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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN TONSL AND MCM2 HBDS BINDING TO A HISTONE H3-H4 TETRAMER
 
Authors :  H. Huang, D. Patel
Date :  11 Apr 16  (Deposition) - 15 Jun 16  (Release) - 13 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.42
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (2x)
Keywords :  Dna Repair And Histone Chaperone, Chaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Saredi, H. Huang, C. M. Hammond, C. Alabert, S. Bekker-Jensen, I. Forne, N. Reveron-Gomez, B. M. Foster, L. Mlejnkova, T. Bartke, P. Cejka, N. Mailand, A. Imhof, D. J. Patel, A. Groth
H4K20Me0 Marks Post-Replicative Chromatin And Recruits The Tonsl-Mms22L Dna Repair Complex.
Nature V. 534 714 2016
PubMed-ID: 27338793  |  Reference-DOI: 10.1038/NATURE18312

(-) Compounds

Molecule 1 - HISTONE H3.3
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21-CODONPLUS(DE3)-RIL
    Expression System Taxid: 469008
    Gene: H3F3A, H3.3A, H3F3, PP781, H3F3B, H3.3B
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - HISTONE H4
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - DNA REPLICATION LICENSING FACTOR MCM2
    Chains: C
    EC Number: 3.6.4.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: MCM2, BM28, CCNL1, CDCL1, KIAA0030
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MINICHROMOSOME MAINTENANCE PROTEIN 2 HOMOLOG,NUCLEAR PROTEIN BM28
 
Molecule 4 - TONSOKU-LIKE PROTEIN
    Chains: D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: TONSL, IKBR, NFKBIL2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: INHIBITOR OF KAPPA B-RELATED PROTEIN,IKAPPABR,NF-KAPPA-B INHIBITOR-LIKE PROTEIN 2,NUCLEAR FACTOR OF KAPPA LIGHT POLYPEPTIDE GENE ENHANCER IN B-CELLS INHIBITOR-LIKE 2

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (2x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2MES2Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:105 , ASP A:106 , ARG A:129 , ILE A:130 , ARG A:131binding site for residue MES A 201
2AC2SOFTWAREGLN B:27 , GLU B:52 , ARG B:55 , ARG D:525 , ASP D:527binding site for residue GOL B 201
3AC3SOFTWAREGLU A:73 , LEU B:22 , ASP B:24 , ASN B:25binding site for residue GOL B 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5JA4)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly D:573 -His D:574
2Gly D:585 -Ala D:586

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5JA4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5JA4)

(-) Exons   (0, 0)

(no "Exon" information available for 5JA4)

(-) Sequences/Alignments

Asymmetric 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:78
                                                                                                              
               SCOP domains ------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------ Transcript
                 5ja4 A  57 STELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGER 134
                                    66        76        86        96       106       116       126        


Chain B from PDB  Type:PROTEIN  Length:89
                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 5ja4 B  12 KGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGF 100
                                    21        31        41        51        61        71        81        91         


Chain C from PDB  Type:PROTEIN  Length:57
                                                                                         
               SCOP domains --------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee....hhhhhhh.......................hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------- Transcript
                 5ja4 C  68 DGEELIGDGMERDYRAIPELDAYEAEGLALDDEDVEELTASQREAAERAMRQRDREA 124
                                    77        87        97       107       117       


Chain D from PDB  Type:PROTEIN  Length:149
                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhh.hhhhhhhh...............hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ja4 D 521 KWNRRNDMGETLLHRACIEGQLRRVQDLVRQGHPLNPRDYCGWTPLHEACNYGHLEIVRFLLDHGAAVDDPGGQGCEGITPLHDALNCGHFEVAELLLERGASVTLRTRKGLSPLETLQQWVKLYRRDLDLETRQKARAMEMLLQAAAS 669
                                   530       540       550       560       570       580       590       600       610       620       630       640       650       660
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 5JA4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5JA4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5JA4)

(-) Gene Ontology  (68, 102)

Asymmetric Unit(hide GO term definitions)

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  5ja4
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  MCM2_HUMAN | P49736
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  TONSL_HUMAN | Q96HA7
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 Related Entries

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

UniProtKB/Swiss-Prot
        H33_HUMAN | P84243: 1pdq 2l43 3ask 3asl 3av2 3jvk 3muk 3mul 3ql9 3qla 3qlc 3wtp 4gne 4gnf 4gng 4gu0 4gur 4gus 4gy5 4h9n 4h9o 4h9p 4h9q 4h9r 4h9s 4hga 4l58 4n4i 4o62 4qq4 4tmp 4u7t 4w5a 5ay8 5b32 5b33 5bnv 5bnx 5dwq 5dx0 5jjy 5jlb 5kdm 5x7x
        H4_HUMAN | P62805: 1kx4 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 3x1v 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 5jrg 5kdm 5teg 5x7x
        MCM2_HUMAN | P49736: 4uuz 5bnv 5bnx 5bo0 5c3i

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5JA4)