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- PDB-4y7r: Crystal structure of WDR5 in complex with MYC MbIIIb peptide -

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Basic information

Entry
Database: PDB / ID: 4y7r
TitleCrystal structure of WDR5 in complex with MYC MbIIIb peptide
Components
  • MYC MbIIIb peptide
  • WD repeat-containing protein 5
KeywordsDNA BINDING PROTEIN / Myc WDR5 Cancer
Function / homology
Function and homology information


positive regulation of metanephric cap mesenchymal cell proliferation / positive regulation of acinar cell proliferation / acinar cell proliferation / negative regulation of transcription initiation by RNA polymerase II / SCF ubiquitin ligase complex binding / NK T cell proliferation / Myc-Max complex / regulation of somatic stem cell population maintenance / regulation of cell cycle process / Binding of TCF/LEF:CTNNB1 to target gene promoters ...positive regulation of metanephric cap mesenchymal cell proliferation / positive regulation of acinar cell proliferation / acinar cell proliferation / negative regulation of transcription initiation by RNA polymerase II / SCF ubiquitin ligase complex binding / NK T cell proliferation / Myc-Max complex / regulation of somatic stem cell population maintenance / regulation of cell cycle process / Binding of TCF/LEF:CTNNB1 to target gene promoters / cellular response to interferon-alpha / RNA polymerase II transcription repressor complex / myotube differentiation / positive regulation of B cell apoptotic process / RUNX3 regulates WNT signaling / TFAP2 (AP-2) family regulates transcription of cell cycle factors / negative regulation of cell division / negative regulation of monocyte differentiation / detection of mechanical stimulus involved in sensory perception of sound / response to growth factor / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / response to alkaloid / MLL3/4 complex / B cell apoptotic process / transcription regulator activator activity / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / protein-DNA complex disassembly / histone H3K4 methyltransferase activity / Transcription of E2F targets under negative control by DREAM complex / Cardiogenesis / negative regulation of stress-activated MAPK cascade / fibroblast apoptotic process / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Regulation of NFE2L2 gene expression / regulation of telomere maintenance / positive regulation of mesenchymal cell proliferation / skeletal system morphogenesis / middle ear morphogenesis / Signaling by ALK / branching involved in ureteric bud morphogenesis / negative regulation of gene expression via chromosomal CpG island methylation / pigmentation / Formation of WDR5-containing histone-modifying complexes / rRNA metabolic process / E-box binding / histone methyltransferase complex / positive regulation of telomere maintenance / regulation of cell division / MLL1 complex / regulation of embryonic development / skeletal muscle cell differentiation / histone acetyltransferase complex / : / chromosome organization / positive regulation of transcription initiation by RNA polymerase II / Cyclin E associated events during G1/S transition / core promoter sequence-specific DNA binding / Cyclin A:Cdk2-associated events at S phase entry / negative regulation of fibroblast proliferation / ERK1 and ERK2 cascade / positive regulation of gluconeogenesis / transcription initiation-coupled chromatin remodeling / positive regulation of epithelial cell proliferation / transcription coregulator binding / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / skeletal system development / gluconeogenesis / MAPK6/MAPK4 signaling / NOTCH1 Intracellular Domain Regulates Transcription / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / G1/S transition of mitotic cell cycle / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / euchromatin / PKMTs methylate histone lysines / protein processing / positive regulation of miRNA transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / spindle / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Wnt signaling pathway / Transcriptional regulation of granulopoiesis / positive regulation of fibroblast proliferation / intrinsic apoptotic signaling pathway in response to DNA damage / mitotic spindle / cellular response to UV / cellular response to xenobiotic stimulus / MAPK cascade / Neddylation / regulation of gene expression / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / DNA-binding transcription activator activity, RNA polymerase II-specific / histone binding / Interleukin-4 and Interleukin-13 signaling / cellular response to hypoxia
Similarity search - Function
Leucine zipper, Myc / Myc leucine zipper domain / Transcription regulator Myc / Transcription regulator Myc, N-terminal / : / Myc amino-terminal region / Helix-loop-helix DNA-binding domain / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. ...Leucine zipper, Myc / Myc leucine zipper domain / Transcription regulator Myc / Transcription regulator Myc, N-terminal / : / Myc amino-terminal region / Helix-loop-helix DNA-binding domain / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Myc proto-oncogene protein / WD repeat-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.898 Å
AuthorsSun, Q. / Phan, J. / Olejniczak, E.T. / Thomas, L.R. / Fesik, S.W. / Tansey, W.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Office of the Director5DP1OD006933 United States
CitationJournal: Mol.Cell / Year: 2015
Title: Interaction with WDR5 Promotes Target Gene Recognition and Tumorigenesis by MYC.
Authors: Thomas, L.R. / Wang, Q. / Grieb, B.C. / Phan, J. / Foshage, A.M. / Sun, Q. / Olejniczak, E.T. / Clark, T. / Dey, S. / Lorey, S. / Alicie, B. / Howard, G.C. / Cawthon, B. / Ess, K.C. / ...Authors: Thomas, L.R. / Wang, Q. / Grieb, B.C. / Phan, J. / Foshage, A.M. / Sun, Q. / Olejniczak, E.T. / Clark, T. / Dey, S. / Lorey, S. / Alicie, B. / Howard, G.C. / Cawthon, B. / Ess, K.C. / Eischen, C.M. / Zhao, Z. / Fesik, S.W. / Tansey, W.P.
History
DepositionFeb 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1May 20, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_entity_src_syn / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: WD repeat-containing protein 5
B: MYC MbIIIb peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4644
Polymers35,2802
Non-polymers1842
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-6 kcal/mol
Surface area12270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.762, 87.177, 44.914
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein WD repeat-containing protein 5 / BMP2-induced 3-kb gene protein


Mass: 34390.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR5, BIG3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Ril / References: UniProt: P61964
#2: Protein/peptide MYC MbIIIb peptide


Mass: 888.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: P01106*PLUS
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M Tris 7.0, 25% PEG 8K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.898→43.589 Å / Num. all: 25709 / Num. obs: 25709 / % possible obs: 99.9 % / Redundancy: 9.7 % / Rsym value: 0.074 / Net I/σ(I): 24.8
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 4.3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1951)refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XL2

2xl2


Resolution: 1.898→43.589 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1879 1275 4.96 %Random selection
Rwork0.1586 ---
obs0.1601 25709 99.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.898→43.589 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2419 0 12 179 2610
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052539
X-RAY DIFFRACTIONf_angle_d0.9583452
X-RAY DIFFRACTIONf_dihedral_angle_d11.803904
X-RAY DIFFRACTIONf_chiral_restr0.048390
X-RAY DIFFRACTIONf_plane_restr0.004430
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8984-1.97440.28471300.22122645X-RAY DIFFRACTION99
1.9744-2.06430.25821380.19012675X-RAY DIFFRACTION100
2.0643-2.17310.21761480.17712673X-RAY DIFFRACTION100
2.1731-2.30920.19951340.16472696X-RAY DIFFRACTION100
2.3092-2.48750.20321450.1672690X-RAY DIFFRACTION100
2.4875-2.73780.18581410.16452687X-RAY DIFFRACTION100
2.7378-3.13390.18551420.16712731X-RAY DIFFRACTION100
3.1339-3.9480.18871450.1492751X-RAY DIFFRACTION100
3.948-43.60.1641520.14512886X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.7443-0.71-0.45751.36920.53941.5301-0.1534-0.0561-0.45390.1932-0.15740.16220.1585-0.11850.18830.28790.00920.01840.25710.02340.36230.039820.18719.203
22.4305-0.26130.40821.65920.24581.80480.0134-0.17440.12360.09680.02550.24180.1385-0.0462-0.03820.23130.02660.01480.21550.01040.22270.074931.030112.6891
31.58170.37160.04771.26060.40772.22080.0118-0.09430.3494-0.10210.04560.1044-0.16440.0077-0.04210.21390.0493-0.00290.2360.02510.28359.633635.28119.6752
42.788-0.4977-0.63582.10480.77181.3581-0.0059-0.13020.4086-0.06070.0676-0.029-0.1760.1164-0.05910.22710.0082-0.00090.2101-0.00090.277115.30537.34258.1262
52.907-0.7572-1.11162.87470.43132.89510.1513-0.21740.72130.1730.1453-0.281-0.08290.1759-0.2970.2567-0.0313-0.00190.3018-0.04190.370724.234737.3286.2489
62.5746-0.5488-0.50972.12540.47821.8221-0.1385-0.3469-0.13350.21290.217-0.25930.06410.3028-0.09910.23280.0369-0.02630.3557-0.00370.264527.397824.88847.3087
72.3051-0.05010.38482.2237-0.84542.7623-0.163-0.1416-0.58890.11560.118-0.28060.29290.0970.04220.30620.05230.03940.34630.03020.37322.69715.5276.8323
81.98520.84820.61271.90140.08551.5248-0.1408-0.1551-0.99470.21830.0804-0.49340.27910.35280.02720.38220.14590.04530.42320.02920.650323.495710.16257.1088
93.0679-0.2688-0.45732.13290.42521.5501-0.18580.0905-0.58990.12760.0830.03860.33470.31050.14090.29790.02230.04180.24920.00330.34510.098913.33785.2362
101.8543-0.7509-0.12020.7127-0.05671.4813-0.19220.0199-0.70330.1439-0.0929-0.1330.57960.0530.28910.36610.01640.06920.22760.00810.54356.28128.16146.8553
112.82020.2681-0.14441.90711.26221.2511-0.1749-0.1094-0.39610.28490.06990.15750.2964-0.10410.05290.22850.00550.05640.18450.03220.25751.51118.674410.1847
125.3837-2.1214-1.71055.34190.84245.4049-0.1882-0.3007-0.31190.19640.094-0.38160.70690.130.10760.62420.1431-0.02650.77090.22380.467421.04718.510921.021
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 53 )
2X-RAY DIFFRACTION2chain 'A' and (resid 54 through 83 )
3X-RAY DIFFRACTION3chain 'A' and (resid 84 through 106 )
4X-RAY DIFFRACTION4chain 'A' and (resid 107 through 148 )
5X-RAY DIFFRACTION5chain 'A' and (resid 149 through 167 )
6X-RAY DIFFRACTION6chain 'A' and (resid 168 through 209 )
7X-RAY DIFFRACTION7chain 'A' and (resid 210 through 233 )
8X-RAY DIFFRACTION8chain 'A' and (resid 234 through 252 )
9X-RAY DIFFRACTION9chain 'A' and (resid 253 through 282 )
10X-RAY DIFFRACTION10chain 'A' and (resid 283 through 303 )
11X-RAY DIFFRACTION11chain 'A' and (resid 304 through 334 )
12X-RAY DIFFRACTION12chain 'B' and (resid 260 through 267 )

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