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(-) Description

Title :  METHYLTRANSFERASE DOMAIN OF HUMAN PR DOMAIN-CONTAINING PROTEIN 1
 
Authors :  M. F. Amaya, H. Zeng, T. Antoshenko, A. Dong, P. Loppnau, C. Bountra, J. Weigelt, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, J. Min, A. N. Plotnikov, H. Wu, Structural Genomics Consortium (Sgc)
Date :  29 May 08  (Deposition) - 12 Aug 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A (1x),B (1x)
Keywords :  Methyltransferase, Prdm1, Structural Genomics, Structural Genomics Consortium, Sgc, Dna-Binding, Metal-Binding, Nucleus, Polymorphism, Repressor, Transcription, Transcription Regulation, Zinc, Zinc-Finger, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Zeng, M. F. Amaya, T. Antoshenko, A. Dong, P. Loppnau, A. Bochkarev, J. Min, A. N. Plotnikov, H. Wu
The Crystal Structure Of Methyltransferase Domain Of Human Pr Domain-Containing Protein 1
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PR DOMAIN ZINC FINGER PROTEIN 1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    GenePRDM1, BLIMP1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPR DOMAIN-CONTAINING PROTEIN 1, BETA-INTERFERON GENE POSITIVE REGULATORY DOMAIN I-BINDING FACTOR, BLIMP-1, POSITIVE REGULATORY DOMAIN I-BINDING FACTOR 1, PRDI- BINDING FACTOR 1, PRDI-BF1

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3DAL)

(-) Sites  (0, 0)

(no "Site" information available for 3DAL)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3DAL)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Pro A:29 -Trp A:30
2Gly A:77 -Pro A:78
3Gly B:77 -Pro B:78

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_024221D203EPRDM1_HUMANPolymorphism811925A/BD166E

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_024221D203EPRDM1_HUMANPolymorphism811925A/BD166E

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SETPS50280 SET domain profile.PRDM1_HUMAN84-201
 
  2A:47-164
B:47-164
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SETPS50280 SET domain profile.PRDM1_HUMAN84-201
 
  2A:47-164
B:47-164

(-) Exons   (0, 0)

(no "Exon" information available for 3DAL)

(-) 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:179
 aligned with PRDM1_HUMAN | O75626 from UniProtKB/Swiss-Prot  Length:825

    Alignment length:203
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   
          PRDM1_HUMAN    21 SSTVRFQGLAEGTKGTMKMDMEDADMTLWTEAEFEEKCTYIVNDHPWDSGADGGTSVQAEASLPRNLLFKYATNSEEVIGVMSKEYIPKGTRFGPLIGEIYTNDTVPKNANRKYFWRIYSRGELHHFIDGFNEEKSNWMRYVNPAHSPREQNLAACQNGMNIYFYTIKPIPANQELLVWYCRDFAERLHYPYPGELTMMNLTQ 223
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..-----hhhh--hh..------......hhhhhhhhh.eee......--------hhhhhh....eeeee......eeeeee.......eee.....eee......---....eeeeee..eeeeeee.......hhhhhhee........eeeeee..eeeeee..........eeeehhhhhhhh........hhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------E-------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------SET  PDB: A:47-164 UniProt: 84-201                                                                                    ---------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dal A -10 SS-----GLVP--RGSK------ADMTLWTEAEFEEKCTYIVNDHPWD--------VQAEASLPRNLLFKYATNSEEVIGVMSKEYIPKGTRFGPLIGEIYTNDTVP---NRKYFWRIYSRGELHHFIDGFNEEKSNWMRYVNPAHSPREQNLAACQNGMNIYFYTIKPIPANQELLVWYCRDFAERLHYPYPGELTMMNLTQ 186
                             |     |-6|  |  |  -   |    13        23       | -      | 43        53        63        73        83      |  -|      103       113       123       133       143       153       163       173       183   
                             |    -8 -5 -4 -1      7                      31       40                                                90  94                                                                                            
                            -9                                                                                                                                                                                                         

Chain B from PDB  Type:PROTEIN  Length:166
 aligned with PRDM1_HUMAN | O75626 from UniProtKB/Swiss-Prot  Length:825

    Alignment length:180
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223
          PRDM1_HUMAN    44 ADMTLWTEAEFEEKCTYIVNDHPWDSGADGGTSVQAEASLPRNLLFKYATNSEEVIGVMSKEYIPKGTRFGPLIGEIYTNDTVPKNANRKYFWRIYSRGELHHFIDGFNEEKSNWMRYVNPAHSPREQNLAACQNGMNIYFYTIKPIPANQELLVWYCRDFAERLHYPYPGELTMMNLTQ 223
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhh.eee....----------hhhhhh....eeeee..-...eeeeee.......eee.....eeehhhhh.---....eeeeee..eeeeeee.......hhhhhhee........eeeeee..eeeeee..........eeeehhhhhhhh........hhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------E-------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------SET  PDB: B:47-164 UniProt: 84-201                                                                                    ---------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3dal B   7 ADMTLWTEAEFEEKCTYIVNDHP----------VQAEASLPRNLLFKYAT-SEEVIGVMSKEYIPKGTRFGPLIGEIYTNDTVP---NRKYFWRIYSRGELHHFIDGFNEEKSNWMRYVNPAHSPREQNLAACQNGMNIYFYTIKPIPANQELLVWYCRDFAERLHYPYPGELTMMNLTQ 186
                                    16        26  |      -   |    46        56 |      66        76        86   |   |96       106       116       126       136       146       156       166       176       186
                                                 29         40              56 |                              90  94                                                                                            
                                                                              58                                                                                                                                

   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 3DAL)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3DAL)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DAL)

(-) Gene Ontology  (42, 42)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PRDM1_HUMAN | O75626)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000978    RNA polymerase II core promoter proximal region sequence-specific DNA binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II.
    GO:0042826    histone deacetylase binding    Interacting selectively and non-covalently with the enzyme histone deacetylase.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0001078    transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    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:0035904    aorta development    The progression of the aorta over time, from its initial formation to the mature structure. An aorta is an artery that carries blood from the heart to other parts of the body.
    GO:0048844    artery morphogenesis    The process in which the anatomical structures of arterial blood vessels are generated and organized. Arteries are blood vessels that transport blood from the heart to the body and its organs.
    GO:0003279    cardiac septum development    The progression of a cardiac septum over time, from its initial formation to the mature structure.
    GO:0045165    cell fate commitment    The commitment of cells to specific cell fates and their capacity to differentiate into particular kinds of cells. Positional information is established through protein signals that emanate from a localized source within a cell (the initial one-cell zygote) or within a developmental field.
    GO:0048869    cellular developmental process    A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition.
    GO:0060976    coronary vasculature development    The process whose specific outcome is the progression of the blood vessels of the heart over time, from its formation to the mature structure.
    GO:0001892    embryonic placenta development    The embryonically driven process whose specific outcome is the progression of the placenta over time, from its formation to the mature structure. The placenta is an organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin.
    GO:0042462    eye photoreceptor cell development    Development of a photoreceptor, a sensory cell in the eye that reacts to the presence of light. They usually contain a pigment that undergoes a chemical change when light is absorbed, thus stimulating a nerve.
    GO:0007281    germ cell development    The process whose specific outcome is the progression of an immature germ cell over time, from its formation to the mature structure (gamete). A germ cell is any reproductive cell in a multicellular organism.
    GO:0003170    heart valve development    The progression of a heart valve over time, from its formation to the mature structure. A heart valve is a structure that restricts the flow of blood to different regions of the heart and forms from an endocardial cushion.
    GO:0001701    in utero embryonic development    The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus.
    GO:0060576    intestinal epithelial cell development    The process whose specific outcome is the progression of a columnar/cuboidal epithelial cell of the intestine over time, from its formation to the mature structure.
    GO:0001893    maternal placenta development    Maternally driven process whose specific outcome is the progression of the placenta over time, from its formation to the mature structure. The placenta is an organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0001763    morphogenesis of a branching structure    The process in which the anatomical structures of branches are generated and organized. A branch is a division or offshoot from a main stem. Examples in animals would include blood vessels, nerves, lymphatics and other endothelial or epithelial tubes.
    GO:0030889    negative regulation of B cell proliferation    Any process that stops, prevents or reduces the rate or extent of B cell proliferation.
    GO:0010629    negative regulation of gene expression    Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0031665    negative regulation of lipopolysaccharide-mediated signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of signaling in response to detection of lipopolysaccharide.
    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:0045579    positive regulation of B cell differentiation    Any process that activates or increases the frequency, rate or extent of B cell differentiation.
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0009791    post-embryonic development    The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development.
    GO:0042127    regulation of cell proliferation    Any process that modulates the frequency, rate or extent of cell proliferation.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:1990654    sebum secreting cell proliferation    The multiplication or reproduction of sebocytes by cell division, resulting in the expansion of their population. A sebocyte is an epithelial cell that makes up the sebaceous glands, and secrete sebum.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0060707    trophoblast giant cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of a trophoblast giant cell of the placenta. Trophoblast giant cells are the cell of the placenta that line the maternal decidua.
    GO:0003281    ventricular septum development    The progression of the ventricular septum over time from its formation to the mature structure.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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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