3NXB - JenaLib

Title :   CRYSTAL STRUCTURE OF THE BROMODOMAIN OF HUMAN CECR2

Authors :   P. Filippakopoulos, S. Picaud, T. Keates, J. Muniz, F. Von Delft, C. H. Arrowsmith, A. Edwards, J. Weigelt, C. Bountra, S. Knapp, Struct Genomics Consortium (Sgc)

Date :   13 Jul 10 (Deposition) - 18 Aug 10 (Release) - 11 Apr 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.83

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

Keywords :   Structural Genomics Consortium, Sgc, Cecr2, Cat Eye Syndrome Chromosome Region Candidate 2, Bromodomain, Structural Genomics, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Filippakopoulos, S. Picaud, M. Mangos, T. Keates, J. P. Lambert, D. Barsyte-Lovejoy, I. Felletar, R. Volkmer, S. Muller, T. Pawson, A. C. Gingras, C. H. Arrowsmith, S. Knapp
Histone Recognition And Large-Scale Structural Analysis Of The Human Bromodomain Family.
Cell(Cambridge, Mass. ) V. 149 214 2012
PubMed-ID: 22464331 | Reference-DOI: 10.1016/J.CELL.2012.02.013

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BROMODOMAIN_2	PS50014	Bromodomain profile.	CECR2_HUMAN	451-521	2	A:451-521 B:451-521
2	BROMODOMAIN_1	PS00633	Bromodomain signature.	CECR2_HUMAN	456-513	2	A:456-513 B:456-513

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BROMODOMAIN_2	PS50014	Bromodomain profile.	CECR2_HUMAN	451-521	1	A:451-521 -
2	BROMODOMAIN_1	PS00633	Bromodomain signature.	CECR2_HUMAN	456-513	1	A:456-513 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BROMODOMAIN_2	PS50014	Bromodomain profile.	CECR2_HUMAN	451-521	1	- B:451-521
2	BROMODOMAIN_1	PS00633	Bromodomain signature.	CECR2_HUMAN	456-513	1	- B:456-513

Exons (0, 0)

Sequences/Alignments

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:101
 aligned with CECR2_HUMAN | Q9BXF3 from UniProtKB/Swiss-Prot  Length:1484

    Alignment length:101
                                   446       456       466       476       486       496       506       516       526       536 
          CECR2_HUMAN   437 DDDFTAMYKVLDVVKAHKDSWPFLEPVDESYAPNYYQIIKAPMDISSMEKKLNGGLYCTKEEFVNDMKTMFRNCRKYNGESSEYTKMSDNLERCFHRAMMK 537
               SCOP domains d3nxba_ A: automated matches                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh..hhhhh.........hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------BROMODOMAIN_2  PDB: A:451-521 UniProt: 451-521                         ---------------- PROSITE (1)
                PROSITE (2) -------------------BROMODOMAIN_1  PDB: A:456-513 UniProt: 456-513            ------------------------ PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 3nxb A 437 DDDFTAMYKVLDVVKAHKDSWPFLEPVDESYAPNYYQIIKAPMDISSMEKKLNGGLYCTKEEFVNDMKTMFRNCRKYNGESSEYTKMSDNLERCFHRAMMK 537
                                   446       456       466       476       486       496       506       516       526       536

Chain B from PDB  Type:PROTEIN  Length:100
 aligned with CECR2_HUMAN | Q9BXF3 from UniProtKB/Swiss-Prot  Length:1484

    Alignment length:100
                                   447       457       467       477       487       497       507       517       527       537
          CECR2_HUMAN   438 DDFTAMYKVLDVVKAHKDSWPFLEPVDESYAPNYYQIIKAPMDISSMEKKLNGGLYCTKEEFVNDMKTMFRNCRKYNGESSEYTKMSDNLERCFHRAMMK 537
               SCOP domains d3nxbb_ B: automated matches                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----Bromodomain-3nxbB01 B:443-526                                                       ----------- Pfam domains (1)
           Pfam domains (2) -----Bromodomain-3nxbB02 B:443-526                                                       ----------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhh...hhhhh.hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------BROMODOMAIN_2  PDB: B:451-521 UniProt: 451-521                         ---------------- PROSITE (1)
                PROSITE (2) ------------------BROMODOMAIN_1  PDB: B:456-513 UniProt: 456-513            ------------------------ PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 3nxb B 438 DDFTAMYKVLDVVKAHKDSWPFLEPVDESYAPNYYQIIKAPMDISSMEKKLNGGLYCTKEEFVNDMKTMFRNCRKYNGESSEYTKMSDNLERCFHRAMMK 537
                                   447       457       467       477       487       497       507       517       527       537

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, 2)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (10, 10)

Asymmetric Unit(hide GO term definitions)

Chain A,B (CECR2_HUMAN | Q9BXF3)

molecular function
	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:0043044	ATP-dependent chromatin remodeling	Dynamic structural changes to eukaryotic chromatin that require energy from the hydrolysis of ATP, ranging from local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation, mediated by ATP-dependent chromatin-remodelling factors.
	GO:0006309	apoptotic DNA fragmentation	The cleavage of DNA during apoptosis, which usually occurs in two stages: cleavage into fragments of about 50 kbp followed by cleavage between nucleosomes to yield 200 bp fragments.
	GO:0000910	cytokinesis	The division of the cytoplasm and the plasma membrane of a cell and its partitioning into two daughter cells.
	GO:0007010	cytoskeleton organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures.
	GO:0097194	execution phase of apoptosis	A stage of the apoptotic process that starts with the controlled breakdown of the cell through the action of effector caspases or other effector molecules (e.g. cathepsins, calpains etc.). Key steps of the execution phase are rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
	GO:0021915	neural tube development	The process whose specific outcome is the progression of the neural tube over time, from its formation to the mature structure. The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium.
	GO:0016192	vesicle-mediated transport	A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
cellular component
	GO:0090537	CERF complex	An ISWI complex that contains an ATPase subunit of the ISWI family (specifically SNF2L in mammals, which contain two ISWI homologs) and a CECR2 homolog. In mammals, CERF is involved in regulation of transcription from RNA polymerase II promoters.
	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.

Visualization

Interactive Views

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		EDO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3nxb)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	3nxb
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	CECR2_HUMAN \| Q9BXF3
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Description