2CV5 | PD0676 - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN NUCLEOSOME CORE PARTICLE

Authors :   Y. Tsunaka, N. Kajimura, S. Tate, K. Morikawa

Date :   31 May 05 (Deposition) - 28 Jun 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : A,B,C,D,E,F,G,H,I,J

Keywords :   Human Nucleosome Structure, X-Ray Crystallography, Supercoiled Dna Path, Metal Binding Site, Structural Protein/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Tsunaka, N. Kajimura, S. Tate, K. Morikawa
Alteration Of The Nucleosomal Dna Path In The Crystal Structure Of A Human Nucleosome Core Particle
Nucleic Acids Res. V. 33 3424 2005
PubMed-ID: 15951514 | Reference-DOI: 10.1093/NAR/GKI663
(for further references see the PDB file header)

Molecule 1 - DNA (146-MER)
	Chains	:	I, J
	Engineered	:	YES
	Synonym	:	PALINDROMIC 146-BP HUMAN A-SATELLITE DNA
	Synthetic	:	YES

Molecule 2 - HISTONE H3.1
	Chains	:	A, E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET22B
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	HISTONE H3

Molecule 3 - HISTONE H4
	Chains	:	B, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET22B
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 4 - HISTONE H2A.A
	Chains	:	C, G
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET22B
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	HISTONE H2A

Molecule 5 - HISTONE H2B K
	Chains	:	D, H
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET22B
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	HISTONE H2B, HIRA-INTERACTING PROTEIN 1

		1	2	3	4	5	6	7	8	9	10
Asymmetric/Biological Unit	:	A	B	C	D	E	F	G	H	I	J

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 13)

No.	Name	Count	Type	Full Name
1	CL	4	Ligand/Ion	CHLORIDE ION
2	MN	9	Ligand/Ion	MANGANESE (II) ION

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	DG J:185 , DG J:186 , HOH J:1043 , HOH J:1046	BINDING SITE FOR RESIDUE MN J 1001
02	AC2	SOFTWARE	DG J:267 , HOH J:1041 , HOH J:1044 , HOH J:1071	BINDING SITE FOR RESIDUE MN J 1002
03	AC3	SOFTWARE	DG J:217 , HOH J:1042	BINDING SITE FOR RESIDUE MN J 1003
04	AC4	SOFTWARE	DG I:68 , HOH I:1039 , HOH J:1081	BINDING SITE FOR RESIDUE MN I 1004
05	AC5	SOFTWARE	DG I:121	BINDING SITE FOR RESIDUE MN I 1005
06	AC6	SOFTWARE	DG J:280	BINDING SITE FOR RESIDUE MN J 1006
07	AC7	SOFTWARE	DG I:134 , HOH I:1042	BINDING SITE FOR RESIDUE MN I 1007
08	AC8	SOFTWARE	VAL D:45 , HOH D:1026 , ASP E:77 , HOH E:2048	BINDING SITE FOR RESIDUE MN D 1008
09	AC9	SOFTWARE	HOH I:1095 , HOH J:1087 , HOH J:1088	BINDING SITE FOR RESIDUE MN J 1009
10	BC1	SOFTWARE	GLY C:46 , ALA C:47 , THR D:87 , SER D:88	BINDING SITE FOR RESIDUE CL C 2001
11	BC2	SOFTWARE	GLY G:44 , ALA G:45 , GLY G:46 , ALA G:47 , THR H:87 , SER H:88	BINDING SITE FOR RESIDUE CL G 2002
12	BC3	SOFTWARE	PRO E:121 , LYS E:122	BINDING SITE FOR RESIDUE CL E 2003
13	BC4	SOFTWARE	PRO A:121 , LYS A:122	BINDING SITE FOR RESIDUE CL A 2004

(no "SS Bond" information available for 2CV5)

Asymmetric/Biological Unit

No.	Residues
1	Lys E:37	-	Pro E:38

Asymmetric/Biological Unit (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/F	E	63	Q

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

Asymmetric/Biological Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HISTONE_H2A	PS00046	Histone H2A signature.	H2A1B_HUMAN	22-28	2	C:21-27 G:21-27
2	HISTONE_H3_2	PS00959	Histone H3 signature 2.	H31_HUMAN	67-75	2	A:66-74 E:66-74
3	HISTONE_H2B	PS00357	Histone H2B signature.	H2B1K_HUMAN	93-115	2	D:89-111 H:89-111

Asymmetric/Biological Unit (3, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000356950	1b	ENSE00001986308	chr6:27114577-27114197	381	H2B1K_HUMAN	1-126	126	2	D:27-122 H:28-121	96 94

2.2b	ENST00000359303	2b	ENSE00001974165	chr6:27858570-27858160	411	H31_HUMAN	1-136	136	2	A:38-134 E:37-135	97 99

3.1	ENST00000377803	1	ENSE00001475159	chr6:26104104-26104518	415	H4_HUMAN	1-127	127	2	B:25-102 F:18-102	78 85

Asymmetric/Biological 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:97
 aligned with H31_HUMAN | P68431 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:97
                                    48        58        68        78        88        98       108       118       128       
            H31_HUMAN    39 PHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGER 135
               SCOP domains d2cv5a_ A: Histone H3                                                                             SCOP domains
               CATH domains 2cv5A00 A:38-134 Histone, subunit A                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------HISTONE_H------------------------------------------------------------ PROSITE
               Transcript 2 Exon 2.2b  PDB: A:38-134 UniProt: 1-136 [INCOMPLETE]                                              Transcript 2
                 2cv5 A  38 PHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGER 134
                                    47        57        67        77        87        97       107       117       127

Chain B from PDB  Type:PROTEIN  Length:78
 aligned with H4_HUMAN | P62805 from UniProtKB/Swiss-Prot  Length:103

    Alignment length:78
                                    35        45        55        65        75        85        95        
             H4_HUMAN    26 NIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG 103
               SCOP domains d2cv5b_ B: Histone H4                                                          SCOP domains
               CATH domains 2cv5B00 B:25-102 Histone, subunit A                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhh..eee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------Q--------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------ PROSITE
               Transcript 3 Exon 3.1  PDB: B:25-102 UniProt: 1-127 [INCOMPLETE]                            Transcript 3
                 2cv5 B  25 NIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG 102
                                    34        44        54        64        74        84        94

Chain C from PDB  Type:PROTEIN  Length:108
 aligned with H2A1B_HUMAN | P04908 from UniProtKB/Swiss-Prot  Length:130

    Alignment length:108
                                    21        31        41        51        61        71        81        91       101       111        
          H2A1B_HUMAN    12 RAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPK 119
               SCOP domains d2cv5c1 C:11-118 Histone H2A                                                                                 SCOP domains
               CATH domains 2cv5C00 C:11-118 Histone, subunit A                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhh...hhhhhhhhhhh.....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhh..eee.........hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------HISTONE------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 2cv5 C  11 RAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPK 118
                                    20        30        40        50        60        70        80        90       100       110

Chain D from PDB  Type:PROTEIN  Length:96
 aligned with H2B1K_HUMAN | O60814 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:96
                                    40        50        60        70        80        90       100       110       120      
          H2B1K_HUMAN    31 KRSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK 126
               SCOP domains d2cv5d1 D:27-122 Histone H2B                                                                     SCOP domains
               CATH domains 2cv5D00 D:27-122 Histone, subunit A                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------HISTONE_H2B            ----------- PROSITE
               Transcript 1 Exon 1.1b  PDB: D:27-122 UniProt: 1-126 [INCOMPLETE]                                             Transcript 1
                 2cv5 D  27 KRSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK 122
                                    36        46        56        66        76        86        96       106       116

Chain E from PDB  Type:PROTEIN  Length:99
 aligned with H31_HUMAN | P68431 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:99
                                    47        57        67        77        87        97       107       117       127         
            H31_HUMAN    38 KPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 136
               SCOP domains d2cv5e_ E: Histone H3                                                                               SCOP domains
               CATH domains 2cv5E00 E:37-135 Histone, subunit A                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhh......hhhhhhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------HISTONE_H------------------------------------------------------------- PROSITE
               Transcript 2 Exon 2.2b  PDB: E:37-135 UniProt: 1-136 [INCOMPLETE]                                                Transcript 2
                 2cv5 E  37 KPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 135
                                    46        56        66        76        86        96       106       116       126

Chain F from PDB  Type:PROTEIN  Length:85
 aligned with H4_HUMAN | P62805 from UniProtKB/Swiss-Prot  Length:103

    Alignment length:85
                                    28        38        48        58        68        78        88        98     
             H4_HUMAN    19 HRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG 103
               SCOP domains d2cv5f_ F: Histone H4                                                                 SCOP domains
               CATH domains 2cv5F00 F:18-102 Histone, subunit A                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhh..eee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------Q--------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
               Transcript 3 Exon 3.1  PDB: F:18-102 UniProt: 1-127 [INCOMPLETE]                                   Transcript 3
                 2cv5 F  18 HRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG 102
                                    27        37        47        57        67        77        87        97

Chain G from PDB  Type:PROTEIN  Length:104
 aligned with H2A1B_HUMAN | P04908 from UniProtKB/Swiss-Prot  Length:130

    Alignment length:104
                                    25        35        45        55        65        75        85        95       105       115    
          H2A1B_HUMAN    16 KTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPK 119
               SCOP domains d2cv5g_ G: Histone H2A                                                                                   SCOP domains
               CATH domains 2cv5G00 G:15-118 Histone, subunit A                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh....hhhhhhhhhhhh....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eehhhhhhhhhhhhhhhhhhh..eee.........hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------HISTONE------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 2cv5 G  15 KTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPK 118
                                    24        34        44        54        64        74        84        94       104       114

Chain H from PDB  Type:PROTEIN  Length:94
 aligned with H2B1K_HUMAN | O60814 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:94
                                    41        51        61        71        81        91       101       111       121    
          H2B1K_HUMAN    32 RSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSA 125
               SCOP domains d2cv5h_ H: Histone H2B                                                                         SCOP domains
               CATH domains 2cv5H00 H:28-121 Histone, subunit A                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------HISTONE_H2B            ---------- PROSITE
               Transcript 1 Exon 1.1b  PDB: H:28-121 UniProt: 1-126 [INCOMPLETE]                                           Transcript 1
                 2cv5 H  28 RSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSA 121
                                    37        47        57        67        77        87        97       107       117

Chain I from PDB  Type:DNA  Length:146
                                                                                                                                                                                  
                 2cv5 I   1 ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCTGAATTCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGAATCTGCAGGTGGATATTGAT 146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain J from PDB  Type:DNA  Length:146
                                                                                                                                                                                  
                 2cv5 J 147 ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCTGAATTCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGAATCTGCAGGTGGATATTGAT 292
                                   156       166       176       186       196       206       216       226       236       246       256       266       276       286

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/Biological 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: Histone H2A (45)

Human (Homo sapiens), H2A.a [TaxId: 9606] (1)

1a	d2cv5c1	C:11-118
1b	d2cv5g_	G:

Protein domain: Histone H2B (48)

Human (Homo sapiens), H2B.k [TaxId: 9606] (1)

2a	d2cv5d1	D:27-122
2b	d2cv5h_	H:

Protein domain: Histone H3 (58)

Human (Homo sapiens) [TaxId: 9606] (10)

3a	d2cv5a_	A:
3b	d2cv5e_	E:

Protein domain: Histone H4 (60)

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

4a	d2cv5b_	B:
4b	d2cv5f_	F:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Histone, subunit A (62)

Homologous Superfamily: Histone, subunit A (62)

[unclassified] (10)

1a	2cv5A00	A:38-134
1b	2cv5E00	E:37-135
1c	2cv5D00	D:27-122
1d	2cv5H00	H:28-121
1e	2cv5F00	F:18-102
1f	2cv5G00	G:15-118
1g	2cv5C00	C:11-118
1h	2cv5B00	B:25-102

(no "Pfam Domain" information available for 2CV5)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,E (H31_HUMAN | P68431)

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:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
biological process
	GO:0006335	DNA replication-dependent nucleosome assembly	The formation of nucleosomes on newly replicated DNA, coupled to strand elongation.
	GO:0007596	blood coagulation	The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
	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: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: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:0002230	positive regulation of defense response to virus by host	Any host process that results in the promotion of antiviral immune response mechanisms, thereby limiting viral replication.
	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:0060968	regulation of gene silencing	Any process that modulates the rate, frequency, or extent of gene silencing, the transcriptional or post-transcriptional process carried out at the cellular level that results in long-term gene inactivation.
	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.
	GO:0098792	xenophagy	The macroautophagy process in which a region of cytoplasm containing an intracellular pathogen or some part of an intracellular pathogen (e.g. viral capsid) is enclosed in a double membrane bound autophagosome, which then fuses with the lysosome leading to degradation of the contents.
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:0000788	nuclear nucleosome	A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA in the nucleus into higher order structures.
	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.

Chain B,F (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.

Chain C,G (H2A1B_HUMAN | P04908)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
biological process
	GO:0006342	chromatin silencing	Repression of transcription by altering the structure of chromatin, e.g. by conversion of large regions of DNA into an inaccessible state often called heterochromatin.
	GO:0008285	negative regulation of cell proliferation	Any process that stops, prevents or reduces the rate or extent of cell proliferation.
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:0000790	nuclear chromatin	The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
	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 D,H (H2B1K_HUMAN | O60814)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003674	molecular_function	Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
	GO:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
biological process
	GO:0019731	antibacterial humoral response	An immune response against bacteria mediated through a body fluid. Examples of this process are the antibacterial humoral responses in Mus musculus and Drosophila melanogaster.
	GO:0050830	defense response to Gram-positive bacterium	Reactions triggered in response to the presence of a Gram-positive bacterium that act to protect the cell or organism.
	GO:0042742	defense response to bacterium	Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
	GO:0002227	innate immune response in mucosa	Any process of the innate immune response that takes place in the mucosal tissues.
	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.
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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	GO:0000788	nuclear nucleosome	A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA in the nucleus into higher order structures.
	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.

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	2cv5
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(no "Related Entries Specified in the PDB File" available for 2CV5)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 13)

Sites (13, 13)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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SAPs(SNPs)/Variants (1, 2)

PROSITE Motifs (3, 6)

Exons (3, 6)

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SCOP Domains (4, 8)

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