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(-) Description

Title :  CRYSTAL STRUCTURE OF CHROMATOSOME AT 3.5 ANGSTROM RESOLUTION
 
Authors :  J. S. Jiang, B. R. Zhou, T. S. Xiao, Y. W. Bai
Date :  11 Jun 14  (Deposition) - 22 Jul 15  (Release) - 12 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.50
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H,I,J,U
Keywords :  Nucleosome Core Particle, Histone Fold, Chromosome, Chromatin, Global Histone H5, Gh5, Ncp167, Regulation, Segregation, Chromatosome, Gh1, Liker Histone H5, Linker Dna, Protein-Dna Complexes, Dna Binding Protein-Dna Complex, Chromatin Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. R. Zhou, J. Jiang, H. Feng, R. Ghirlando, T. S. Xiao, Y. Bai
Structural Mechanisms Of Nucleosome Recognition By Linker Histones.
Mol. Cell V. Pl 1 2 2015
PubMed-ID: 26212454  |  Reference-DOI: 10.1016/J.MOLCEL.2015.06.025

(-) Compounds

Molecule 1 - DNA (167-MER)
    Chains: I
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: 167BP WIDOM 601 DNA
    Gene: DNA
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - DNA (167-MER)
    Chains: J
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: 167BP WIDOM 601 DNA
    Gene: DNA
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - HISTONE H3
    Chains: A, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: 562
    Expression System Taxid: 562
    His3: CG33866
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227
    Strain: 7227
 
Molecule 4 - HISTONE H4
    Cg33907, Cg33909, H4, H4r, H4 Drome, His4, His4: CG31611,
    Chains: B, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: 562
    Expression System Taxid: 562
    Gene: CG31611, CG3379, CG33869, CG33871, CG33873, CG33875, CG33877, CG33879, CG33881, CG33883, CG33885, CG33887, CG33889, CG33891, CG33893, CG33895, CG33897, CG33899, CG33901, CG33903, CG33905,
    His4: CG33909, HIS4R
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227
    Strain: 7227
 
Molecule 5 - HISTONE H2A
    Cg33850, Cg33862, Cg33865, H2a, H2a Drome, His2a, His2a: CG31618,
    Chains: C, G
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: 562
    Expression System Taxid: 562
    Gene: CG31618, CG33808, CG33814, CG33817, CG33820, CG33823, CG33826, CG33829, CG33832, CG33835, CG33838, CG33841, CG33844, CG33847,
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227
    Strain: 7227
 
Molecule 6 - HISTONE H2B
    Chains: D, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: 562
    Expression System Taxid: 562
    His2b: CG33910
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227
    Strain: 7227
 
Molecule 7 - H5
    Chains: U
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: 562
    Expression System Taxid: 562
    Gene: H5_CHICK
    Organism Scientific: GALLUS GALLUS
    Organism Taxid: 9031
    Strain: 9031

 Structural Features

(-) Chains, Units

  1234567891011
Asymmetric/Biological Unit : ABCDEFGHIJU

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1CIT3Ligand/IonCITRIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:129 , ARG A:134BINDING SITE FOR RESIDUE CIT A 201
2AC2SOFTWAREGLU G:60 , GLU G:63BINDING SITE FOR RESIDUE CIT G 201
3AC3SOFTWARELYS A:64 , GLN G:103BINDING SITE FOR RESIDUE CIT G 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4QLC)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4QLC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4QLC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4QLC)

(-) Exons   (0, 0)

(no "Exon" information available for 4QLC)

(-) 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.....hhhhhhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 4qlc A  38 PHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 135
                                    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 hhhhhhhhhhhhhhhhhh..ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhh..eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------ Transcript
                 4qlc B  25 NIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG 102
                                    34        44        54        64        74        84        94        


Chain C from PDB  Type:PROTEIN  Length:104
                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh....hhhhhhhhhhh.....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhh..eee.........hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 4qlc C  14 KSRSNRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPK 117
                                    23        33        43        53        63        73        83        93       103       113    


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...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 4qlc D  29 KRKESYAIYIYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSS 121
                                    38        48        58        68        78        88        98       108       118   


Chain E from PDB  Type:PROTEIN  Length:98
                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 4qlc E  38 PHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 135
                                    47        57        67        77        87        97       107       117       127        


Chain F from PDB  Type:PROTEIN  Length:80
                                                                                                                
               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
                 4qlc F  23 RDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG 102
                                    32        42        52        62        72        82        92       102


Chain G from PDB  Type:PROTEIN  Length:104
                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh....hhhhhhhhhhh.....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eehhhhhhhhhhhhhhhhhhh..eee.........hhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 4qlc G  13 AKSRSNRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLP 116
                                    22        32        42        52        62        72        82        92       102       112    


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...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                 4qlc H  28 RKRKESYAIYIYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSS 121
                                    37        47        57        67        77        87        97       107       117    


Chain I from PDB  Type:DNA  Length:166
                                                                                                                                                                                                      
                 4qlc I   1 ACTGGCCGCCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTGCATGTAAG 166
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160      


Chain J from PDB  Type:DNA  Length:166
                                                                                                                                                                                                      
                 4qlc J   1 ACTTACATGCACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAGGGCGGCCAG 166
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160      


Chain U from PDB  Type:PROTEIN  Length:76
                                                                                                            
               SCOP domains ---------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhh......eehhhhhhhhhhhh....hhhhhhhhhhhhhhhh..eeeeee....eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                 4qlc U  22 SASHPTYSEMIAAAIRAEKSRGGSSRQSIQKYIKSHYKVGHNADLQIKLSIRRLLAAGVLKQTKGVGASGSFRLAK  97
                                    31        41        51        61        71        81        91
   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 4QLC)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4QLC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4QLC)

(-) Gene Ontology  (24, 60)

Asymmetric/Biological Unit(hide GO term definitions)

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  4qlc
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 Related Entries

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

UniProtKB/Swiss-Prot
        H2A_DROME | P84051: 2nqb 2pyo 4x23
        H2B_DROME | P02283: 2nqb 2pyo 4x23 5cve
        H3_DROME | P02299: 1kna 1kne 2nqb 2pyo 2yba 4uuz 4x23
        H4_DROME | P84040: 2nqb 2pyo 2xyi 3c9c 4uuz 4x23
        H5_CHICK | P02259: 1hst

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4QLC)