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(-) Description

Title :  X-RAY STRUCTURE OF THE MMTV-A NUCLEOSOME CORE PARTICLE
 
Authors :  T. D. Frouws, T. J. Richmond
Date :  09 Dec 15  (Deposition) - 03 Feb 16  (Release) - 10 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.63
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H,I,J
Keywords :  Nucleosome Core Particle Histone Dna, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. D. Frouws, S. C. Duda, T. J. Richmond
X-Ray Structure Of The Mmtv-A Nucleosome Core.
Proc. Natl. Acad. Sci. Usa V. 113 1214 2016
PubMed-ID: 26787910  |  Reference-DOI: 10.1073/PNAS.1524607113

(-) Compounds

Molecule 1 - HISTONE H3.2
    Chains: A, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET3A
    Expression System Taxid: 469008
    Expression System Variant: PLYSS
    Mutation: YES
    Organism Common: AFRICAN CLAWED FROG
    Organism Scientific: XENOPUS LAEVIS
    Organism Taxid: 8355
 
Molecule 2 - HISTONE H4
    Chains: B, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET3A
    Expression System Taxid: 469008
    Expression System Variant: PLYSS
    Mutation: YES
    Organism Common: AFRICAN CLAWED FROG
    Organism Scientific: XENOPUS LAEVIS
    Organism Taxid: 8355
 
Molecule 3 - HISTONE H2A TYPE 1
    Chains: C, G
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET3A
    Expression System Taxid: 469008
    Expression System Variant: PLYSS
    Organism Common: AFRICAN CLAWED FROG
    Organism Scientific: XENOPUS LAEVIS
    Organism Taxid: 8355
 
Molecule 4 - HISTONE H2B 1.1
    Chains: D, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET3A
    Expression System Taxid: 469008
    Expression System Variant: PLYSS
    Organism Common: AFRICAN CLAWED FROG
    Organism Scientific: XENOPUS LAEVIS
    Organism Taxid: 8355
    Synonym: H2B1.1
 
Molecule 5 - DNA (147-MER)
    Chains: I
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PUC57
    Expression System Strain: DH10B
    Expression System Taxid: 316385
    Organism Scientific: MOUSE MAMMARY TUMOR VIRUS
    Organism Taxid: 11757
 
Molecule 6 - DNA (147-MER)
    Chains: J
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PUC57
    Expression System Strain: DH10B
    Expression System Taxid: 316385
    Organism Scientific: MOUSE MAMMARY TUMOR VIRUS
    Organism Taxid: 11757

 Structural Features

(-) Chains, Units

  12345678910
Asymmetric/Biological Unit : ABCDEFGHIJ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:120 , PRO A:121 , LYS A:122binding site for residue CL A 201
2AC2SOFTWAREGLY C:44 , ALA C:45 , GLY C:46 , ALA C:47 , THR D:90 , SER D:91binding site for residue CL C 201
3AC3SOFTWAREMET E:120 , PRO E:121 , LYS E:122 , HOH F:294binding site for residue CL E 201
4AC4SOFTWAREGLU C:64 , HOH C:346 , VAL D:48 , ASP E:77 , HOH E:301 , HOH E:324 , HOH F:205binding site for residue MG E 202
5AC5SOFTWAREGLY G:46 , ALA G:47 , THR H:90 , SER H:91binding site for residue CL G 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5F99)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5F99)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5F99)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5F99)

(-) Exons   (0, 0)

(no "Exon" information available for 5F99)

(-) 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:100
                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee.hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 5f99 A  36 KKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLAAIHAKRVTIMPKDIQLARRIRGERA 135
                                    45        55        65        75        85        95       105       115       125       135


Chain B from PDB  Type:PROTEIN  Length:83
                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh.hhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh..eee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                 5f99 B  20 KVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG 102
                                    29        39        49        59        69        79        89        99   


Chain C from PDB  Type:PROTEIN  Length:111
                                                                                                                                               
               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
                 5f99 C  11 RAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKTE 121
                                    20        30        40        50        60        70        80        90       100       110       120 


Chain D from PDB  Type:PROTEIN  Length:100
                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 5f99 D  26 GKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK 125
                                    35        45        55        65        75        85        95       105       115       125


Chain E from PDB  Type:PROTEIN  Length:99
                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 5f99 E  37 KPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLAAIHAKRVTIMPKDIQLARRIRGERA 135
                                    46        56        66        76        86        96       106       116       126         


Chain F from PDB  Type:PROTEIN  Length:92
                                                                                                                            
               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
                 5f99 F  11 GKGGAKRRRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG 102
                                    20        30        40        50        60        70        80        90       100  


Chain G from PDB  Type:PROTEIN  Length:121
                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................hhhhhhhhhhhh....ee.hhhhhhhhhhhhhhhhhhhhhhhh........eehhhhhhhhhhhhhhhhhhh..eee........................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f99 G   9 KTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKTESSKSAKSK 129
                                    18        28        38        48        58        68        78        88        98       108       118       128 


Chain H from PDB  Type:PROTEIN  Length:97
                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhh...ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 5f99 H  29 RRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK 125
                                    38        48        58        68        78        88        98       108       118       


Chain I from PDB  Type:DNA  Length:147
                                                                                                                                                                                   
                 5f99 I -73 ATCTGCAACAGTCCTAACATTCACCTCTTGTGTGTTTGTGTCTGTTCGCCATCCCGTCTCCGCTCGTCACTTATCCTTCACTTTCCAGAGGGTCCCCCCGCAGACCCCGGCGACCCTCAGGTCGGCCGACTGCGGCACAGTTTTGAT  73
                                   -64       -54       -44       -34       -24       -14        -4         6        16        26        36        46        56        66       


Chain J from PDB  Type:DNA  Length:147
                                                                                                                                                                                   
                 5f99 J -73 ATCAAAACTGTGCCGCAGTCGGCCGACCTGAGGGTCGCCGGGGTCTGCGGGGGGACCCTCTGGAAAGTGAAGGATAAGTGACGAGCGGAGACGGGATGGCGAACAGACACAAACACACAAGAGGTGAATGTTAGGACTGTTGCAGAT  73
                                   -64       -54       -44       -34       -24       -14        -4         6        16        26        36        46        56        66
   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 5F99)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5F99)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5F99)

(-) Gene Ontology  (9, 25)

Asymmetric/Biological Unit(hide GO term definitions)

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  5f99
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  H2B11_XENLA | P02281
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  H32_XENLA | P84233
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  H4_XENLA | P62799
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 Related Entries

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

UniProtKB/Swiss-Prot
        H2A1_XENLA | P06897: 1aoi 1kx3 1kx4 1kx5 1m18 1m19 1m1a 1p34 1p3a 1p3b 1p3f 1p3g 1p3i 1p3k 1p3l 1p3m 1p3o 1p3p 1s32 1zbb 1zla 2fj7 2nzd 3b6f 3b6g 3c1b 3c1c 3kuy 3kwq 3lja 3mnn 3o62 3reh 3rei 3rej 3rek 3rel 3tu4 3ut9 3uta 3utb 4j8u 4j8v 4j8w 4j8x 4ld9 4wu8 4wu9 4xuj 4xzq 4ys3 4z66 4zux 5cp6 5dnm 5dnn 5e5a 5g2e 5hq2 5mlu 5nl0
        H2B11_XENLA | P02281: 1aoi 1f66 1kx3 1kx4 1kx5 1m18 1m19 1m1a 1p34 1p3a 1p3b 1p3f 1p3g 1p3i 1p3k 1p3l 1p3m 1p3o 1p3p 1s32 1zbb 1zla 2f8n 2fj7 2nzd 3b6f 3b6g 3kuy 3kwq 3kxb 3lel 3lja 3lz0 3lz1 3mgp 3mgq 3mgr 3mgs 3mnn 3mvd 3o62 3reh 3rei 3rej 3rek 3rel 3tu4 3ut9 3uta 3utb 4j8u 4j8v 4j8w 4j8x 4kgc 4kha 4ld9 4r8p 4wu8 4wu9 4xuj 4xzq 4ys3 4z66 4zux 5cp6 5dnm 5dnn 5e5a 5g2e 5hq2 5nl0 5x0x 5x0y
        H32_XENLA | P84233: 1f66 1kx3 1kx4 1kx5 1p34 1p3a 1p3b 1p3f 1p3g 1p3i 1p3k 1p3l 1p3m 1p3o 1p3p 1s32 1zbb 1zla 2f8n 2fj7 2hue 2io5 2nzd 3b6f 3b6g 3c1b 3c1c 3gv6 3kuy 3kwq 3kxb 3lel 3lja 3lz0 3lz1 3mgp 3mgq 3mgr 3mgs 3mnn 3mvd 3o62 3reh 3rei 3rej 3rek 3rel 3tu4 3ut9 3uta 3utb 4eo5 4j8u 4j8v 4j8w 4j8x 4kgc 4ld9 4r8p 4wu8 4wu9 4xuj 4xzq 4ys3 4z66 4zux 5bs7 5bsa 5cp6 5dnm 5dnn 5e5a 5hq2 5kgf 5mlu 5nl0 5x0x 5x0y
        H4_XENLA | P62799: 1aoi 1kx3 1kx4 1kx5 1m18 1m19 1m1a 1p34 1p3a 1p3b 1p3f 1p3g 1p3i 1p3k 1p3l 1p3m 1p3o 1p3p 1s32 1zbb 1zla 2f8n 2fj7 2hue 2io5 2nzd 3b6f 3b6g 3c1b 3c1c 3kuy 3kwq 3kxb 3lel 3lja 3lz0 3lz1 3mgp 3mgq 3mgr 3mgs 3mnn 3mvd 3o62 3reh 3rei 3rej 3rek 3rel 3tu4 3ut9 3uta 3utb 4eo5 4j8u 4j8v 4j8w 4j8x 4kgc 4ld9 4r8p 4wu8 4wu9 4xuj 4xzq 4ys3 4z66 4zbj 4zux 5bs7 5bsa 5cp6 5dnm 5dnn 5e5a 5hq2 5kgf 5mlu 5nl0 5x0x 5x0y

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5F99)