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- PDB-3uvn: Crystal structure of WDR5 in complex with the WDR5-interacting mo... -

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Basic information

Entry
Database: PDB / ID: 3uvn
TitleCrystal structure of WDR5 in complex with the WDR5-interacting motif of SET1A
Components
  • Histone-lysine N-methyltransferase SETD1A
  • WD repeat-containing protein 5
KeywordsTRANSCRIPTION / trithorax / chromatin biology / beta-propeller / scaffolding / histone H3 / nucleus
Function / homology
Function and homology information


regulation of chromatin organization / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / histone H3K4 trimethyltransferase activity / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity ...regulation of chromatin organization / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / histone H3K4 trimethyltransferase activity / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / regulation of hematopoietic stem cell differentiation / histone methyltransferase complex / regulation of tubulin deacetylation / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / regulation of embryonic development / MLL1 complex / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / histone acetyltransferase complex / positive regulation of gluconeogenesis / transcription initiation-coupled chromatin remodeling / methylated histone binding / skeletal system development / gluconeogenesis / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / brain development / mitotic spindle / PKMTs methylate histone lysines / beta-catenin binding / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Neddylation / HATs acetylate histones / histone binding / methylation / RNA polymerase II-specific DNA-binding transcription factor binding / regulation of cell cycle / nuclear speck / DNA damage response / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Set1A, RNA recognition motif / Histone-lysine N-methyltransferase SETD1A / Histone-lysine N-methyltransferase Set1-like / COMPASS complex Set1 subunit, N-SET domain / COMPASS (Complex proteins associated with Set1p) component N / COMPASS (Complex proteins associated with Set1p) component N / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain ...Set1A, RNA recognition motif / Histone-lysine N-methyltransferase SETD1A / Histone-lysine N-methyltransferase Set1-like / COMPASS complex Set1 subunit, N-SET domain / COMPASS (Complex proteins associated with Set1p) component N / COMPASS (Complex proteins associated with Set1p) component N / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Nucleotide-binding alpha-beta plait domain superfamily / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Histone-lysine N-methyltransferase SETD1A / WD repeat-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.792 Å
AuthorsZhang, P. / Lee, H. / Brunzelle, J.S. / Couture, J.-F.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: The plasticity of WDR5 peptide-binding cleft enables the binding of the SET1 family of histone methyltransferases.
Authors: Zhang, P. / Lee, H. / Brunzelle, J.S. / Couture, J.F.
History
DepositionNov 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2012Group: Database references
Revision 1.2May 30, 2012Group: Database references
Revision 1.3Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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: Histone-lysine N-methyltransferase SETD1A
C: WD repeat-containing protein 5
D: Histone-lysine N-methyltransferase SETD1A


Theoretical massNumber of molelcules
Total (without water)71,9894
Polymers71,9894
Non-polymers00
Water4,666259
1
A: WD repeat-containing protein 5
B: Histone-lysine N-methyltransferase SETD1A


Theoretical massNumber of molelcules
Total (without water)35,9952
Polymers35,9952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-4 kcal/mol
Surface area11410 Å2
MethodPISA
2
C: WD repeat-containing protein 5
D: Histone-lysine N-methyltransferase SETD1A


Theoretical massNumber of molelcules
Total (without water)35,9952
Polymers35,9952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-4 kcal/mol
Surface area11350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.890, 47.100, 102.520
Angle α, β, γ (deg.)90.00, 108.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein WD repeat-containing protein 5 / WDR5 / BMP2-induced 3-kb gene protein


Mass: 34794.449 Da / Num. of mol.: 2 / Fragment: UNP residues 21-334
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR5, BIG3 / Production host: Escherichia coli (E. coli) / References: UniProt: P61964
#2: Protein/peptide Histone-lysine N-methyltransferase SETD1A / Lysine N-methyltransferase 2F / SET domain-containing protein 1A / hSET1A / Set1/Ash2 histone ...Lysine N-methyltransferase 2F / SET domain-containing protein 1A / hSET1A / Set1/Ash2 histone methyltransferase complex subunit SET1


Mass: 1200.280 Da / Num. of mol.: 2 / Fragment: WDR5-interacting motif (UNP residues 1492-1502) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: O15047, histone-lysine N-methyltransferase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 25% PEG3350, 0.1 M sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12718 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 10, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12718 Å / Relative weight: 1
ReflectionResolution: 1.792→42.401 Å / Num. all: 69653 / Num. obs: 68329 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 23.36 Å2 / Rsym value: 0.09 / Net I/σ(I): 22
Reflection shellResolution: 1.792→2.2 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 4.8 / Rsym value: 0.3 / % possible all: 91.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
BUSTER2.8.0refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2H13

2h13


Resolution: 1.792→42.401 Å / Cor.coef. Fo:Fc: 0.9368 / Cor.coef. Fo:Fc free: 0.9127 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2303 2799 5.07 %RANDOM
Rwork0.1935 ---
obs0.1953 55234 --
all-69653 --
Displacement parametersBiso mean: 35.6 Å2
Baniso -1Baniso -2Baniso -3
1-4.6442 Å20 Å2-4.1052 Å2
2--5.4907 Å20 Å2
3----10.135 Å2
Refine analyzeLuzzati coordinate error obs: 0.329 Å
Refinement stepCycle: LAST / Resolution: 1.792→42.401 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4749 0 0 259 5008
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1593SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes104HARMONIC2
X-RAY DIFFRACTIONt_gen_planes708HARMONIC5
X-RAY DIFFRACTIONt_it4866HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion658SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5712SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4866HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6624HARMONIC21.19
X-RAY DIFFRACTIONt_omega_torsion4.19
X-RAY DIFFRACTIONt_other_torsion15.88
LS refinement shellResolution: 1.792→1.84 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 177 4.65 %
Rwork0.242 3633 -
all-3810 -
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)
11.7123-0.2132-0.37041.5427-0.00910.9271-0.04380.00330.2488-0.07540.08340.09350.0056-0.0518-0.0396-0.1341-0.0246-0.016-0.03120.03110.0093-16.71818.3524-5.2692
20.495-0.32080.29581.6805-1.28592.5480.11010.18010.07880.1205-0.6166-0.2711-0.07570.98980.5065-0.2339-0.0575-0.02290.40140.2093-0.11360.707611.8861-43.569
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|31 - A|334 }A31 - 334
2X-RAY DIFFRACTION2{ C|31 - C|334 }C31 - 334

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