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(-) Description

Title :  CRYSTAL STRUCTURE OF WDR5 IN COMPLEX WITH THE WDR5-INTERACTING MOTIF OF SET1B
 
Authors :  P. Zhang, H. Lee, J. S. Brunzelle, J. -F. Couture
Date :  30 Nov 11  (Deposition) - 14 Dec 11  (Release) - 30 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Trithorax, Chromatin Biology, Beta-Propeller, Scaffolding, Histone H3, Nucleus, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Zhang, H. Lee, J. S. Brunzelle, J. F. Couture
The Plasticity Of Wdr5 Peptide-Binding Cleft Enables The Binding Of The Set1 Family Of Histone Methyltransferases.
Nucleic Acids Res. V. 40 4237 2012
PubMed-ID: 22266653  |  Reference-DOI: 10.1093/NAR/GKR1235

(-) Compounds

Molecule 1 - WD REPEAT-CONTAINING PROTEIN 5
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 21-334
    GeneWDR5, BIG3
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymWDR5, BMP2-INDUCED 3-KB GENE PROTEIN
 
Molecule 2 - HISTONE-LYSINE N-METHYLTRANSFERASE SETD1B
    ChainsB
    EC Number2.1.1.43
    EngineeredYES
    FragmentWDR5-INTERACTING MOTIF (UNP RESIDUES 1702-1712)
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymLYSINE N-METHYLTRANSFERASE 2G, SET DOMAIN-CONTAINING PROTEIN 1B, HSET1B
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 3UVO)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3UVO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3UVO)

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1WD_REPEATS_1PS00678 Trp-Asp (WD) repeats signature.WDR5_HUMAN102-116
144-158
186-200
274-288
  4A:102-116
A:144-158
A:186-200
A:274-288

(-) Exons   (12, 12)

Asymmetric/Biological Unit (12, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003586251ENSE00001422154chr9:137001210-137001322113WDR5_HUMAN-00--
1.2bENST000003586252bENSE00001399325chr9:137004942-137005080139WDR5_HUMAN1-27270--
1.3ENST000003586253ENSE00001378987chr9:137005825-137005933109WDR5_HUMAN28-64371A:31-6434
1.4ENST000003586254ENSE00001370072chr9:137006632-13700670574WDR5_HUMAN64-88251A:64-8825
1.5ENST000003586255ENSE00001422107chr9:137007071-13700716090WDR5_HUMAN89-118301A:89-11830
1.6ENST000003586256ENSE00001415339chr9:137007455-13700754490WDR5_HUMAN119-148301A:119-14830
1.7ENST000003586257ENSE00001416091chr9:137007758-13700784184WDR5_HUMAN149-176281A:149-17628
1.8ENST000003586258ENSE00001401373chr9:137013410-13701346556WDR5_HUMAN177-195191A:177-19519
1.9ENST000003586259ENSE00001430459chr9:137017105-13701715147WDR5_HUMAN195-211171A:195-21016
1.10ENST0000035862510ENSE00001411527chr9:137019588-13701966376WDR5_HUMAN211-236261A:215-23622
1.11ENST0000035862511ENSE00001429531chr9:137020462-13702049534WDR5_HUMAN236-247121A:236-24712
1.12ENST0000035862512ENSE00001431152chr9:137020815-13702088975WDR5_HUMAN248-272251A:248-27225
1.13ENST0000035862513ENSE00001417345chr9:137021628-13702171588WDR5_HUMAN273-302301A:273-30230
1.14aENST0000035862514aENSE00001833493chr9:137023015-1370250902076WDR5_HUMAN302-334331A:302-33433

(-) Sequences/Alignments

Asymmetric/Biological 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:300
 aligned with WDR5_HUMAN | P61964 from UniProtKB/Swiss-Prot  Length:334

    Alignment length:304
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330    
          WDR5_HUMAN     31 VKPNYALKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIWGAYDGKFEKTISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSGKCLKTLKGHSNYVFCCNFNPQSNLIVSGSFDESVRIWDVKTGKCLKTLPAHSDPVSAVHFNRDGSLIVSSSYDGLCRIWDTASGQCLKTLIDDDNPPVSFVKFSPNGKYILAATLDNTLKLWDYSKGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLVYIWNLQTKEIVQKLQGHTDVVISTACHPTENIIASAALENDKTIKLWKSDC  334
               SCOP domains d3uvoa_ A: automated matches                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee......eeeeee.....eeeeee....eeeee.....eeeee......eeeeee.....eeeeee....eeeee.....eeeee......eeeeee.....eeeeee....eeeee.....eeeee......eeeeee.....eeeeee....eeeee.....eeeee.----..eeeeee......eeeee...eeeeee....eeeeee...........eeee.....eeee.....eeeeee.....eeeeee.....eeeeee.....eeeeee......eeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------WD_REPEATS_1   ---------------------------WD_REPEATS_1   ---------------------------WD_REPEATS_1   -------------------------------------------------------------------------WD_REPEATS_1   ---------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: A:31-64            ------------------------Exon 1.5  PDB: A:89-118       Exon 1.6  PDB: A:119-148      Exon 1.7  PDB: A:149-176    Exon 1.8           ---------------Exon 1.10  PDB: A:215-236 -----------Exon 1.12  PDB: A:248-272Exon 1.13  PDB: A:273-302     -------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------Exon 1.4  PDB: A:64-88   ----------------------------------------------------------------------------------------------------------Exon 1.9         ------------------------Exon 1.11   ------------------------------------------------------Exon 1.14a  PDB: A:302-334        Transcript 1 (2)
                3uvo A   31 VKPNYALKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIWGAYDGKFEKTISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSGKCLKTLKGHSNYVFCCNFNPQSNLIVSGSFDESVRIWDVKTGKCLKTLPAHSDPVSAVHFNRDGSLIVSSSYDGLCRIWDTASGQCLKTLI----PPVSFVKFSPNGKYILAATLDNTLKLWDYSKGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLVYIWNLQTKEIVQKLQGHTDVVISTACHPTENIIASAALENDKTIKLWKSDC  334
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210    |  220       230       240       250       260       270       280       290       300       310       320       330    
                                                                                                                                                                                                             210  215                                                                                                                       

Chain B from PDB  Type:PROTEIN  Length:9
 aligned with SET1B_HUMAN | Q9UPS6 from UniProtKB/Swiss-Prot  Length:1966

    Alignment length:9
         SET1B_HUMAN   1746 CARSEGFYT 1754
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author .hhhhh... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                3uvo B 1883 CARSEGFYT 1891

   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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (35, 45)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (WDR5_HUMAN | P61964)
molecular function
    GO:0046972    histone acetyltransferase activity (H4-K16 specific)    Catalysis of the reaction: acetyl-CoA + histone H4 L-lysine (position 16) = CoA + histone H4 N6-acetyl-L-lysine (position 16). This reaction represents the addition of an acetyl group to the lysine at position 16 of histone H4.
    GO:0043995    histone acetyltransferase activity (H4-K5 specific)    Catalysis of the reaction: acetyl-CoA + histone H4 L-lysine (position 5) = CoA + histone H4 N6-acetyl-L-lysine (position 5).
    GO:0043996    histone acetyltransferase activity (H4-K8 specific)    Catalysis of the reaction: acetyl-CoA + histone H4 L-lysine (position 8) = CoA + histone H4 N6-acetyl-L-lysine (position 8).
    GO:0042800    histone methyltransferase activity (H3-K4 specific)    Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 4) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 4). This reaction is the addition of a methyl group onto lysine at position 4 of the histone H3 protein.
    GO:0018024    histone-lysine N-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + histone L-lysine = S-adenosyl-L-homocysteine + histone N6-methyl-L-lysine. The methylation of peptidyl-lysine in histones forms N6-methyl-L-lysine, N6,N6-dimethyl-L-lysine and N6,N6,N6-trimethyl-L-lysine derivatives.
    GO:0035064    methylated histone binding    Interacting selectively and non-covalently with a histone in which a residue has been modified by methylation. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes.
    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).
biological process
    GO:0043966    histone H3 acetylation    The modification of histone H3 by the addition of an acetyl group.
    GO:0051568    histone H3-K4 methylation    The modification of histone H3 by addition of one or more methyl groups to lysine at position 4 of the histone.
    GO:0043984    histone H4-K16 acetylation    The modification of histone H4 by the addition of an acetyl group to a lysine residue at position 16 of the histone.
    GO:0043981    histone H4-K5 acetylation    The modification of histone H4 by the addition of an acetyl group to a lysine residue at position 5 of the histone.
    GO:0043982    histone H4-K8 acetylation    The modification of histone H4 by the addition of an acetyl group to a lysine residue at position 8 of the histone.
    GO:0031175    neuron projection development    The process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
    GO:0035948    positive regulation of gluconeogenesis by positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of gluconeogenesis by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0001501    skeletal system development    The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton).
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005671    Ada2/Gcn5/Ada3 transcription activator complex    A multiprotein complex that possesses histone acetyltransferase and is involved in regulation of transcription. Contains either GCN5 or PCAF in a mutually exclusive manner. The budding yeast complex includes Gcn5p, two proteins of the Ada family, and two TBP-associate proteins (TAFs); analogous complexes in other species have analogous compositions, and usually contain homologs of the yeast proteins. Both ATAC- or SAGA (see GO:0000124, SAGA complex) are involved in the acetylation of histone H3K9 and K14 residues.
    GO:0071339    MLL1 complex    A protein complex that can methylate lysine-4 of histone H3. MLL1/MLL is the catalytic methyltransferase subunit, and the complex also contains the core components ASH2L, HCFC1/HCF1 WDR5 and RBBP5.
    GO:0044666    MLL3/4 complex    A protein complex that can methylate lysine-4 of histone H3, and which contains either of the protein subunits MLL3 or MLL4 in mammals, or equivalent in other species.
    GO:0048188    Set1C/COMPASS complex    A conserved protein complex that catalyzes methylation of histone H3. In Saccharomyces the complex contains Shg1p, Sdc1p, Swd1p, Swd2p, Swd3p, Spp1p, Bre2p, and the trithorax-related Set1p; in mammals it contains the catalytic subunit (SETD1A or SETD1B), WDR5, WDR82, RBBP5, ASH2L/ASH2, CXXC1/CFP1, HCFC1 and DPY30.
    GO:0000123    histone acetyltransferase complex    A protein complex that possesses histone acetyltransferase activity.
    GO:0035097    histone methyltransferase complex    A multimeric complex that is able to catalyze the addition of methyl groups to histone proteins.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    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.

Chain B   (SET1B_HUMAN | Q9UPS6)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0042800    histone methyltransferase activity (H3-K4 specific)    Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 4) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 4). This reaction is the addition of a methyl group onto lysine at position 4 of the histone H3 protein.
    GO:0018024    histone-lysine N-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + histone L-lysine = S-adenosyl-L-homocysteine + histone N6-methyl-L-lysine. The methylation of peptidyl-lysine in histones forms N6-methyl-L-lysine, N6,N6-dimethyl-L-lysine and N6,N6,N6-trimethyl-L-lysine derivatives.
    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:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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: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:0051568    histone H3-K4 methylation    The modification of histone H3 by addition of one or more methyl groups to lysine at position 4 of the histone.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    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:0048188    Set1C/COMPASS complex    A conserved protein complex that catalyzes methylation of histone H3. In Saccharomyces the complex contains Shg1p, Sdc1p, Swd1p, Swd2p, Swd3p, Spp1p, Bre2p, and the trithorax-related Set1p; in mammals it contains the catalytic subunit (SETD1A or SETD1B), WDR5, WDR82, RBBP5, ASH2L/ASH2, CXXC1/CFP1, HCFC1 and DPY30.
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0035097    histone methyltransferase complex    A multimeric complex that is able to catalyze the addition of methyl groups to histone proteins.
    GO:0016607    nuclear speck    A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        SET1B_HUMAN | Q9UPS64es0
        WDR5_HUMAN | P619642cnx 2co0 2g99 2g9a 2gnq 2h13 2h14 2h68 2h6k 2h6n 2h6q 2h9l 2h9m 2h9n 2h9p 2o9k 3eg6 3emh 3mxx 3n0d 3n0e 3p4f 3psl 3smr 3ur4 3uvk 3uvl 3uvm 3uvn 4a7j 4cy1 4cy2 4erq 4ery 4erz 4es0 4esg 4ewr 4gm3 4gm8 4gm9 4gmb 4ia9 4o45 4ql1 4qqe 4y7r 5eal 5eam 5eap 5ear 5m23 5m25 5sxm 5vfc

(-) Related Entries Specified in the PDB File

3uvk CRYSTAL STRUCTURE OF WDR5 IN COMPLEX WITH THE WDR5- INTERACTING MOTIF OF MLL2
3uvl CRYSTAL STRUCTURE OF WDR5 IN COMPLEX WITH THE WDR5- INTERACTING MOTIF OF MLL3
3uvm CRYSTAL STRUCTURE OF WDR5 IN COMPLEX WITH THE WDR5- INTERACTING MOTIF OF MLL4
3uvn CRYSTAL STRUCTURE OF WDR5 IN COMPLEX WITH THE WDR5- INTERACTING MOTIF OF SET1A