2BZF | PD0799 - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Title :   STRUCTURAL BASIS FOR DNA BRIDGING BY BARRIER-TO-AUTOINTEGRATION FACTOR (BAF)

Authors :   C. M. Bradley, D. R. Ronning, R. Ghirlando, R. Craigie, F. Dyda

Date :   16 Aug 05 (Deposition) - 15 Sep 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.87

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

Keywords :   Dna-Binding Protein, Retroviral Integration, Non-Specific Dna-Binding, Dna Compaction, Nuclear Organization, Lem Family (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. M. Bradley, D. R. Ronning, R. Ghirlando, R. Craigie, F. Dyda
Structural Basis For Dna Bridging By Barrier-To- Autointegration Factor.
Nat. Struct. Mol. Biol. V. 12 935 2005
PubMed-ID: 16155580 | Reference-DOI: 10.1038/NSMB989

Molecule 1 - BARRIER-TO-AUTOINTEGRATION FACTOR
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

*Molecule 2 - 5'-D(GPTPGPGPAPGPGP)-3'**
	Chains	:	B
	Synthetic	:	YES

*Molecule 3 - 5'-D(CPCPTPCPCPAPCP)-3'**
	Chains	:	C
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2BZF)

(no "Site" information available for 2BZF)

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

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

Asymmetric Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_065954	A	12	T	BAF_HUMAN	Disease (NGPS)	387906871	A	A	12	T

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_065954	A	12	T	BAF_HUMAN	Disease (NGPS)	387906871	A	A	12	T

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

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

Asymmetric Unit (2, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000312175	1a	ENSE00001189984	chr11:65769550-65770041	492	BAF_HUMAN	-	0	0	-	-
1.3b	ENST00000312175	3b	ENSE00001189976	chr11:65770706-65770844	139	BAF_HUMAN	1-41	41	1	A:2-41	40
1.4f	ENST00000312175	4f	ENSE00002191965	chr11:65771097-65771620	524	BAF_HUMAN	42-89	48	1	A:42-89	48

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:88
 aligned with BAF_HUMAN | O75531 from UniProtKB/Swiss-Prot  Length:89

    Alignment length:88
                                    11        21        31        41        51        61        71        81        
             BAF_HUMAN    2 TTSQKHRDFVAEPMGEKPVGSLAGIGEVLGKKLEERGFDKAYVVLGQFLVLKKDEDLFREWLKDTCGANAKQSRDCFGCLREWCDAFL 89
               SCOP domains d2bzfa_ A: Barrier-to-autointegration factor, BAF                                        SCOP domains
               CATH domains 2bzfA00 A:2-89  [code=1.10.150.40, no name defined]                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh.....hhhhh...hhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------T----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.3b  PDB: A:2-41 UniProt: 1-41    Exon 1.4f  PDB: A:42-89 UniProt: 42-89           Transcript 1
                  2bzf A  2 TTSQKHRDFVAEPMGEKPVGSLAGIGEVLGKKLEERGFDKAYVVLGQFLVLKKDEDLFREWLKDTCGANAKQSRDCFGCLREWCDAFL 89
                                    11        21        31        41        51        61        71        81

Chain B from PDB  Type:DNA  Length:7
                                      
                  2bzf B  1 GTGGAGG  7

Chain C from PDB  Type:DNA  Length:7
                                      
                  2bzf C  8 CCTCCAC 14

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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: All alpha proteins (14657)

Fold: SAM domain-like (639)

Superfamily: Barrier-to-autointegration factor, BAF (7)

Family: Barrier-to-autointegration factor, BAF (7)

Protein domain: Barrier-to-autointegration factor, BAF (7)

Human (Homo sapiens) [TaxId: 9606] (7)

d2bzfa_

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: DNA polymerase; domain 1 (617)

Homologous Superfamily: [code=1.10.150.40, no name defined] (7)

Human (Homo sapiens) (7)

2bzfA00

A:2-89

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

Asymmetric Unit(hide GO term definitions)

Chain A (BAF_HUMAN | O75531)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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.
biological process
	GO:0015074	DNA integration	The process in which a segment of DNA is incorporated into another, usually larger, DNA molecule such as a chromosome.
	GO:0075713	establishment of integrated proviral latency	A process by which the virus integrates into the host genome and establishes as a stable provirus or prophage.
	GO:0007077	mitotic nuclear envelope disassembly	The cell cycle process in which the controlled breakdown of the nuclear envelope during mitotic cell division occurs.
	GO:0007084	mitotic nuclear envelope reassembly	The cell cycle process that results in reformation of the nuclear envelope during mitotic cell division.
	GO:0051169	nuclear transport	The directed movement of substances into, out of, or within the nucleus.
	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: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:0005694	chromosome	A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
	GO:0000793	condensed chromosome	A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct structure.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	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:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2bzf)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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Access by PDB/NDB ID
	2bzf
		Family and Domain Information	:	ProDom \| SYSTERS
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		Orientation in Membranes	:	OPM
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Access by UniProt ID/Accession number
	BAF_HUMAN \| O75531
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	614008
		Disease Information	:	OMIM

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	BAF_HUMAN \| O75531
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UniProtKB/Swiss-Prot
	BAF_HUMAN \| O75531	:	1ci4 1qck 2ezx 2ezy 2ezz 2odg

1ci4	THE CRYSTAL STRUCTURE OF HUMAN BARRIER-TO- AUTOINTEGRATION FACTOR (BAF)
1qck	SOLUTION STRUCTURE OF HUMAN BARRIER-TO- AUTOINTEGRATION FACTOR BAF, NMR, REGULARIZED MEAN STRUCTURE PLUS 20 INDIVIDUAL SIMULATED ANNEALING STRUCTURES
2ezx	SOLUTION STRUCTURE OF HUMAN BARRIER-TO- AUTOINTEGRATION FACTOR BAF, NMR, REGULARIZED MEAN STRUCTURE
2ezy	SOLUTION STRUCTURE OF HUMAN BARRIER-TO- AUTOINTEGRATION FACTOR BAF, NMR, ENSEMBLE OF 20 SIMULATED ANNEALING STRUCTURES
2ezz	SOLUTION STRUCTURE OF HUMAN BARRIER-TO- AUTOINTEGRATION FACTOR BAF NMR, ENSEMBLE OF 20 SIMULATED ANNEALING STRUCTURES

Description

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Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (0, 0)

Exons (2, 2)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (17, 17)

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