

(no "Exon" information available for 3MQC)

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:100
 aligned with BST2_HUMAN | Q10589 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:100
                                    59        69        79        89        99       109       119       129       139       149
           BST2_HUMAN    50 SEACRDGLRAVMECRNVTHLLQQELTEAQKGFQDVEAQAATCNHTVMALMASLDAEKAQGQKKVEELEGEITTLNHKLQDASAEVERLRRENQVLSVRIA 149
               SCOP domains ---------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------F------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 3mqc A  10 SEACRDGLRAVmECRNVTHLLQQELTEAQKGFQDVEAQAATCNHTVmALmASLDAEKAQGQKKVEELEGEITTLNHKLQDASAEVERLRRENQVLSVRIA 109
                                    19 |      29        39        49      | 59        69        79        89        99       109
                                      21-MSE                             56-MSE                                                 
                                                                            59-MSE

Chain B from PDB  Type:PROTEIN  Length:100
 aligned with BST2_HUMAN | Q10589 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:100
                                    59        69        79        89        99       109       119       129       139       149
           BST2_HUMAN    50 SEACRDGLRAVMECRNVTHLLQQELTEAQKGFQDVEAQAATCNHTVMALMASLDAEKAQGQKKVEELEGEITTLNHKLQDASAEVERLRRENQVLSVRIA 149
               SCOP domains ---------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------F------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 3mqc B  10 SEACRDGLRAVmECRNVTHLLQQELTEAQKGFQDVEAQAATCNHTVmALmASLDAEKAQGQKKVEELEGEITTLNHKLQDASAEVERLRRENQVLSVRIA 109
                                    19 |      29        39        49      | 59        69        79        89        99       109
                                      21-MSE                             56-MSE                                                 
                                                                            59-MSE

Chain C from PDB  Type:PROTEIN  Length:100
 aligned with BST2_HUMAN | Q10589 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:100
                                    59        69        79        89        99       109       119       129       139       149
           BST2_HUMAN    50 SEACRDGLRAVMECRNVTHLLQQELTEAQKGFQDVEAQAATCNHTVMALMASLDAEKAQGQKKVEELEGEITTLNHKLQDASAEVERLRRENQVLSVRIA 149
               SCOP domains ---------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------F------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 3mqc C  10 SEACRDGLRAVmECRNVTHLLQQELTEAQKGFQDVEAQAATCNHTVmALmASLDAEKAQGQKKVEELEGEITTLNHKLQDASAEVERLRRENQVLSVRIA 109
                                    19 |      29        39        49      | 59        69        79        89        99       109
                                      21-MSE                             56-MSE                                                 
                                                                            59-MSE

Chain D from PDB  Type:PROTEIN  Length:100
 aligned with BST2_HUMAN | Q10589 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:100
                                    59        69        79        89        99       109       119       129       139       149
           BST2_HUMAN    50 SEACRDGLRAVMECRNVTHLLQQELTEAQKGFQDVEAQAATCNHTVMALMASLDAEKAQGQKKVEELEGEITTLNHKLQDASAEVERLRRENQVLSVRIA 149
               SCOP domains ---------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------F------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 3mqc D  10 SEACRDGLRAVmECRNVTHLLQQELTEAQKGFQDVEAQAATCNHTVmALmASLDAEKAQGQKKVEELEGEITTLNHKLQDASAEVERLRRENQVLSVRIA 109
                                    19 |      29        39        49      | 59        69        79        89        99       109
                                      21-MSE                             56-MSE                                                 
                                                                            59-MSE

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 3MQC)

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

(no "Pfam Domain" information available for 3MQC)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (BST2_HUMAN | Q10589)

molecular function
	GO:0008191	metalloendopeptidase inhibitor activity	Stops, prevents or reduces the activity of metalloendopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain and contain a chelated metal ion at their active sites which is essential to their catalytic activity.
	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:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0004871	signal transducer activity	Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
biological process
	GO:0042113	B cell activation	The change in morphology and behavior of a mature or immature B cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.
	GO:0008283	cell proliferation	The multiplication or reproduction of cells, resulting in the expansion of a cell population.
	GO:0007267	cell-cell signaling	Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions.
	GO:0051607	defense response to virus	Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
	GO:0006959	humoral immune response	An immune response mediated through a body fluid.
	GO:0002376	immune system process	Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	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:0030308	negative regulation of cell growth	Any process that stops, prevents, or reduces the frequency, rate, extent or direction of cell growth.
	GO:0030336	negative regulation of cell migration	Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration.
	GO:0010951	negative regulation of endopeptidase activity	Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
	GO:1901253	negative regulation of intracellular transport of viral material	Any process that stops, prevents or reduces the frequency, rate or extent of intracellular transport of viral material.
	GO:0002737	negative regulation of plasmacytoid dendritic cell cytokine production	Any process that stops, prevents, or reduces the frequency, rate, or extent of plasmacytoid dendritic cell cytokine production.
	GO:0045071	negative regulation of viral genome replication	Any process that stops, prevents, or reduces the frequency, rate or extent of viral genome replication.
	GO:0043123	positive regulation of I-kappaB kinase/NF-kappaB signaling	Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling.
	GO:0032956	regulation of actin cytoskeleton organization	Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
	GO:0035455	response to interferon-alpha	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interferon-alpha stimulus. Interferon-alpha is a type I interferon.
	GO:0035456	response to interferon-beta	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interferon-beta stimulus. Interferon-beta is a type I interferon.
	GO:0034341	response to interferon-gamma	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interferon-gamma stimulus. Interferon-gamma is also known as type II interferon.
	GO:0009615	response to virus	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a virus.
	GO:0060337	type I interferon signaling pathway	A series of molecular signals initiated by the binding of a type I interferon to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
cellular component
	GO:0005794	Golgi apparatus	A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
	GO:0031225	anchored component of membrane	The component of a membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping.
	GO:0016324	apical plasma membrane	The region of the plasma membrane located at the apical end of the cell.
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005768	endosome	A vacuole to which materials ingested by endocytosis are delivered.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	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:0005887	integral component of plasma membrane	The component of the plasma 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:0005770	late endosome	A prelysosomal endocytic organelle differentiated from early endosomes by lower lumenal pH and different protein composition. Late endosomes are more spherical than early endosomes and are mostly juxtanuclear, being concentrated near the microtubule organizing center.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0045121	membrane raft	Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
	GO:0005771	multivesicular body	A type of endosome in which regions of the limiting endosomal membrane invaginate to form internal vesicles; membrane proteins that enter the internal vesicles are sequestered from the cytoplasm.
	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.

Asymmetric Unit
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	3mqc
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	BST2_HUMAN \| Q10589	:	2lk9 2x7a 2xg7 3mq7 3mq9 3mqb 3nwh 4p6z

3mq7	CRYSTAL STRUCTURE OF ECTODOMAIN MUTANT OF BST-2/TETHERIN/ CD317
3mq9	CRYSTAL STRUCTURE OF ECTODOMAIN MUTANT OF BST-2/TETHERIN/ CD317 FUSED TO MBP
3mqb	CRYSTAL STRUCTURE OF ECTODOMAIN OF BST-2/TETHERIN/CD317

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 12)

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SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

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