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(-) Description

Title :  THE MOUSE NUCLEOSOME STRUCTURE CONTAINING H3T
 
Authors :  T. Urahama, S. Machida, N. Horikoshi, A. Osakabe, H. Tachiwana, H. Tagu H. Kurumizaka
Date :  08 Dec 15  (Deposition) - 15 Feb 17  (Release) - 15 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H,I,J
Keywords :  Chromatin, Spermatogenesis, Histone-Fold, Structural Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Ueda, A. Harada, T. Urahama, S. Machida, K. Maehara, M. Hada, Y. Makino, J. Nogami, N. Horikoshi, A. Osakabe, H. Taguchi, H. Tanaka, H. Tachiwana, T. Yao, M. Yamada, T. Iwamoto, A. Isotani, M. Ikawa, T. Tachibana, Y. Okada, H. Kimura, Y. Ohkawa, H. Kurumizaka, K. Yamagata
Testis-Specific Histone Variant H3T Gene Is Essential For Entry Into Spermatogenesis
Cell Rep V. 18 593 2017
PubMed-ID: 28099840  |  Reference-DOI: 10.1016/J.CELREP.2016.12.065

(-) Compounds

Molecule 1 - HISTONE H3T
    Chains: A, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: GM12260
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - HISTONE H4
    Chains: B, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: JM109(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: HIST1H4A, HIST1H4B, H4-53, HIST1H4C, H4-12, HIST1H4D, HIST1H4F, HIST1H4H, HIST1H4I, HIST1H4J, HIST1H4K, HIST1H4M, HIST2H4A, HIST2H4, HIST4H4
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 3 - HISTONE H2A TYPE 1
    Chains: C, G
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: HIST1H2AB, HIST1H2AC, HIST1H2AD, HIST1H2AE, HIST1H2AG, HIST1H2AI, HIST1H2AN, HIST1H2AO
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 4 - HISTONE H2B TYPE 3-A
    Chains: D, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: HIST3H2BA
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 5 - DNA (146-MER)
    Chains: I, J
    Engineered: YES
    Expression System: ESCHERICHIA COLI DH5[ALPHA]
    Expression System Plasmid: PGEM-T EASY
    Expression System Strain: DH5[ALPHA]
    Expression System Taxid: 668369
    Expression System Vector Type: PLASMID
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12345678910
Asymmetric/Biological Unit : ABCDEFGHIJ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 17)

Asymmetric/Biological Unit (2, 17)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2MN13Ligand/IonMANGANESE (II) ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:121 , LYS A:122binding site for residue CL A 301
02AC2SOFTWAREGLY C:44 , GLY C:46 , ALA C:47 , THR D:90 , SER D:91binding site for residue CL C 301
03AC3SOFTWAREHOH C:409 , VAL D:48 , HOH D:402 , HOH D:409 , ASP E:77 , HOH E:412binding site for residue MN D 301
04AC4SOFTWAREPRO E:121 , LYS E:122binding site for residue CL E 301
05AC5SOFTWAREGLY G:44 , GLY G:46 , ALA G:47 , SER H:91binding site for residue CL G 301
06AC6SOFTWAREDG I:121 , HOH I:406 , HOH I:435binding site for residue MN I 301
07AC7SOFTWAREHOH I:414 , HOH I:441 , HOH J:511 , HOH J:538binding site for residue MN I 302
08AC8SOFTWAREDG I:134 , HOH I:432 , HOH I:437binding site for residue MN I 303
09AC9SOFTWAREDG I:68 , HOH I:409 , HOH J:517binding site for residue MN I 304
10AD1SOFTWAREHOH I:419 , HOH J:540binding site for residue MN I 305
11AD2SOFTWAREDA I:17binding site for residue MN I 306
12AD3SOFTWAREDG J:267 , HOH J:505 , HOH J:532 , HOH J:537 , HOH J:545binding site for residue MN J 401
13AD4SOFTWAREDG J:185 , DG J:186 , HOH J:522 , HOH J:530 , HOH J:531binding site for residue MN J 402
14AD5SOFTWAREDG J:280 , HOH J:519 , HOH J:544binding site for residue MN J 403
15AD6SOFTWAREDT J:183 , HOH J:541binding site for residue MN J 404
16AD7SOFTWAREDG J:217 , HOH J:502binding site for residue MN J 405
17AD8SOFTWAREHOH J:542binding site for residue MN J 406

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5B1L)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5B1L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5B1L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5B1L)

(-) Exons   (0, 0)

(no "Exon" information available for 5B1L)

(-) 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:97
                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 5b1l A  38 PHRYHPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACESYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGER 134
                                    47        57        67        77        87        97       107       117       127       


Chain B from PDB  Type:PROTEIN  Length:78
                                                                                                              
               SCOP domains ------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhh...ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------ Transcript
                 5b1l B  25 NIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG 102
                                    34        44        54        64        74        84        94        


Chain C from PDB  Type:PROTEIN  Length:108
                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhh...hhhhhhhhhhhh....ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhh...ee.........hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 5b1l C  11 RAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPK 118
                                    20        30        40        50        60        70        80        90       100       110        


Chain D from PDB  Type:PROTEIN  Length:93
                                                                                                                             
               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
                 5b1l D  32 GRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIASEASRLAHYNKRSTITSREVQTAVRLLLPGELAKHAVSEGTKAVTKYTSS 124
                                    41        51        61        71        81        91       101       111       121   


Chain E from PDB  Type:PROTEIN  Length:97
                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 5b1l E  38 PHRYHPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACESYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGER 134
                                    47        57        67        77        87        97       107       117       127       


Chain F from PDB  Type:PROTEIN  Length:84
                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhh...ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                 5b1l F  19 RKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG 102
                                    28        38        48        58        68        78        88        98    


Chain G from PDB  Type:PROTEIN  Length:104
                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh...hhhhhhhhhhhh....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhh...ee.........hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 5b1l G  15 KTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPK 118
                                    24        34        44        54        64        74        84        94       104       114    


Chain H from PDB  Type:PROTEIN  Length:92
                                                                                                                            
               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
                 5b1l H  33 RKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIASEASRLAHYNKRSTITSREVQTAVRLLLPGELAKHAVSEGTKAVTKYTSS 124
                                    42        52        62        72        82        92       102       112       122  


Chain I from PDB  Type:DNA  Length:145
                                                                                                                                                                                 
                 5b1l I   2 TCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCTGAATTCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGAATCTGCAGGTGGATATTGAT 146
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141     


Chain J from PDB  Type:DNA  Length:145
                                                                                                                                                                                 
                 5b1l J 147 ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCTGAATTCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGAATCTGCAGGTGGATATTGA 291
                                   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 5B1L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5B1L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5B1L)

(-) Gene Ontology  (32, 66)

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  5b1l
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 Related Entries

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

UniProtKB/Swiss-Prot
        H2A1B_MOUSE | C0HKE1: 5b1m
        H2A1C_MOUSE | C0HKE2: 5b1m
        H2A1D_MOUSE | C0HKE3: 5b1m
        H2A1E_MOUSE | C0HKE4: 5b1m
        H2A1G_MOUSE | C0HKE5: 5b1m
        H2A1I_MOUSE | C0HKE6: 5b1m
        H2A1N_MOUSE | C0HKE7: 5b1m
        H2A1O_MOUSE | C0HKE8: 5b1m
        H2A1P_MOUSE | C0HKE9: 5b1m
        H2B3A_MOUSE | Q9D2U9: 1u35 2f8n 5b1m
        H31_MOUSE | P68433: 1cs9 1ct6 1guw 1q3l 1u35 2v83 2w5z 2wp1 2xl3 4ezh 5b1m 5ix1 5ix2
        H4_MOUSE | P62806: 1f66 1kx4 1kx5 1m18 1m19 1m1a 1s32 1u35 2wp2 4au7 4dow 5b1m

(-) Related Entries Specified in the PDB File

5b1m