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(-) Description

Title :  CRYSTAL STRUCTURE OF NUCLEOSOME CORE PARTICLE IN THE PRESENCE OF HISTONE VARIANT INVOLVED IN REPROGRAMMING
 
Authors :  P. Sivaraman, T. S. Kumarevel
Date :  28 Nov 14  (Deposition) - 23 Sep 15  (Release) - 23 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.92
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H,I,J
Keywords :  Nucleosome, Chromatin, Histone Variant, Reprogramming, Structural Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Padavattan, T. Shinagawa, K. Hasegawa, T. Kumasaka, S. Ishii, T. Kumarevel
Structural And Functional Analyses Of Nucleosome Complexes With Mouse Histone Variants Th2A And Th2B, Involved In Reprogramming
Biochem. Biophys. Res. Commun. V. 464 929 2015
PubMed-ID: 26188507  |  Reference-DOI: 10.1016/J.BBRC.2015.07.070

(-) Compounds

Molecule 1 - DNA (146-MER)
    ChainsI, J
    EngineeredYES
    Organism ScientificSYNTHETIC
    Organism Taxid32630
    SyntheticYES
 
Molecule 2 - HISTONE H3.1
    ChainsA, E
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPHCE
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneH3.1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHISTONE H3/A, HISTONE H3/B, HISTONE H3/C, HISTONE H3/D, HISTONE H3/F, HISTONE H3/H, HISTONE H3/I, HISTONE H3/J, HISTONE H3/K, HISTONE H3/L
 
Molecule 3 - HISTONE H4
    ChainsB, F
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B
    Expression System StrainJM109(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneH4
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 4 - HISTONE H2A TYPE 1-B/E
    ChainsC, G
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPHCE
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneH2A
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHISTONE H2A.2, HISTONE H2A/A, HISTONE H2A/M
 
Molecule 5 - HISTONE H2B TYPE 1-A
    ChainsD, H
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPHCE
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneH2BA
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymHISTONE H2B, TESTIS, TESTIS-SPECIFIC HISTONE H2B

 Structural Features

(-) Chains, Units

  12345678910
Asymmetric/Biological Unit ABCDEFGHIJ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 25)

Asymmetric/Biological Unit (2, 25)
No.NameCountTypeFull Name
1CL6Ligand/IonCHLORIDE ION
2MN19Ligand/IonMANGANESE (II) ION

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREDG I:68BINDING SITE FOR RESIDUE MN I 201
02AC2SOFTWAREDT I:120 , DG I:121 , MN I:207BINDING SITE FOR RESIDUE MN I 202
03AC3SOFTWAREDG I:134 , HOH I:310BINDING SITE FOR RESIDUE MN I 203
04AC4SOFTWAREDG I:78 , HOH J:401BINDING SITE FOR RESIDUE MN I 204
05AC5SOFTWAREDG I:87BINDING SITE FOR RESIDUE MN I 205
06AC6SOFTWAREDG I:134BINDING SITE FOR RESIDUE MN I 206
07AC7SOFTWAREDG I:121 , MN I:202BINDING SITE FOR RESIDUE MN I 207
08AC8SOFTWAREDT I:6 , DC I:84BINDING SITE FOR RESIDUE MN I 208
09AC9SOFTWAREARG E:42 , DA I:145 , DT I:146BINDING SITE FOR RESIDUE MN I 209
10BC1SOFTWAREDA I:17BINDING SITE FOR RESIDUE MN I 210
11BC2SOFTWAREDA I:56BINDING SITE FOR RESIDUE MN I 211
12BC3SOFTWAREDT J:289 , DG J:290BINDING SITE FOR RESIDUE CL I 212
13BC4SOFTWAREDG I:135 , DT I:136BINDING SITE FOR RESIDUE CL I 213
14BC5SOFTWAREDG J:164BINDING SITE FOR RESIDUE MN J 301
15BC6SOFTWAREDG J:280BINDING SITE FOR RESIDUE MN J 302
16BC7SOFTWAREDG J:185 , DG J:186BINDING SITE FOR RESIDUE MN J 303
17BC8SOFTWAREDG J:267BINDING SITE FOR RESIDUE MN J 304
18BC9SOFTWAREDT J:183BINDING SITE FOR RESIDUE MN J 305
19CC1SOFTWAREDG J:217BINDING SITE FOR RESIDUE CL J 308
20CC2SOFTWAREVAL D:48 , CL D:202 , ASP E:77BINDING SITE FOR RESIDUE MN D 201
21CC3SOFTWAREVAL D:48 , MN D:201 , GLN E:76 , ASP E:77BINDING SITE FOR RESIDUE CL D 202
22CC4SOFTWAREGLY G:44 , GLY G:46 , ALA G:47 , THR H:90 , SER H:91BINDING SITE FOR RESIDUE MN G 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3X1V)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3X1V)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3X1V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3X1V)

(-) Exons   (0, 0)

(no "Exon" information available for 3X1V)

(-) Sequences/Alignments

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:98
                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhh.....hhhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 3x1v A  38 PHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 135
                                    47        57        67        77        87        97       107       117       127        

Chain B from PDB  Type:PROTEIN  Length:79
                                                                                                               
               SCOP domains ------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhh..eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------- Transcript
                 3x1v B  24 DNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG 102
                                    33        43        53        63        73        83        93         

Chain C from PDB  Type:PROTEIN  Length:106
                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhh...hhhhhhhhhhh.....ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhh..eee.........hhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 3x1v C  13 KAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPK 118
                                    22        32        42        52        62        72        82        92       102       112      

Chain D from PDB  Type:PROTEIN  Length:99
                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 3x1v D  27 RKRKRCRKESYSIYIYKVLKQVHPDTGISSKAMSIMNSFVTDIFERIASEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 125
                                    36        46        56        66        76        86        96       106       116         

Chain E from PDB  Type:PROTEIN  Length:99
                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 3x1v E  37 KPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 135
                                    46        56        66        76        86        96       106       116       126         

Chain F from PDB  Type:PROTEIN  Length:87
                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhh..eee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 3x1v F  16 KRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG 102
                                    25        35        45        55        65        75        85        95       

Chain G from PDB  Type:PROTEIN  Length:109
                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhh...hhhhhhhhhhhh....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eehhhhhhhhhhhhhhhhhhh..eee.........hhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 3x1v G  11 RAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKK 119
                                    20        30        40        50        60        70        80        90       100       110         

Chain H from PDB  Type:PROTEIN  Length:94
                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                 3x1v H  32 CRKESYSIYIYKVLKQVHPDTGISSKAMSIMNSFVTDIFERIASEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 125
                                    41        51        61        71        81        91       101       111       121    

Chain I from PDB  Type:DNA  Length:146
                                                                                                                                                                                  
                 3x1v 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
                                                                                                                                                                                  
                 3x1v 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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3X1V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3X1V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3X1V)

(-) Gene Ontology  (47, 85)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        H2A1B_HUMAN | P049082cv5 2rvq 3a6n 3afa 3an2 3av1 3av2 3ayw 3aze 3azf 3azg 3azh 3azi 3azj 3azk 3azl 3azm 3azn 3w96 3w97 3w98 3w99 3wkj 3wtp 3x1s 4ym5 4ym6 4z5t 5av5 5av6 5av8 5av9 5avb 5avc 5ay8 5b0y 5b0z 5b24 5b2i 5b2j 5b31 5b32 5b40 5cpi 5cpj 5cpk 5gse 5gtc 5gxq 5jrg 5vey 5x7x
        H2B1A_MOUSE | P706963x1t
        H31_HUMAN | P684311cs9 1ct6 1guw 1o9s 1q3l 2b2t 2b2u 2b2v 2b2w 2c1j 2c1n 2cv5 2kwj 2kwk 2l75 2lbm 2m0o 2ndf 2ndg 2oq6 2ot7 2ox0 2ri7 2uxn 2v89 2vpg 2x0l 3a1b 3afa 3avr 3ayw 3aze 3azf 3azg 3azh 3azi 3azj 3azk 3azl 3azm 3azn 3b95 3kmt 3kqi 3lqi 3lqj 3o34 3o35 3o37 3qj6 3rig 3riy 3sou 3sow 3u31 3u3d 3u4s 3u5n 3u5o 3u5p 3uee 3uef 3uig 3uii 3uik 3v43 3w96 3w97 3w98 3w99 3wa9 3waa 3wkj 3x1s 3x1t 3x1u 3zg6 3zvy 4a0j 4a0n 4a7j 4bd3 4c1q 4f4u 4f56 4ft2 4ft4 4fwf 4hon 4i51 4l7x 4lk9 4lka 4llb 4lxl 4n4h 4qbq 4qbr 4qbs 4tn7 4u68 4up0 4uy4 4x3k 4y6l 4yhp 4yhz 4ym5 4ym6 4z0r 4z2m 5av5 5av6 5av8 5av9 5avb 5avc 5b24 5b2i 5b2j 5b31 5c11 5c13 5c3i 5cpi 5cpj 5cpk 5d6y 5dah 5fb0 5fb1 5ffv 5gse 5gsu 5gt0 5gt3 5gtc 5hjb 5hjc 5hjd 5hyn 5iql 5j3v 5j9s 5jhn 5jin 5jiy 5jj0 5jrg 5kjh 5kji 5kkl 5m5g 5svx 5svy 5t0k 5t0m 5t1g 5t1i 5t8r 5tbn 5tdr 5tdw 5v21 5v22 5va6
        H4_HUMAN | P628051kx4 1kx5 1m18 1m19 1m1a 1s32 1zkk 2bqz 2cv5 2ig0 2kwn 2kwo 2lvm 2qqs 2rje 2rny 2rs9 3a6n 3afa 3an2 3av1 3av2 3ayw 3aze 3azf 3azg 3azh 3azi 3azj 3azk 3azl 3azm 3azn 3cfs 3cfv 3f9w 3f9x 3f9y 3f9z 3ij1 3jpx 3nqj 3nqu 3o36 3qby 3qzs 3qzt 3qzv 3r45 3uvw 3uvx 3uvy 3uw9 3w96 3w97 3w98 3w99 3wa9 3waa 3wkj 3wtp 3x1s 3x1t 3x1u 4gqb 4h9n 4h9o 4h9p 4h9q 4h9r 4h9s 4hga 4m38 4n3w 4n4f 4qut 4quu 4qyd 4u9w 4ym5 4ym6 4yy6 4yyd 4yyg 4yyh 4yyi 4yyj 4yyk 4yym 4yyn 4z2m 4z5t 5av5 5av6 5av8 5av9 5avb 5avc 5ay8 5b0y 5b0z 5b24 5b2i 5b2j 5b31 5b32 5b33 5b40 5bnv 5bnx 5bo0 5c3i 5cpi 5cpj 5cpk 5fa5 5ffw 5fwe 5gse 5gsu 5gt0 5gt3 5gtc 5gxq 5ja4 5jrg 5kdm 5teg 5x7x

(-) Related Entries Specified in the PDB File

3x1s 3x1t 3x1u