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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN NRMT1 IN COMPLEX WITH ALPHA-N-DIMETHYLATED HUMAN CENP-A PEPTIDE
 
Authors :  R. Wu, H. Li
Date :  26 Jul 15  (Deposition) - 25 Nov 15  (Release) - 02 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym. Unit :  A,B,D,E
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,E  (1x)
Keywords :  Alpha-N-Methyltransferase, Histone Methylation, Sam-Mtase, Cenp-A, Transferase-Peptide Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Wu, Y. Yue, X. Zheng, H. Li
Molecular Basis For Histone N-Terminal Methylation By Nrmt1
Genes Dev. V. 29 2337 2015
PubMed-ID: 26543159  |  Reference-DOI: 10.1101/GAD.270926.115

(-) Compounds

Molecule 1 - N-TERMINAL XAA-PRO-LYS N-METHYLTRANSFERASE 1
    Chains: A, B
    EC Number: 2.1.1.244
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: NTMT1, NRMT1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ALPHA N-TERMINAL PROTEIN METHYLTRANSFERASE 1A, METHYLTRANSFERASE-LIKE PROTEIN 11A,N-TERMINAL RCC1 METHYLTRANSFERASE, X-PRO-LYS N-TERMINAL PROTEIN METHYLTRANSFERASE 1A,NTM1A
 
Molecule 2 - N-TEMINAL PEPTIDE FROM HISTONE H3-LIKE CENTROMERIC PROTEIN A
    Chains: D, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: UNP RESIDUES 2-10
    Gene: CENPA
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CENTROMERE AUTOANTIGEN A,CENTROMERE PROTEIN A,CENP-A

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABDE
Biological Unit 1 (1x): A D 
Biological Unit 2 (1x):  B E

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1DMG2Mod. Amino AcidN,N-DIMETHYLGLYCINE
2SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1DMG1Mod. Amino AcidN,N-DIMETHYLGLYCINE
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1DMG1Mod. Amino AcidN,N-DIMETHYLGLYCINE
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:20 , MET A:30 , GLY A:69 , GLY A:71 , ARG A:74 , ILE A:75 , ASP A:91 , ILE A:92 , THR A:93 , PHE A:96 , CYS A:117 , GLY A:118 , LEU A:119 , GLN A:120 , GLN A:135 , TRP A:136 , VAL A:137 , HIS A:140 , HOH A:435 , HOH A:530 , HOH A:574 , DMG D:1binding site for residue SAH A 301
2AC2SOFTWARETRP B:20 , MET B:30 , GLY B:69 , GLY B:71 , ARG B:74 , ILE B:75 , ASP B:91 , ILE B:92 , THR B:93 , PHE B:96 , GLY B:118 , LEU B:119 , GLN B:120 , GLN B:135 , TRP B:136 , VAL B:137 , HIS B:140 , HOH B:428 , HOH B:511 , HOH B:557 , DMG E:1binding site for residue SAH B 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5CVD)

(-) 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:231
                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhh..hhhhhhhhhhhhhhh...hhhhhh..hhhhhhhhhhhhhhhhhhhhhh........eeeee....hhhhhhh......eeeeee.hhhhhhhhhhhhhhhhh.eeeeee.hhhhh......eeeeeee.hhhhhhhhhhhhhhhhhhhheeeeeeeeeeeeee...eeee....eeeeehhhhhhhhhhh..eeeeeee.........eeeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cvd A  -7 GLVPRGSHMTSEVIEDEKQFYSKAKTYWKQIPPTVDGMLGGYGHISSIDINSSRKFLQRFLREGPNKTGTSCALDCGAGIGRITKRLLLPLFREVDMVDITEDFLVQAKTYLGEEGKRVRNYFCCGLQDFTPEPDSYDVIWIQWVIGHLTDQHLAEFLRRCKGSLRPNGIIVIKDNMAQEGVILDDVDSSVCRDLDVVRRIICSAGLSLLAEERQENLPDEIYHVYSFALR 223
                                     2        12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222 


Chain B from PDB  Type:PROTEIN  Length:226
                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh..hhhhhhhhhhhhhhh...hhhhhh..hhhhhhhhhhhhhhhhhhhhh.........eeeee....hhhhhhh......eeeeee.hhhhhhhhhhhhhhhhh.eeeeee.hhhhh......eeeeeee.hhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeee....eeee....eeeehhhhhhhhhhhh..eeeeeee.........eeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cvd B  -2 GSHMTSEVIEDEKQFYSKAKTYWKQIPPTVDGMLGGYGHISSIDINSSRKFLQRFLREGPNKTGTSCALDCGAGIGRITKRLLLPLFREVDMVDITEDFLVQAKTYLGEEGKRVRNYFCCGLQDFTPEPDSYDVIWIQWVIGHLTDQHLAEFLRRCKGSLRPNGIIVIKDNMAQEGVILDDVDSSVCRDLDVVRRIICSAGLSLLAEERQENLPDEIYHVYSFALR 223
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217      


Chain D from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 5cvd D   1 gPRRRS   6
                            |     
                            1-DMG 


Chain E from PDB  Type:PROTEIN  Length:7
                                       
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 5cvd E   1 gPRRRSR   7
                            |      
                            1-DMG
   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 5CVD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (35, 37)

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  NTM1A_HUMAN | Q9BV86
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 Related Entries

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

UniProtKB/Swiss-Prot
        CENPA_HUMAN | P49450: 3an2 3nqj 3nqu 3r45 3wtp
        NTM1A_HUMAN | Q9BV86: 2ex4 5cve 5e1b 5e1d 5e1m 5e1o 5e2a 5e2b

(-) Related Entries Specified in the PDB File

5cve