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Biological Unit 3 (Jmol Viewer)

Title :   THE CRYSTAL STRUCTURE OF THE BAR DOMAIN FROM HUMAN BIN1/AMPHIPHYSIN II AND ITS IMPLICATIONS FOR MOLECULAR RECOGNITION

Authors :   E. Casal, L. Federici, W. Zhang, J. Fernandez-Recio, E. M. Priego, R. N. J. B. Duhadaway, G. C. Prendergast, B. F. Luisi, E. D. Laue

Date :   29 Dec 05 (Deposition) - 14 Nov 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.99

Chains :   Asym. Unit : A,B
Biol. Unit 1: A (1x),B (1x)
Biol. Unit 2: A  (1x)
Biol. Unit 3: B  (1x)

Keywords :   Bar Domain, Homodimer, Coiled-Coils, Endocytosis/Exocytosis, Membrane Protein Complex, Endocytosis-Exocytosis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Casal, L. Federici, W. Zhang, J. Fernandez-Recio, E. M. Priego, R. N. Miguel, J. B. Duhadaway, G. C. Prendergast, B. F. Luisi, E. D. Laue
The Crystal Structure Of The Bar Domain From Human Bin1/Amphiphysin Ii And Its Implications For Molecular Recognition
Biochemistry V. 45 12917 2006
PubMed-ID: 17059209 | Reference-DOI: 10.1021/BI060717K

Molecule 1 - BRIDGING INTEGRATOR 1
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET14B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	BAR DOMAIN (1-251)
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	BIN1, AMPHIPHYSIN II

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	XE	2	Ligand/Ion	XENON

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	XE	-1	Ligand/Ion	XENON

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	XE	-1	Ligand/Ion	XENON

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	XE	-1	Ligand/Ion	XENON

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL B:218	BINDING SITE FOR RESIDUE XE B 1002

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

(no "Cis Peptide Bond" information available for 2FIC)

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_037426	D	151	N	BIN1_HUMAN	Disease (CNM2)	121909274	A/B	D	161	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_037426	D	151	N	BIN1_HUMAN	Disease (CNM2)	121909274	A/B	D	161	N

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

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_037426	D	151	N	BIN1_HUMAN	Disease (CNM2)	121909274	A	D	161	N

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

Biological Unit 3 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_037426	D	151	N	BIN1_HUMAN	Disease (CNM2)	121909274	B	D	161	N

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

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

Asymmetric Unit (8, 16)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000316724	1a	ENSE00001918151	chr2:127864931-127864436	496	BIN1_HUMAN	1-28	28	0	-	-
1.2	ENST00000316724	2	ENSE00000925832	chr2:127834282-127834202	81	BIN1_HUMAN	29-55	27	2	A:52-65 B:50-65	14 16
1.3	ENST00000316724	3	ENSE00000925829	chr2:127828392-127828338	55	BIN1_HUMAN	56-74	19	2	A:66-84 B:66-84	19 19
1.4	ENST00000316724	4	ENSE00000925827	chr2:127828223-127828129	95	BIN1_HUMAN	74-105	32	2	A:84-115 B:84-115	32 32
1.5	ENST00000316724	5	ENSE00000925826	chr2:127827666-127827571	96	BIN1_HUMAN	106-137	32	2	A:116-147 B:116-147	32 32
1.6	ENST00000316724	6	ENSE00000925823	chr2:127826607-127826500	108	BIN1_HUMAN	138-173	36	2	A:148-183 (gaps) B:148-183	36 36
1.7	ENST00000316724	7	ENSE00000925822	chr2:127825831-127825739	93	BIN1_HUMAN	174-204	31	0	-	-
1.9	ENST00000316724	9	ENSE00000925821	chr2:127821594-127821509	86	BIN1_HUMAN	205-233	29	2	A:184-212 B:184-212	29 29
1.10	ENST00000316724	10	ENSE00000925819	chr2:127821222-127821147	76	BIN1_HUMAN	233-258	26	2	A:212-237 B:212-237	26 26
1.11	ENST00000316724	11	ENSE00000925816	chr2:127819773-127819691	83	BIN1_HUMAN	259-286	28	2	A:238-249 B:238-250	12 13
1.13	ENST00000316724	13	ENSE00000925814	chr2:127816731-127816587	145	BIN1_HUMAN	286-334	49	0	-	-
1.14	ENST00000316724	14	ENSE00000925812	chr2:127815177-127815049	129	BIN1_HUMAN	335-377	43	0	-	-
1.15b	ENST00000316724	15b	ENSE00000925811	chr2:127811588-127811481	108	BIN1_HUMAN	378-413	36	0	-	-
1.15c	ENST00000316724	15c	ENSE00001417047	chr2:127811021-127810998	24	BIN1_HUMAN	414-421	8	0	-	-
1.15d	ENST00000316724	15d	ENSE00001236385	chr2:127809938-127809831	108	BIN1_HUMAN	422-457	36	0	-	-
1.16	ENST00000316724	16	ENSE00000964173	chr2:127808819-127808730	90	BIN1_HUMAN	458-487	30	0	-	-
1.17	ENST00000316724	17	ENSE00000925804	chr2:127808488-127808378	111	BIN1_HUMAN	488-524	37	0	-	-
1.18a	ENST00000316724	18a	ENSE00000925801	chr2:127808098-127807997	102	BIN1_HUMAN	525-558	34	0	-	-
1.19c	ENST00000316724	19c	ENSE00001928062	chr2:127806209-127805603	607	BIN1_HUMAN	559-593	35	0	-	-

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:191
 aligned with BIN1_HUMAN | O00499 from UniProtKB/Swiss-Prot  Length:593

    Alignment length:229
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261         
           BIN1_HUMAN    42 EQFEQCVQNFNKQLTEGTRLQKDLRTYLASVKAMHEASKKLNECLQEVYEPDWPGRDEANKIAENNDLLWMDYHQKLVDQALLTMDTYLGQFPDIKSRIAKRGRKLVDYDSARHHYESLQTAKKKDEAKIAKPVSLLEKAAPQWCQGKLQAHLVAQTNLLRNQAEEELIKAQKVFEEMNVDLQEELPSLWNSRVGFYVNTFQSIAGLEENFHKEMSKLNQNLNDVLVGL 270
               SCOP domains d2fica_ A: automated matches                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh-------hhhh-------------------------------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------N----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2      Exon 1.3           -------------------------------Exon 1.5  PDB: A:116-147        Exon 1.6  PDB: A:148-183 (gaps)     Exon 1.7  PDB: -               ----------------------------Exon 1.10  PDB: A:212-237 Exon 1.11    Transcript 1 (1)
           Transcript 1 (2) --------------------------------Exon 1.4  PDB: A:84-115         ---------------------------------------------------------------------------------------------------Exon 1.9  PDB: A:184-212     ------------------------------------- Transcript 1 (2)
                 2fic A  52 EQFEQCVQNFNKQLTEGTRLQKDLRTYLASVKAMHEASKKLNECLQEVYEPDWPGRDEANKIAENNDLLWMDYHQKLVDQALLTMDTYLGQFPDIKSRIAKRGRKLVDYDSARHHYESLQT-------KIAK-------------------------------AEEELIKAQKVFEEMNVDLQEELPSLWNSRVGFYVNTFQSIAGLEENFHKEMSKLNQNLNDVLVGL 249
                                    61        71        81        91       101       111       121       131       141       151       161       171|      181 |       -         -         -   |   190       200       210       220       230       240         
                                                                                                                                                  172     180  |                             184                                                                 
                                                                                                                                                             183

Chain B from PDB  Type:PROTEIN  Length:201
 aligned with BIN1_HUMAN | O00499 from UniProtKB/Swiss-Prot  Length:593

    Alignment length:232
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269  
           BIN1_HUMAN    40 KDEQFEQCVQNFNKQLTEGTRLQKDLRTYLASVKAMHEASKKLNECLQEVYEPDWPGRDEANKIAENNDLLWMDYHQKLVDQALLTMDTYLGQFPDIKSRIAKRGRKLVDYDSARHHYESLQTAKKKDEAKIAKPVSLLEKAAPQWCQGKLQAHLVAQTNLLRNQAEEELIKAQKVFEEMNVDLQEELPSLWNSRVGFYVNTFQSIAGLEENFHKEMSKLNQNLNDVLVGLE 271
               SCOP domains d2ficb_ B: automated matches                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhh-------------------------------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------N------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2        Exon 1.3           -------------------------------Exon 1.5  PDB: B:116-147        Exon 1.6  PDB: B:148-183            Exon 1.7  PDB: -               ----------------------------Exon 1.10  PDB: B:212-237 Exon 1.11     Transcript 1 (1)
           Transcript 1 (2) ----------------------------------Exon 1.4  PDB: B:84-115         ---------------------------------------------------------------------------------------------------Exon 1.9  PDB: B:184-212     -------------------------------------- Transcript 1 (2)
                 2fic B  50 KDEQFEQCVQNFNKQLTEGTRLQKDLRTYLASVKAMHEASKKLNECLQEVYEPDWPGRDEANKIAENNDLLWMDYHQKLVDQALLTMDTYLGQFPDIKSRIAKRGRKLVDYDSARHHYESLQTAKKKDEAKIAK-------------------------------AEEELIKAQKVFEEMNVDLQEELPSLWNSRVGFYVNTFQSIAGLEENFHKEMSKLNQNLNDVLVGLE 250
                                    59        69        79        89        99       109       119       129       139       149       159       169       179   |     -         -         -     | 188       198       208       218       228       238       248  
                                                                                                                                                               183                             184

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)

1a	d2fica_	A:
1b	d2ficb_	B:

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

(no "Pfam Domain" information available for 2FIC)

Asymmetric Unit(hide GO term definitions)

Chain A,B (BIN1_HUMAN | O00499)

molecular function
	GO:0070063	RNA polymerase binding	Interacting selectively and non-covalently with an RNA polymerase molecule or complex.
	GO:0051015	actin filament binding	Interacting selectively and non-covalently with an actin filament, also known as F-actin, a helical filamentous polymer of globular G-actin subunits.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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:0048156	tau protein binding	Interacting selectively and non-covalently with tau protein. tau is a microtubule-associated protein, implicated in Alzheimer's disease, Down Syndrome and ALS.
biological process
	GO:0030154	cell differentiation	The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
	GO:0008283	cell proliferation	The multiplication or reproduction of cells, resulting in the expansion of a cell population.
	GO:0006897	endocytosis	A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
	GO:0060988	lipid tube assembly	The aggregation, arrangement and bonding together of a set of macromolecules to form a macromolecular complex that contains a tube of lipid surrounded by a protein coat involved in membrane shaping of vesicle membranes as they fuse or undergo fission.
	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:0042692	muscle cell differentiation	The process in which a relatively unspecialized cell acquires specialized features of a muscle cell.
	GO:0006997	nucleus organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleus.
	GO:0043065	positive regulation of apoptotic process	Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
	GO:0048711	positive regulation of astrocyte differentiation	Any process that activates or increases the frequency, rate or extent of astrocyte differentiation.
	GO:0071156	regulation of cell cycle arrest	Any process that modulates the rate, frequency, or extent of cell cycle arrest, the process in which the cell cycle is halted during one of the normal phases.
	GO:0030100	regulation of endocytosis	Any process that modulates the frequency, rate or extent of endocytosis.
	GO:0045664	regulation of neuron differentiation	Any process that modulates the frequency, rate or extent of neuron differentiation.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	GO:0031674	I band	A region of a sarcomere that appears as a light band on each side of the Z disc, comprising a region of the sarcomere where thin (actin) filaments are not overlapped by thick (myosin) filaments; contains actin, troponin, and tropomyosin; each sarcomere includes half of an I band at each end.
	GO:0030315	T-tubule	Invagination of the plasma membrane of a muscle cell that extends inward from the cell surface around each myofibril. The ends of T-tubules make contact with the sarcoplasmic reticulum membrane.
	GO:0030018	Z disc	Platelike region of a muscle sarcomere to which the plus ends of actin filaments are attached.
	GO:0015629	actin cytoskeleton	The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
	GO:0030424	axon	The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
	GO:0043194	axon initial segment	Portion of the axon proximal to the neuronal cell body, at the level of the axon hillock. The action potentials that propagate along the axon are generated at the level of this initial segment.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0060987	lipid tube	A macromolecular complex that contains a tube of lipid surrounded by a protein coat.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0033268	node of Ranvier	An axon part that is a gap in the myelin where voltage-gated sodium channels cluster and saltatory conduction is executed.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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	BIN1_HUMAN \| O00499	:	1muz 1mv0 1mv3 2rmy 2rnd 5i22

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