2CNX - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   WDR5 AND HISTONE H3 LYSINE 4 DIMETHYL COMPLEX AT 2.1 ANGSTROM

Authors :   A. J. Ruthenburg, W. Wang, D. M. Graybosch, H. Li, C. D. Allis, D. J. Patel, G. L. Verdine

Date :   25 May 06 (Deposition) - 03 Jul 06 (Release) - 21 Dec 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym./Biol. Unit : A,P

Keywords :   Histone Presenter, Lysine Methylation, Mll1, Leukemia, Hox Gene Activation, Transcription Activation, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. J. Ruthenburg, W. 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

Molecule 1 - WD-REPEAT PROTEIN 5
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	ROSETTA 2 PLYSS
	Fragment	:	RESIDUES 20-334
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	BMP2-INDUCED 3-KB GENE PROTEIN

Molecule 2 - HISTONE H3 DIMETHYL-LYSINE 4
	Chains	:	P
	Fragment	:	HISTONE TAIL, UNP RESIDUES 2-6
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synthetic	:	YES

		1	2
Asymmetric/Biological Unit	:	A	P

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	MLY	1	Mod. Amino Acid	N-DIMETHYL-LYSINE

(no "Site" information available for 2CNX)

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

Asymmetric/Biological Unit

No.	Residues
1	Asn A:214	-	Pro A:215

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

Asymmetric/Biological Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	WD_REPEATS_1	PS00678	Trp-Asp (WD) repeats signature.	WDR5_HUMAN	102-116 144-158 186-200 274-288	4	A:102-116 A:144-158 A:186-200 A:274-288

Asymmetric/Biological Unit (12, 12)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000358625	1	ENSE00001422154	chr9:137001210-137001322	113	WDR5_HUMAN	-	0	0	-	-
1.2b	ENST00000358625	2b	ENSE00001399325	chr9:137004942-137005080	139	WDR5_HUMAN	1-27	27	0	-	-
1.3	ENST00000358625	3	ENSE00001378987	chr9:137005825-137005933	109	WDR5_HUMAN	28-64	37	1	A:29-64	36
1.4	ENST00000358625	4	ENSE00001370072	chr9:137006632-137006705	74	WDR5_HUMAN	64-88	25	1	A:64-88	25
1.5	ENST00000358625	5	ENSE00001422107	chr9:137007071-137007160	90	WDR5_HUMAN	89-118	30	1	A:89-118	30
1.6	ENST00000358625	6	ENSE00001415339	chr9:137007455-137007544	90	WDR5_HUMAN	119-148	30	1	A:119-148	30
1.7	ENST00000358625	7	ENSE00001416091	chr9:137007758-137007841	84	WDR5_HUMAN	149-176	28	1	A:149-176	28
1.8	ENST00000358625	8	ENSE00001401373	chr9:137013410-137013465	56	WDR5_HUMAN	177-195	19	1	A:177-195	19
1.9	ENST00000358625	9	ENSE00001430459	chr9:137017105-137017151	47	WDR5_HUMAN	195-211	17	1	A:195-211	17
1.10	ENST00000358625	10	ENSE00001411527	chr9:137019588-137019663	76	WDR5_HUMAN	211-236	26	1	A:211-236	26
1.11	ENST00000358625	11	ENSE00001429531	chr9:137020462-137020495	34	WDR5_HUMAN	236-247	12	1	A:236-247	12
1.12	ENST00000358625	12	ENSE00001431152	chr9:137020815-137020889	75	WDR5_HUMAN	248-272	25	1	A:248-272	25
1.13	ENST00000358625	13	ENSE00001417345	chr9:137021628-137021715	88	WDR5_HUMAN	273-302	30	1	A:273-302	30
1.14a	ENST00000358625	14a	ENSE00001833493	chr9:137023015-137025090	2076	WDR5_HUMAN	302-334	33	1	A:302-334	33

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:306
 aligned with WDR5_HUMAN | P61964 from UniProtKB/Swiss-Prot  Length:334

    Alignment length:306
                                    38        48        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      
           WDR5_HUMAN    29 TPVKPNYALKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIWGAYDGKFEKTISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSGKCLKTLKGHSNYVFCCNFNPQSNLIVSGSFDESVRIWDVKTGKCLKTLPAHSDPVSAVHFNRDGSLIVSSSYDGLCRIWDTASGQCLKTLIDDDNPPVSFVKFSPNGKYILAATLDNTLKLWDYSKGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLVYIWNLQTKEIVQKLQGHTDVVISTACHPTENIIASAALENDKTIKLWKSDC 334
               SCOP domains d2cnxa_ A: automated matches                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeeee......eeeeee.....eeeeee...eeeeee.....eeeeee.....eeeeee.....eeeeee...eeeeee....eeeeeee.....eeeeee.....eeeeee....eeeee.....eeeee......eeeeee.....eeeeee....eeeee.....eeeeee......eeeeee.....eeeeee...eeeeee....eeeeee...........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:29-64 [INCOMPLETE] ------------------------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)
                 2cnx A  29 TPVKPNYALMFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIWGAYDGKFEKTISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSGKCLKTLKGHSNYVFCCNFNPQSNLIVSGSFDESVRIWDVKTGMCLKTLPAHSDPVSAVHFNRDGSLIVSSSYDGLCRIWDTASGQCLKTLIDDDNPPVSFVKFSPNGKYILAATLDNTLKLWDYSKGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNMVYIWNLQTKEIVQKLQGHTDVVISTACHPTENIIASAALENDKTIKLWKSDC 334
                                    38        48        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

Chain P from PDB  Type:PROTEIN  Length:5
 aligned with H3_YEAST | P61830 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:5
             H3_YEAST     2 ARTKQ   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
                 2cnx P   1 ARTkQ   5
                               | 
                               | 
                               4-MLY

Chain P from PDB  Type:PROTEIN  Length:5
 aligned with Q5TEC6_HUMAN | Q5TEC6 from UniProtKB/TrEMBL  Length:136

    Alignment length:5
         Q5TEC6_HUMAN     2 ARTKQ   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
                 2cnx P   1 ARTkQ   5
                               | 
                               | 
                               4-MLY

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: 7-bladed beta-propeller (245)

Superfamily: WD40 repeat-like (95)

Family: automated matches (36)

Protein domain: automated matches (36)

Human (Homo sapiens) [TaxId: 9606] (34)

d2cnxa_

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

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

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 P (H3_YEAST | P61830)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic 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:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
biological process
	GO:0006333	chromatin assembly or disassembly	The formation or destruction of chromatin structures.
	GO:0070911	global genome nucleotide-excision repair	The nucleotide-excision repair process in which DNA lesions are removed from nontranscribed strands and from transcriptionally silent regions over the entire genome.
	GO:0009303	rRNA transcription	The synthesis of ribosomal RNA (rRNA), any RNA that forms part of the ribosomal structure, from a DNA template.
	GO:0043935	sexual sporulation resulting in formation of a cellular spore	The formation of spores derived from the products of meiosis. A cellular spore is a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction.
cellular component
	GO:0043505	CENP-A containing nucleosome	A form of nucleosome located only at the centromere, in which the histone H3 is replaced by the variant form CENP-A (sometimes known as CenH3).
	GO:0005694	chromosome	A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
	GO:0000788	nuclear nucleosome	A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA in the nucleus into higher order structures.
	GO:0000786	nucleosome	A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures.
	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.
	GO:0031298	replication fork protection complex	A protein complex conserved in eukaryotes and associated with the replication fork; the complex stabilizes stalled replication forks and is thought to be involved in coordinating leading- and lagging-strand synthesis and in replication checkpoint signaling.

Chain P (Q5TEC6_HUMAN | Q5TEC6)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
cellular component
	GO:0005694	chromosome	A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
	GO:0000786	nucleosome	A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures.
	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.

Asymmetric/Biological Unit
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		Asn A:214 - Pro A:215	[ RasMol ]

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2co0	WDR5 AND UNMODIFIED HISTONE H3 COMPLEX AT 2.25 ANGSTROM
2gnq	STRUCTURE OF WDR5

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

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SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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Exons (12, 12)

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