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(-) Description

Title :  HISTONE H3 RECOGNITION AND PRESENTATION BY THE WDR5 MODULE OF THE MLL1 COMPLEX
 
Authors :  A. J. Ruthenburg, W. -K. Wang, D. M. Graybosch, H. Li, C. D. Allis, D. J. Pa G. L. Verdine
Date :  01 Jun 06  (Deposition) - 04 Jul 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.87
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Wdr5 Wd40 Wd-Repeat Histone H3 Modification Mll Set Chromatin, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. J. Ruthenburg, W. -K. Wang, D. M. Graybosch, H. Li, C. D. Allis, D. J. Patel, G. L. Verdine
Histone H3 Recognition And Presentation By The Wdr5 Module Of The Mll1 Complex.
Nat. Struct. Mol. Biol. V. 13 704 2006
PubMed-ID: 16829959  |  Reference-DOI: 10.1038/NSMB1119

(-) Compounds

Molecule 1 - WD-REPEAT PROTEIN 5
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPMCSG7-PET BASED
    Expression System StrainROSETTA 2 (DE3) PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES 23-334
    GeneWDR5, BIG3
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymBMP2-INDUCED 3-KB GENE PROTEIN
 
Molecule 2 - HISTONE H3 K4-ME3 9-RESIDUE PEPTIDE
    ChainsC, D
    EngineeredYES
    Other DetailsTHE PEPTIDE WAS CHEMICALLY SYNTHESIZED USING SOLID PHASE SYNTHESIS
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A C 
Biological Unit 2 (1x) B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1M3L2Mod. Amino AcidN-TRIMETHYLLYSINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1M3L1Mod. Amino AcidN-TRIMETHYLLYSINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1M3L1Mod. Amino AcidN-TRIMETHYLLYSINE

(-) Sites  (0, 0)

(no "Site" information available for 2H6Q)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2H6Q)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2H6Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2H6Q)

(-) PROSITE Motifs  (1, 8)

Asymmetric Unit (1, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1WD_REPEATS_1PS00678 Trp-Asp (WD) repeats signature.WDR5_HUMAN102-116
 
144-158
 
186-200
 
274-288
 
  8A:102-116
B:102-116
A:144-158
B:144-158
A:186-200
B:186-200
A:274-288
B:274-288
Biological Unit 1 (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
-
Biological Unit 2 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1WD_REPEATS_1PS00678 Trp-Asp (WD) repeats signature.WDR5_HUMAN102-116
 
144-158
 
186-200
 
274-288
 
  4-
B:102-116
-
B:144-158
-
B:186-200
-
B:274-288

(-) Exons   (12, 24)

Asymmetric Unit (12, 24)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003586251ENSE00001422154chr9:137001210-137001322113WDR5_HUMAN-00--
1.2bENST000003586252bENSE00001399325chr9:137004942-137005080139WDR5_HUMAN1-27270--
1.3ENST000003586253ENSE00001378987chr9:137005825-137005933109WDR5_HUMAN28-64372A:31-64
B:31-64
34
34
1.4ENST000003586254ENSE00001370072chr9:137006632-13700670574WDR5_HUMAN64-88252A:64-88
B:64-88
25
25
1.5ENST000003586255ENSE00001422107chr9:137007071-13700716090WDR5_HUMAN89-118302A:89-118
B:89-118
30
30
1.6ENST000003586256ENSE00001415339chr9:137007455-13700754490WDR5_HUMAN119-148302A:119-148
B:119-148
30
30
1.7ENST000003586257ENSE00001416091chr9:137007758-13700784184WDR5_HUMAN149-176282A:149-176
B:149-176
28
28
1.8ENST000003586258ENSE00001401373chr9:137013410-13701346556WDR5_HUMAN177-195192A:177-195
B:177-195
19
19
1.9ENST000003586259ENSE00001430459chr9:137017105-13701715147WDR5_HUMAN195-211172A:195-211
B:195-211
17
17
1.10ENST0000035862510ENSE00001411527chr9:137019588-13701966376WDR5_HUMAN211-236262A:211-236
B:211-236
26
26
1.11ENST0000035862511ENSE00001429531chr9:137020462-13702049534WDR5_HUMAN236-247122A:236-247
B:236-247
12
12
1.12ENST0000035862512ENSE00001431152chr9:137020815-13702088975WDR5_HUMAN248-272252A:248-272
B:248-272
25
25
1.13ENST0000035862513ENSE00001417345chr9:137021628-13702171588WDR5_HUMAN273-302302A:273-302
B:273-302
30
30
1.14aENST0000035862514aENSE00001833493chr9:137023015-1370250902076WDR5_HUMAN302-334332A:302-334
B:302-334
33
33

(-) 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:304
 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 d2h6qa_ A: automated matches                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee......eeeeee.....eeeeee...eeeeee.....eeeeee.....eeeeee.....eeeeee...eeeeee.....eeeeee.....eeeeee.....eeeeee....eeeee.....eeeee......eeeeee.....eeeeee....eeeee.....eeeee.......eeeeee.....eeeeee...eeeeee....eeeeeee..........eeee.....eeee......eeeee.....eeeee......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:211-236 -----------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)
                 2h6q A  31 VKPNYALKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIWGAYDGKFEKTISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSGKCLKTLKGHSNYVFCCNFNPQSNLIVSGSFDESVRIWDVKTGKCLKTLPAHSDPVSAVHFNRDGSLIVSSSYDGLCRIWDTASGQCLKTLIDDDNPPVSFVKFSPNGKYILAATLDNTLKLWDYSKGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLVYIWNLQTKEIVQKLQGHTDVVISTACHPTENIIASAALENDKTIKLWKSDC 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    

Chain B from PDB  Type:PROTEIN  Length:304
 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 d2h6qb_ B: automated matches                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee......eeeeee.....eeeeee....eeeee.....eeeee......eeeeee.....eeeeee...eeeeee.....eeeeee.....eeeeee.....eeeeee....eeeee.....eeeee......eeeeee.....eeeeee....eeeee.....eeeee.......eeeeee......eeeee...eeeeee....eeeeeee..........eeee.....eeee......eeeee.....eeeee......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: B:31-64            ------------------------Exon 1.5  PDB: B:89-118       Exon 1.6  PDB: B:119-148      Exon 1.7  PDB: B:149-176    Exon 1.8           ---------------Exon 1.10  PDB: B:211-236 -----------Exon 1.12  PDB: B:248-272Exon 1.13  PDB: B:273-302     -------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------Exon 1.4  PDB: B:64-88   ----------------------------------------------------------------------------------------------------------Exon 1.9         ------------------------Exon 1.11   ------------------------------------------------------Exon 1.14a  PDB: B:302-334        Transcript 1 (2)
                 2h6q B  31 VKPNYALKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIWGAYDGKFEKTISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSGKCLKTLKGHSNYVFCCNFNPQSNLIVSGSFDESVRIWDVKTGKCLKTLPAHSDPVSAVHFNRDGSLIVSSSYDGLCRIWDTASGQCLKTLIDDDNPPVSFVKFSPNGKYILAATLDNTLKLWDYSKGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLVYIWNLQTKEIVQKLQGHTDVVISTACHPTENIIASAALENDKTIKLWKSDC 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    

Chain C 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
                 2h6q C   1 ARTkQTA   7
                               |   
                               4-M3L

Chain D 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
                 2h6q D   1 ARTkQTA   7
                               |   
                               4-M3L

   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, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2H6Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2H6Q)

(-) Gene Ontology  (26, 26)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        WDR5_HUMAN | P619642cnx 2co0 2g99 2g9a 2gnq 2h13 2h14 2h68 2h6k 2h6n 2h9l 2h9m 2h9n 2h9p 2o9k 3eg6 3emh 3mxx 3n0d 3n0e 3p4f 3psl 3smr 3ur4 3uvk 3uvl 3uvm 3uvn 3uvo 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

2cnx WDR5 WITH HISTONE H3 DIMETHYLATED AT K4, COMPLEX II
2co0 WDR5 WITH UNMODIFIED HISTONE H3
2h68 APO-WDR5
2h6k WDR5 WITH HISTONE H3 MONOMETHYLATED AT K4
2h6n WDR5 WITH HISTONE H3 DIMETHYLATED AT K4, COMPLEX I