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(-) Description

Title :  HUMAN PRDM9 ALLELE-A ZNF DOMAIN WITH ASSOCIATED RECOMBINATION HOTSPOT DNA SEQUENCE II
 
Authors :  A. Patel, J. R. Horton, G. G. Wilson, X. Zhang, X. Cheng
Date :  26 Oct 15  (Deposition) - 17 Feb 16  (Release) - 17 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.98
Chains :  Asym./Biol. Unit :  A,C,D
Keywords :  Protein-Dna Complex, Zinc Finger Protein, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Patel, J. R. Horton, G. G. Wilson, X. Zhang, X. Cheng
Structural Basis For Human Prdm9 Action At Recombination Ho Spots.
Genes Dev. V. 30 257 2016
PubMed-ID: 26833727  |  Reference-DOI: 10.1101/GAD.274928.115

(-) Compounds

Molecule 1 - DNA (5'- D(*AP*CP*CP*AP*CP*GP*TP*GP*GP*CP*TP*AP*GP*GP*GP*AP*GP*GP*CP*CP*T)- 3')
    Chains: C
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES
 
Molecule 2 - DNA (5'- D(*TP*AP*GP*GP*CP*CP*TP*CP*CP*CP*TP*AP*GP*CP*CP*AP*CP*GP*TP*GP*G)- 3')
    Chains: D
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES
 
Molecule 3 - HISTONE-LYSINE N-METHYLTRANSFERASE PRDM9
    Chains: A
    EC Number: 2.1.1.43
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX6P-1
    Expression System Strain: BL21 (DE3) CODON-PLUS RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: ZNF8-12 (UNP RESIDUES 717-858)
    Gene: PRDM9, PFM6
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PR DOMAIN ZINC FINGER PROTEIN 9,PR DOMAIN-CONTAINING PROTEIN 9
    Variant: ALLELE-A

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ACD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1ZN4Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:721 , CYS A:724 , HIS A:737 , HIS A:741binding site for residue ZN A 1001
2AC2SOFTWARECYS A:749 , CYS A:752 , HIS A:765 , HIS A:769binding site for residue ZN A 1002
3AC3SOFTWARECYS A:777 , CYS A:780 , HIS A:793 , HIS A:797binding site for residue ZN A 1003
4AC4SOFTWARECYS A:805 , CYS A:808 , HIS A:821 , HIS A:825binding site for residue ZN A 1004

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5EGB)

(-) 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    
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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:111
                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee......ee.hhhhhhhhhhhhhh...ee......ee.hhhhhhhhhhhhh....ee......ee.hhhhhhhhhhhhhh...ee......ee.hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 5egb A 716 EKPYVCRECGRGFSNKSHLLRHQRTHTGEKPYVCRECGRGFRDKSHLLRHQRTHTGEKPYVCRECGRGFRDKSNLLSHQRTHTGEKPYVCRECGRGFSNKSHLLRHQRTHT 826
                                   725       735       745       755       765       775       785       795       805       815       825 


Chain C from PDB  Type:DNA  Length:21
                                                     
                 5egb C   1 ACCACGTGGCTAGGGAGGCCT  21
                                    10        20 


Chain D from PDB  Type:DNA  Length:21
                                                     
                 5egb D   1 TAGGCCTCCCTAGCCACGTGG  21
                                    10        20
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5EGB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 16)

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
        PRDM9_HUMAN | Q9NQV7: 4ijd 5eh2 5ei9

(-) Related Entries Specified in the PDB File

5eh2 5ei9