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

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Basic information

Entry
Database: PDB / ID: 3uvo
TitleCrystal structure of WDR5 in complex with the WDR5-interacting motif of SET1B
Components
  • Histone-lysine N-methyltransferase SETD1B
  • WD repeat-containing protein 5
KeywordsTRANSCRIPTION / trithorax / chromatin biology / beta-propeller / scaffolding / histone H3 / nucleus
Function / homology
Function and homology information


[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 / : ...[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 / histone H3 methyltransferase activity / histone methyltransferase complex / regulation of tubulin deacetylation / regulation of cell division / Formation of WDR5-containing histone-modifying complexes / MLL1 complex / regulation of embryonic development / 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 / mitotic spindle / PKMTs methylate histone lysines / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / chromosome / Neddylation / methylation / HATs acetylate histones / histone binding / regulation of cell cycle / nuclear speck / regulation of DNA-templated transcription / 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
Similarity search - Function
Set1B, 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 ...Set1B, 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. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
WD repeat-containing protein 5 / Histone-lysine N-methyltransferase SETD1B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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

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Assembly

Deposited unit
A: WD repeat-containing protein 5
B: Histone-lysine N-methyltransferase SETD1B


Theoretical massNumber of molelcules
Total (without water)35,9992
Polymers35,9992
Non-polymers00
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-6 kcal/mol
Surface area11510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.270, 69.920, 88.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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.: 1 / 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 SETD1B / Lysine N-methyltransferase 2G / SET domain-containing protein 1B / hSET1B


Mass: 1204.334 Da / Num. of mol.: 1 / Fragment: WDR5-interacting motif (UNP residues 1702-1712) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q9UPS6, histone-lysine N-methyltransferase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.11 Å3/Da / Density % sol: 41.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M ammonium sulfate, 25% PEG3350, 0.1 M Tris, pH 8.5, 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: 2.2→50 Å / Num. all: 15927 / Num. obs: 15927 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 48.78 Å2 / Rsym value: 0.077 / Net I/σ(I): 43.7
Reflection shellResolution: 2.2→2.35 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 6.9 / Rsym value: 0.246 / % possible all: 86.8

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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: 2.2→43.01 Å / Cor.coef. Fo:Fc: 0.9359 / Cor.coef. Fo:Fc free: 0.9313 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2187 794 4.99 %RANDOM
Rwork0.1869 ---
obs0.1884 15926 --
all-15927 --
Displacement parametersBiso mean: 60.66 Å2
Baniso -1Baniso -2Baniso -3
1--7.2373 Å20 Å20 Å2
2---8.8792 Å20 Å2
3---16.1165 Å2
Refine analyzeLuzzati coordinate error obs: 0.385 Å
Refinement stepCycle: LAST / Resolution: 2.2→43.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2340 0 0 98 2438
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d782SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes48HARMONIC2
X-RAY DIFFRACTIONt_gen_planes348HARMONIC5
X-RAY DIFFRACTIONt_it2394HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion327SEMIHARMONIC5
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_contact2816SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2394HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3256HARMONIC21.27
X-RAY DIFFRACTIONt_omega_torsion3.91
X-RAY DIFFRACTIONt_other_torsion17.26
LS refinement shellResolution: 2.2→2.35 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2655 152 5.5 %
Rwork0.2092 2613 -
all0.2126 2765 -
Refinement TLS params.Method: refined / Origin x: -13.2497 Å / Origin y: -9.6388 Å / Origin z: 17.732 Å
111213212223313233
T-0.0822 Å2-0.0503 Å2-0.0034 Å2--0.2311 Å2-0.0398 Å2---0.2551 Å2
L2.2449 °2-0.2167 °2-0.4389 °2-4.7402 °22.9865 °2--4.8643 °2
S0.1535 Å °-0.0326 Å °-0.1147 Å °0.8873 Å °0.078 Å °-0.1346 Å °0.0018 Å °0.3831 Å °-0.2315 Å °
Refinement TLS groupSelection details: { A|31 - A|334 }

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