3NQU - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF PARTIALLY TRYPSINIZED (CENP-A/H4)2 HETEROTETRAMER

Authors :   N. Sekulic, B. E. Black

Date :   29 Jun 10 (Deposition) - 25 Aug 10 (Release) - 13 Oct 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Alpha Helix, Histone Fold, Centromere, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Sekulic, E. A. Bassett, D. J. Rogers, B. E. Black
The Structure Of (Cenp-A-H4)(2) Reveals Physical Features That Mark Centromeres.
Nature V. 467 347 2010
PubMed-ID: 20739937 | Reference-DOI: 10.1038/NATURE09323

Molecule 1 - HISTONE H3-LIKE CENTROMERIC PROTEIN A
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	CENPA
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CENTROMERE PROTEIN A, CENP-A, CENTROMERE AUTOANTIGEN A

Molecule 2 - HISTONE H4
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	HIST1H4A, H4/A, H4FA
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 5)

No.	Name	Count	Type	Full Name
1	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 10)

No.	Name	Count	Type	Full Name
1	SO4	10	Ligand/Ion	SULFATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:118 , VAL A:119 , THR A:120	BINDING SITE FOR RESIDUE SO4 A 141
2	AC2	SOFTWARE	ARG A:80 , LYS B:31 , TYR B:51 , ARG B:67	BINDING SITE FOR RESIDUE SO4 A 142
3	AC3	SOFTWARE	ARG B:78 , LYS B:79 , THR B:80	BINDING SITE FOR RESIDUE SO4 B 103
4	AC4	SOFTWARE	THR B:30 , PRO B:32 , ARG B:36	BINDING SITE FOR RESIDUE SO4 B 104
5	AC5	SOFTWARE	PRO B:32 , ARG B:35	BINDING SITE FOR RESIDUE SO4 B 105

(no "SS Bond" information available for 3NQU)

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

Asymmetric Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_036206	E	64	Q	H4_HUMAN	Unclassified	747622981	B	E	63	Q

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_036206	E	64	Q	H4_HUMAN	Unclassified	747622981	B	E	63	Q

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HISTONE_H3_2	PS00959	Histone H3 signature 2.	CENPA_HUMAN	66-74	1	A:66-74

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HISTONE_H3_2	PS00959	Histone H3 signature 2.	CENPA_HUMAN	66-74	2	A:66-74

Asymmetric Unit (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000377803	1	ENSE00001475159	chr6:26104104-26104518	415	H4_HUMAN	1-127	127	1	B:25-91	67

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:76
 aligned with CENPA_HUMAN | P49450 from UniProtKB/Swiss-Prot  Length:140

    Alignment length:76
                                    68        78        88        98       108       118       128      
          CENPA_HUMAN    59 HLLIRKLPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVTLFPKDVQLARRIRG 134
               SCOP domains d3nqua_ A: automated matches                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains Histone-3nquA01 A:59-133                                                   - Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhh....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------HISTONE_H------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                 3nqu A  59 HLLIRKLPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVTLFPKDVQLARRIRG 134
                                    68        78        88        98       108       118       128

Chain B from PDB  Type:PROTEIN  Length:67
 aligned with H4_HUMAN | P62805 from UniProtKB/Swiss-Prot  Length:103

    Alignment length:67
                                    35        45        55        65        75        85       
             H4_HUMAN    26 NIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALK  92
               SCOP domains d3nqub_ B: Histone H4                                               SCOP domains
               CATH domains ------------------------------------------------------------------- CATH domains
               Pfam domains Histone-3nquB01 B:25-91                                             Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------Q---------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:25-91 UniProt: 1-127 [INCOMPLETE]                  Transcript 1
                 3nqu B  25 NIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALK  91
                                    34        44        54        64        74        84

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: Histone-fold (277)

Superfamily: Histone-fold (277)

Family: Nucleosome core histones (247)

Protein domain: automated matches (34)

Human (Homo sapiens) [TaxId: 9606] (25)

d3nqua_

Protein domain: Histone H4 (60)

Human (Homo sapiens) [TaxId: 9606] (11)

d3nqub_

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Histone (49)

Family: Histone (46)

Homo sapiens (Human) (6)

1a	Histone-3nquA01	A:59-133
1b	Histone-3nquB01	B:25-91

Asymmetric Unit(hide GO term definitions)

Chain A (CENPA_HUMAN | P49450)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003682	chromatin binding	Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
	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:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
biological process
	GO:0034080	CENP-A containing nucleosome assembly	The formation of nucleosomes containing the histone H3 variant CENP-A to form centromeric chromatin. This specialised chromatin occurs at centromeric region in point centromeres, and the central core in modular centromeres.
	GO:0000132	establishment of mitotic spindle orientation	A cell cycle process that sets the alignment of mitotic spindle relative to other cellular structures.
	GO:0051382	kinetochore assembly	The aggregation, arrangement and bonding together of a set of components to form the kinetochore, a multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules.
	GO:0071459	protein localization to chromosome, centromeric region	Any process in which a protein is transported to, or maintained at, the centromeric region of a chromosome.
	GO:0007062	sister chromatid cohesion	The cell cycle process in which the sister chromatids of a replicated chromosome become tethered to each other.
	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:0000775	chromosome, centromeric region	The region of a chromosome that includes the centromeric DNA and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.
	GO:0000939	condensed chromosome inner kinetochore	The region of a condensed chromosome kinetochore closest to centromeric DNA; in mammals the CREST antigens (CENP proteins) are found in this layer; this layer may help define underlying centromeric chromatin structure and position of the kinetochore on the chromosome.
	GO:0000777	condensed chromosome kinetochore	A multisubunit complex that is located at the centromeric region of a condensed chromosome and provides an attachment point for the spindle microtubules.
	GO:0000778	condensed nuclear chromosome kinetochore	A multisubunit complex that is located at the centromeric region of a condensed nuclear chromosome and provides an attachment point for the spindle microtubules.
	GO:0000780	condensed nuclear chromosome, centromeric region	The region of a condensed nuclear chromosome that includes the centromere and associated proteins, including the kinetochore. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.
	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:0000776	kinetochore	A multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0000786	nucleosome	A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures.
	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.

Chain B (H4_HUMAN | P62805)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0042393	histone binding	Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene 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:0019904	protein domain specific binding	Interacting selectively and non-covalently with a specific domain of a protein.
	GO:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
biological process
	GO:0034080	CENP-A containing nucleosome assembly	The formation of nucleosomes containing the histone H3 variant CENP-A to form centromeric chromatin. This specialised chromatin occurs at centromeric region in point centromeres, and the central core in modular centromeres.
	GO:0006335	DNA replication-dependent nucleosome assembly	The formation of nucleosomes on newly replicated DNA, coupled to strand elongation.
	GO:0006336	DNA replication-independent nucleosome assembly	The formation of nucleosomes outside the context of DNA replication.
	GO:0006352	DNA-templated transcription, initiation	Any process involved in the assembly of the RNA polymerase preinitiation complex (PIC) at the core promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. The initiation phase ends just before and does not include promoter clearance, or release, which is the transition between the initiation and elongation phases of transcription.
	GO:1904837	beta-catenin-TCF complex assembly	The aggregation, arrangement and bonding together of a set of components to form a beta-catenin-TCF complex.
	GO:0044267	cellular protein metabolic process	The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
	GO:0000183	chromatin silencing at rDNA	Repression of transcription of ribosomal DNA by altering the structure of chromatin.
	GO:0006303	double-strand break repair via nonhomologous end joining	The repair of a double-strand break in DNA in which the two broken ends are rejoined with little or no sequence complementarity. Information at the DNA ends may be lost due to the modification of broken DNA ends. This term covers instances of separate pathways, called classical (or canonical) and alternative nonhomologous end joining (C-NHEJ and A-NHEJ). These in turn may further branch into sub-pathways, but evidence is still unclear.
	GO:0031047	gene silencing by RNA	Any process in which RNA molecules inactivate expression of target genes.
	GO:0045814	negative regulation of gene expression, epigenetic	Any epigenetic process that stops, prevents or reduces the rate of gene expression.
	GO:0045653	negative regulation of megakaryocyte differentiation	Any process that stops, prevents, or reduces the frequency, rate or extent of megakaryocyte differentiation.
	GO:0006334	nucleosome assembly	The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.
	GO:0045815	positive regulation of gene expression, epigenetic	Any epigenetic process that activates or increases the rate of gene expression.
	GO:0051290	protein heterotetramerization	The formation of a protein heterotetramer, a macromolecular structure consisting of four noncovalently associated subunits, of which not all are identical.
	GO:0016233	telomere capping	A process in which telomeres are protected from degradation and fusion, thereby ensuring chromosome stability by protecting the ends from both degradation and from being recognized as damaged DNA. May be mediated by specific single- or double-stranded telomeric DNA binding proteins.
	GO:0032200	telomere organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of telomeres, terminal regions of a linear chromosome that include the telomeric DNA repeats and associated proteins.
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: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:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0000228	nuclear chromosome	A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact.
	GO:0000784	nuclear chromosome, telomeric region	The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0000786	nucleosome	A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures.
	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.
	GO:0043234	protein complex	A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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	3nqu
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3nqj	HIGHER RESOLUTION STRUCTURE OF THE SAME COMPLEX

Description

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Ligands, Modified Residues, Ions (1, 5)

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SS Bonds (0, 0)

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