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(-) Description

Title :  CRYSTAL STRUCTURE OF METHYLTRANSFERASE DOMAIN OF HUMAN PR DOMAIN-CONTAINING PROTEIN 9
 
Authors :  A. Dong, L. Dombrovski, Y. Li, W. Tempel, C. Bountra, C. H. Arrowsmith, A. M. Edwards, P. J. Brown, H. Wu, Structural Genomics Consortium (
Date :  21 Dec 12  (Deposition) - 13 Feb 13  (Release) - 13 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Prdm9, Methyltransferase, Structural Genomics, Structural Genomics Consortium, Sgc, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Dombrovski, A. Dong, Y. Li, W. Tempel, C. Bountra, C. H. Arrowsmith, A. M. Edwards, P. J. Brown, H. Wu, Structural Genomics Consortium (Sgc)
Crystal Structure Of Methyltransferase Domain Of Human Pr Domain-Containing Protein 9
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HISTONE-LYSINE N-METHYLTRANSFERASE PRDM9
    Chains: A, B
    EC Number: 2.1.1.43
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28-MHL
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 195-415
    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

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 34)

Asymmetric Unit (3, 34)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2UNX24Ligand/IonUNKNOWN ATOM OR ION
3ZN4Ligand/IonZINC ION
Biological Unit 1 (2, 19)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
2UNX16Ligand/IonUNKNOWN ATOM OR ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 11)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
2UNX8Ligand/IonUNKNOWN ATOM OR ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:205 , CYS A:208 , CYS A:216 , HIS A:219BINDING SITE FOR RESIDUE ZN A 501
2AC2SOFTWARECYS A:390 , CYS A:393 , HIS A:406 , HIS A:411BINDING SITE FOR RESIDUE ZN A 502
3AC3SOFTWARECYS B:205 , CYS B:208 , CYS B:216 , HIS B:219BINDING SITE FOR RESIDUE ZN B 501
4AC4SOFTWARECYS B:390 , CYS B:393 , HIS B:406 , HIS B:411BINDING SITE FOR RESIDUE ZN B 502

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:351 -A:394
2B:351 -B:394

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:274 -Pro A:275
2Gly B:274 -Pro B:275

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4IJD)

(-) 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:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhheee....eee...........ee..........hhhhhh....eeeee.......eeeee.........ee.....eee.hhhhh....eeeeeee..eeeeee.......hhhhhhee........eeeeee..eeeeee..........eee....hhhhhhhh...hhhhhhh.....ee......ee.hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ijd A 195 SEPQDDDYLYCEmCQNFFIDSCAAHGPPTFVKDSAVDKGHPNRSALSLPPGLRIGPSGIPQAGLGVWNEASDLPLGLHFGPYEGRITEDEEAANNGYSWLITKGRNCYEYVDGKDKSWANWmRYVNCARDDEEQNLVAFQYHRQIFYRTCRVIRPGCELLVWYGDEYGQELGIKWGSKWKKELmPKPEIHPCPSCCLAFSSQKFLSQHVERNHSS 413
                                   204  |    214       224       234       244       254       264       274       284       294       304       314 |     324       334       344       354       364       374   ||  388       398       408     
                                      207-MSE                                                                                                      316-MSE                                                       378-MSE                           
                                                                                                                                                                                                                  383                              


Chain B from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhheee....eee...........ee..........hhhhhhh...eeeee.......eeeee.........ee.....eee.hhhhh....eeeee.....eeeee..hhhhhhhhhhhee........eeeeee..eeeeee..........eee....hhhhhhhh...hhhhhhh.......ee......ee.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ijd B 195 SEPQDDDYLYCEmCQNFFIDSCAAHGPPTFVKDSAVDKGHPNRSALSLPPGLRIGPSGIPQAGLGVWNEASDLPLGLHFGPYEGRITEDEEAANNGYSWLITKGRNCYEYVDGKDKSWANWmRYVNCARDDEEQNLVAFQYHRQIFYRTCRVIRPGCELLVWYGDEYGQELGIKWGSKWKKELmREPKPEIHPCPSCCLAFSSQKFLSQHVERNH 411
                                   204  |    214       224       234       244       254       264       274       284       294       304       314 |     324       334       344       354       364       374   ||  386       396       406     
                                      207-MSE                                                                                                      316-MSE                                                       378-MSE                           
                                                                                                                                                                                                                  381
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  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 4IJD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)

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  PRDM9_HUMAN | Q9NQV7
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 Related Entries

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        PRDM9_HUMAN | Q9NQV7: 5egb 5eh2 5ei9

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