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(-) Description

Title :  CRYSTAL STRUCTURE OF M. MUSCULUS PROTEIN ARGININE METHYLTRANSFERASE PRMT6 WITH CACL2 AT 1.34 ANGSTROMS
 
Authors :  L. Bonnefond, V. Cura, N. Troffer-Charlier, J. Mailliot, J. M. Wurtz, J. Cavarelli
Date :  31 Jul 13  (Deposition) - 30 Jul 14  (Release) - 12 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.34
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Transferase, S-Adenosyl-L-Methionine (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Bonnefond, J. Stojko, J. Mailliot, N. Troffer-Charlier, V. Cura, J. M. Wurtz, S. Cianferani, J. Cavarelli
Functional Insights From High Resolution Structures Of Mouse Protein Arginine Methyltransferase 6.
J. Struct. Biol. V. 191 175 2015
PubMed-ID: 26094878  |  Reference-DOI: 10.1016/J.JSB.2015.06.017

(-) Compounds

Molecule 1 - PROTEIN ARGININE N-METHYLTRANSFERASE 6
    ChainsA
    EC Number2.1.1.-, 2.1.1.125
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymHISTONE-ARGININE N-METHYLTRANSFERASE PRMT6

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2CA5Ligand/IonCALCIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
11PE2Ligand/IonPENTAETHYLENE GLYCOL
2CA-1Ligand/IonCALCIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:81 , GLN A:105 , SER A:117 , ALA A:118 , GLU A:144BINDING SITE FOR RESIDUE 1PE A1378
2AC2SOFTWAREGLU A:158 , MET A:160 , HOH A:2019 , HOH A:2125 , HOH A:2126 , HOH A:2129BINDING SITE FOR RESIDUE CA A1379
3AC3SOFTWAREGLY A:275 , HOH A:2162 , HOH A:2228 , HOH A:2236 , HOH A:2241 , HOH A:2242BINDING SITE FOR RESIDUE CA A1380
4AC4SOFTWAREARG A:255 , HOH A:2223 , HOH A:2224 , HOH A:2225 , HOH A:2226 , HOH A:2229BINDING SITE FOR RESIDUE CA A1381
5AC5SOFTWAREGLU A:167 , HOH A:2137 , HOH A:2141 , HOH A:2143 , HOH A:2144BINDING SITE FOR RESIDUE CA A1382
6AC6SOFTWAREGLN A:242 , ASP A:243 , HOH A:2199 , HOH A:2200 , HOH A:2203BINDING SITE FOR RESIDUE CA A1383

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:53 -A:232

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Leu A:188 -Pro A:189

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4C08)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4C08)

(-) Exons   (0, 0)

(no "Exon" information available for 4C08)

(-) 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:325
 aligned with ANM6_MOUSE | Q6NZB1 from UniProtKB/Swiss-Prot  Length:378

    Alignment length:328
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368        
           ANM6_MOUSE    49 LYYECYSDVSVHEEMIADQVRTEAYRLGILKNWAALRGKTVLDVGAGTGILSIFCAQAGARRVYAVEASAIWQQAREVVRLNGLEDRVHVLPGPVETVELPERVDAIVSEWMGYGLLHESMLSSVLHARTKWLKEGGLLLPASAELFVAPISDQMLEWRLGFWSQVKQHYGVDMSCMESFATRCLMGHSEIVVQDLSGEDVLARPQRFAQLELARAGLEQELEAGVGGRFRCSCYGSAPLHGFAVWFQVTFPGGDSEKPLVLSTSPFHPATHWKQALLYLNEPVPVEQDTDISGEITLLPSPDNPRRLRILLRYKVGDHEEKTKDFAM 376
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhh...eeeeee...hhhhhhhhhhhh.....eeeee...........eeeee............hhhhhhhhhhhheeeeeeee..eeeeeeeee.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh....eee..hhhh.....eeeeeee....hhhhhhhhheeeeeeee....eeeeeeeeeeeeee...---..eeee...........eeeeeeeeeeee....eeeeeeeeeee..eeeeeeeeeeeee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c08 A  49 LYYECYSDVSVHEEMIADQVRTEAYRLGILKNWAALRGKTVLDVGAGTGILSIFCAQAGARRVYAVEASAIWQQAREVVRLNGLEDRVHVLPGPVETVELPERVDAIVSEWMGYGLLHESMLSSVLHARTKWLKEGGLLLPASAELFVAPISDQMLEWRLGFWSQVKQHYGVDMSCMESFATRCLMGHSEIVVQDLSGEDVLARPQRFAQLELARAGLEQELEAGVGGRFRCSCYGSAPLHGFAVWFQVTFPGG---KPLVLSTSPLHPATHWKQALLYLNEPVPVEQDTDISGEITLLPSPDNPRRLRILLRYKVGDHEEKTKDFAM 376
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298   |   308       318       328       338       348       358       368        
                                                                                                                                                                                                                                                                                       302 306                                                                      

   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 4C08)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4C08)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4C08)

(-) Gene Ontology  (28, 28)

Asymmetric Unit(hide GO term definitions)
Chain A   (ANM6_MOUSE | Q6NZB1)
molecular function
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    GO:0042393    histone binding    Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
    GO:0042054    histone methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + histone = S-adenosyl-L-homocysteine + methyl-histone. Histone methylation generally occurs on either an arginine or lysine residue.
    GO:0070612    histone methyltransferase activity (H2A-R3 specific)    Catalysis of the reaction: S-adenosyl-L-methionine + (histone H2A)-arginine (position 3) = S-adenosyl-L-homocysteine + (histone H2A)-N-methyl-arginine (position 3). This reaction is the addition of a methyl group to arginine at position 3 of histone H2A.
    GO:0070611    histone methyltransferase activity (H3-R2 specific)    Catalysis of the reaction: S-adenosyl-L-methionine + (histone H3)-arginine (position 2) = S-adenosyl-L-homocysteine + (histone H3)-N-methyl-arginine (position 2). This reaction is the addition of a methyl group to arginine at position 2 of histone H3.
    GO:0044020    histone methyltransferase activity (H4-R3 specific)    Catalysis of the reaction: S-adenosyl-L-methionine + (histone H4)-arginine (position 3) = S-adenosyl-L-homocysteine + (histone H4)-N-methyl-arginine (position 3). This reaction is the addition of a methyl group to arginine at position 3 of histone H4.
    GO:0008469    histone-arginine N-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + (histone)-arginine = S-adenosyl-L-homocysteine + (histone)-N-methyl-arginine.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0016274    protein-arginine N-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + (protein)-arginine = S-adenosyl-L-homocysteine + (protein)-N-methyl-arginine.
    GO:0035242    protein-arginine omega-N asymmetric methyltransferase activity    Catalysis of the addition of a second methyl group to methylated peptidyl-arginine. Methylation is on the same terminal nitrogen (omega nitrogen) residue that was previously methylated, resulting in asymmetrical peptidyl-N(omega),N(omega)-dimethylated arginine residues.
    GO:0035241    protein-arginine omega-N monomethyltransferase activity    Catalysis of the addition of a methyl group to either of the unmethylated terminal nitrogen atoms (also called omega nitrogen) in peptidyl-arginine to form an omega-N-G-monomethylated arginine residue. The reaction is S-adenosyl-L-methionine + [protein]-L-arginine = S-adenosyl-L-homocysteine + [protein]-Nomega-methyl-L-arginine.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0016049    cell growth    The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0090398    cellular senescence    A cell aging process stimulated in response to cellular stress, whereby normal cells lose the ability to divide through irreversible cell cycle arrest.
    GO:0034970    histone H3-R2 methylation    The modification of histone H3 by addition of a methyl group to arginine at position 2 of the histone.
    GO:0043985    histone H4-R3 methylation    The modification of histone H4 by addition of a methyl group to arginine at position 3 of the histone.
    GO:0016571    histone methylation    The modification of histones by addition of methyl groups.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0019919    peptidyl-arginine methylation, to asymmetrical-dimethyl arginine    The process of methylation of peptidyl-arginine to form peptidyl-N(omega),N(omega)-dimethyl-L-arginine.
    GO:0006479    protein methylation    The addition of a methyl group to a protein amino acid. A methyl group is derived from methane by the removal of a hydrogen atom.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ANM6_MOUSE | Q6NZB14c03 4c04 4c05 4c06 4c07 5fqn 5fqo

(-) Related Entries Specified in the PDB File

4c03 CRYSTAL STRUCTURE OF M. MUSCULUS PROTEIN ARGININE METHYLTRANSFERASE PRMT6 REDUCED
4c04 CRYSTAL STRUCTURE OF M. MUSCULUS PROTEIN ARGININE METHYLTRANSFERASE PRMT6 WITH SINEFUNGIN
4c05 CRYSTAL STRUCTURE OF M. MUSCULUS PROTEIN ARGININE METHYLTRANSFERASE PRMT6 WITH SAH
4c06 CRYSTAL STRUCTURE OF M. MUSCULUS PROTEIN ARGININE METHYLTRANSFERASE PRMT6 WITH MGCL2
4c07 CRYSTAL STRUCTURE OF M. MUSCULUS PROTEIN ARGININE METHYLTRANSFERASE PRMT6 WITH CACL2 AT 1.5 ANGSTROMS