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Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE N-BAR DOMAIN OF HUMAN BRIDGING INTEGRATOR 2.

Authors :   C. K. Allerston, T. Krojer, C. D. O. Cooper, M. Vollmar, C. H. Arrowsmith A. Edwards, C. Bountra, F. Von Delft, O. Gileadi

Date :   28 May 12 (Deposition) - 20 Jun 12 (Release) - 05 Dec 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.91

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

Keywords :   Protein Binding, Plasma Membrane, Bar Adaptor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. K. Allerston, T. Krojer, C. D. O. Cooper, M. Vollmar, C. H. Arrowsmith, A. Edwards, C. Bountra, F. Von Delft, O. Gileadi
Crystal Structure Of The N-Bar Domain Of Human Bridging Integrator 2.
To Be Published
PubMed: search

Molecule 1 - BRIDGING INTEGRATOR 2
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC28-BSA4
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	R3-PRARE2
	Expression System Vector Type	:	PLASMID
	Fragment	:	N-BAR DOMAIN, RESIDUES 11-245
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	BREAST CANCER-ASSOCIATED PROTEIN 1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 5)

No.	Name	Count	Type	Full Name
1	EDO	3	Ligand/Ion	1,2-ETHANEDIOL
2	EPE	2	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID

Biological Unit 1 (2, 10)

No.	Name	Count	Type	Full Name
1	EDO	6	Ligand/Ion	1,2-ETHANEDIOL
2	EPE	4	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:26 , VAL A:36 , ASP A:150 , HIS A:154 , GLU A:157 , HOH A:2028	BINDING SITE FOR RESIDUE EDO A1245
2	AC2	SOFTWARE	ASP A:112 , TYR A:113 , LEU A:216 , VAL A:219 , HOH A:2167	BINDING SITE FOR RESIDUE EDO A1246
3	AC3	SOFTWARE	THR A:38 , TYR A:149 , GLN A:181 , PHE A:184 , THR A:208	BINDING SITE FOR RESIDUE EDO A1247
4	AC4	SOFTWARE	ASP A:94 , GLY A:95 , HIS A:96 , GLU A:97 , GLU A:98 , LYS A:179 , HOH A:2092	BINDING SITE FOR RESIDUE EPE A1248
5	AC5	SOFTWARE	ARG A:144 , LYS A:145 , GLN A:241 , HOH A:2009 , HOH A:2115	BINDING SITE FOR RESIDUE EPE A1249

(no "SS Bond" information available for 4AVM)

(no "Cis Peptide Bond" information available for 4AVM)

Asymmetric Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_028883	S	48	N	BIN2_HUMAN	Polymorphism	7312857	A	S	48	N

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

Biological Unit 1 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_028883	S	48	N	BIN2_HUMAN	Polymorphism	7312857	A	S	48	N

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BAR	PS51021	BAR domain profile.	BIN2_HUMAN	28-244	1	A:28-244

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BAR	PS51021	BAR domain profile.	BIN2_HUMAN	28-244	2	A:28-244

(no "Exon" information available for 4AVM)

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:230
 aligned with BIN2_HUMAN | Q9UBW5 from UniProtKB/Swiss-Prot  Length:565

    Alignment length:230
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244
           BIN2_HUMAN    15 KQVQKKFSRAQEKVLQKLGKAVETKDERFEQSASNFYQQQAEGHKLYKDLKNFLSAVKVMHESSKRVSETLQEIYSSEWDGHEELKAIVWNNDLLWEDYEEKLADQAVRTMEIYVAQFSEIKERIAKRGRKLVDYDSARHHLEAVQNAKKKDEAKTAKAEEEFNKAQTVFEDLNQELLEELPILYNSRIGCYVTIFQNISNLRDVFYREMSKLNHNLYEVMSKLEKQHSN 244
               SCOP domains d4avma_ A: automated matches                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------N---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------BAR  PDB: A:28-244 UniProt: 28-244                                                                                                                                                                                        PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4avm A  15 KQVQKKFSRAQEKVLQKLGKAVETKDERFEQSASNFYQQQAEGHKLYKDLKNFLSAVKVMHESSKRVSETLQEIYSSEWDGHEELKAIVWNNDLLWEDYEEKLADQAVRTMEIYVAQFSEIKERIAKRGRKLVDYDSARHHLEAVQNAKKKDEAKTAKAEEEFNKAQTVFEDLNQELLEELPILYNSRIGCYVTIFQNISNLRDVFYREMSKLNHNLYEVMSKLERQHSN 244
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: BAR/IMD domain-like (27)

Superfamily: BAR/IMD domain-like (27)

Family: automated matches (6)

Protein domain: automated matches (6)

Human (Homo sapiens) [TaxId: 9606] (5)

d4avma_

(no "CATH Domain" information available for 4AVM)

(no "Pfam Domain" information available for 4AVM)

Asymmetric Unit(hide GO term definitions)

Chain A (BIN2_HUMAN | Q9UBW5)

molecular function
	GO:0005543	phospholipid binding	Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester.
	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:0060326	cell chemotaxis	The directed movement of a motile cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
	GO:0006911	phagocytosis, engulfment	The internalization of bacteria, immune complexes and other particulate matter or of an apoptotic cell by phagocytosis, including the membrane and cytoskeletal processes required, which involves one of three mechanisms: zippering of pseudopods around a target via repeated receptor-ligand interactions, sinking of the target directly into plasma membrane of the phagocytosing cell, or induced uptake via an enhanced membrane ruffling of the phagocytosing cell similar to macropinocytosis.
	GO:0097320	plasma membrane tubulation	A membrane tubulation process occurring in a plasma membrane.
	GO:0071800	podosome assembly	The aggregation, arrangement and bonding together of a set of components to form a podosome, an actin-rich adhesion structure characterized by formation upon cell substrate contact and localization at the substrate-attached part of the cell.
cellular component
	GO:0005938	cell cortex	The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins.
	GO:0030054	cell junction	A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
	GO:0042995	cell projection	A prolongation or process extending from a cell, e.g. a flagellum or axon.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0001891	phagocytic cup	An invagination of the cell membrane formed by an actin dependent process during phagocytosis. Following internalization it is converted into a phagosome.
	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.
	GO:0002102	podosome	An actin-rich adhesion structure characterized by formation upon cell substrate contact and localization at the substrate-attached part of the cell, contain an F-actin-rich core surrounded by a ring structure containing proteins such as vinculin and talin, and have a diameter of 0.5 mm.

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Biological Unit
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Description

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Ligands, Modified Residues, Ions (2, 5)

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SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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