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(-) Description

Title :  HUMAN PRDM9 ALLELE-A ZNF DOMAIN WITH ASSOCIATED RECOMBINATION HOTSPOT DNA SEQUENCE I
 
Authors :  A. Patel, J. R. Horton, G. G. Wilson, X. Zhang, X. Cheng
Date :  29 Oct 15  (Deposition) - 17 Feb 16  (Release) - 17 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.92
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,E  (1x)
Biol. Unit 2:  C,D,F  (1x)
Keywords :  Protein-Dna Complex, Recombination, 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*TP*CP*CP*AP*CP*GP*TP*GP*GP*CP*TP*AP*GP*GP*GP*AP*GP*GP*CP*C)- 3')
    Chains: A, C
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES
 
Molecule 2 - HISTONE-LYSINE N-METHYLTRANSFERASE PRDM9
    Chains: F, E
    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
 
Molecule 3 - DNA (5'- D(*TP*GP*GP*CP*CP*TP*CP*CP*CP*TP*AP*GP*CP*CP*AP*CP*GP*TP*GP*GP*A)- 3')
    Chains: B, D
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB  E 
Biological Unit 2 (1x):   CD F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1ZN8Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS F:721 , CYS F:724 , HIS F:737 , HIS F:741binding site for residue ZN F 1001
2AC2SOFTWARECYS F:749 , CYS F:752 , HIS F:765 , HIS F:769binding site for residue ZN F 1002
3AC3SOFTWARECYS F:777 , CYS F:780 , HIS F:793 , HIS F:797binding site for residue ZN F 1003
4AC4SOFTWARECYS F:805 , CYS F:808 , HIS F:821 , HIS F:825binding site for residue ZN F 1004
5AC5SOFTWARECYS E:721 , CYS E:724 , HIS E:737 , HIS E:741binding site for residue ZN E 1001
6AC6SOFTWARECYS E:749 , CYS E:752 , HIS E:765 , HIS E:769binding site for residue ZN E 1002
7AC7SOFTWARECYS E:777 , CYS E:780 , HIS E:793 , HIS E:797binding site for residue ZN E 1003
8AC8SOFTWARECYS E:805 , CYS E:808 , HIS E:821 , HIS E:825binding site for residue ZN E 1004

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5EI9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5EI9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5EI9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5EI9)

(-) Exons   (0, 0)

(no "Exon" information available for 5EI9)

(-) 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:DNA  Length:21
                                                     
                 5ei9 A   1 ATCCACGTGGCTAGGGAGGCC  21
                                    10        20 


Chain B from PDB  Type:DNA  Length:21
                                                     
                 5ei9 B  22 TGGCCTCCCTAGCCACGTGGA  42
                                    31        41 


Chain C from PDB  Type:DNA  Length:21
                                                     
                 5ei9 C   1 ATCCACGTGGCTAGGGAGGCC  21
                                    10        20 


Chain D from PDB  Type:DNA  Length:21
                                                     
                 5ei9 D  22 TGGCCTCCCTAGCCACGTGGA  42
                                    31        41 


Chain E from PDB  Type:PROTEIN  Length:111
                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee......ee.hhhhhhhhhhhhh....ee......ee.hhhhhhhhhhhhhh...ee......ee.hhhhhhhhhhhhhh...ee......ee.hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 5ei9 E 716 EKPYVCRECGRGFSNKSHLLRHQRTHTGEKPYVCRECGRGFRDKSHLLRHQRTHTGEKPYVCRECGRGFRDKSNLLSHQRTHTGEKPYVCRECGRGFSNKSHLLRHQRTHT 826
                                   725       735       745       755       765       775       785       795       805       815       825 


Chain F from PDB  Type:PROTEIN  Length:110
                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee......ee.hhhhhhhhhhhhhh...ee......ee.hhhhhhhhhhhhhh...ee......ee.hhhhhhhhhhhhhh...ee......ee.hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 5ei9 F 717 KPYVCRECGRGFSNKSHLLRHQRTHTGEKPYVCRECGRGFRDKSHLLRHQRTHTGEKPYVCRECGRGFRDKSNLLSHQRTHTGEKPYVCRECGRGFSNKSHLLRHQRTHT 826
                                   726       736       746       756       766       776       786       796       806       816       826
   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 5EI9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5EI9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5EI9)

(-) Gene Ontology  (16, 16)

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 Related Entries

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

UniProtKB/Swiss-Prot
        PRDM9_HUMAN | Q9NQV7: 4ijd 5egb 5eh2

(-) Related Entries Specified in the PDB File

5egb 5eh2