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- PDB-7bed: X-ray structure of WDR5 bound to the WDR5 win motif peptide -

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Basic information

Entry
Database: PDB / ID: 7bed
TitleX-ray structure of WDR5 bound to the WDR5 win motif peptide
ComponentsWD repeat-containing protein 5
KeywordsTRANSFERASE / WD repeat-containing protein 5 LANA Histone Methyltransferase H3K4 / TRANSCRIPTION
Function / homology
Function and homology information


MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / : / Cardiogenesis / histone methyltransferase complex / regulation of tubulin deacetylation ...MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / : / Cardiogenesis / histone methyltransferase complex / regulation of tubulin deacetylation / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / 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 / Neddylation / HATs acetylate histones / histone binding / regulation of cell cycle / 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 / nucleoplasm / nucleus
Similarity search - Function
G-protein beta WD-40 repeat / WD40 repeat, conserved site / 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
Similarity search - Domain/homology
WD repeat-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å
AuthorsMcVey, C.E. / Kaye, K.M.
Funding support Portugal, United States, 5items
OrganizationGrant numberCountry
Foundation for Science and Technology (FCT)LISBOA-01-0145-FEDER-007344 Portugal
Foundation for Science and Technology (FCT)IF/01023/2013/CP1173/CT0003 Portugal
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)CA082036 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)DE025208 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)DE024971 United States
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: MLL1 is regulated by KSHV LANA and is important for virus latency.
Authors: Tan, M. / Li, S. / Juillard, F. / Chitas, R. / Custodio, T.F. / Xue, H. / Szymula, A. / Sun, Q. / Liu, B. / Alvarez, A.L. / Chen, S. / Huang, J. / Simas, J.P. / McVey, C.E. / Kaye, K.M.
History
DepositionDec 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 15, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 29, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: WD repeat-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,3673
Polymers73,2712
Non-polymers961
Water6,521362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, HiLoad 16/60 Superdex, 75 PG
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-13 kcal/mol
Surface area12250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.008, 54.469, 117.140
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

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


Mass: 36635.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR5, BIG3 / Plasmid: pET47b
Details (production host): 6XHis tag;3C protease site;T7 promoter:KanR
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: P61964
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 362 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.24 Å3/Da / Density % sol: 45.18 % / Description: Capped bipyrimidal
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 26% PEG 3350, 100mM Bis-Tris pH 5.5, 50mM (NH4)2SO4,WDR5 at 14,65 mg/ml with 2:1 (protein:well) drop ratio.
PH range: 5.5 - 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 25, 2016 / Details: DCM (Double Crystal Monochromator)
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.26→27.23 Å / Num. obs: 157708 / % possible obs: 99.3 % / Redundancy: 3.8 % / Biso Wilson estimate: 10.07 Å2 / CC1/2: 0.999 / R split: 0.068 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.045 / Rrim(I) all: 0.09 / Χ2: 0.57 / Net I/av σ(I): 9 / Net I/σ(I): 7.9
Reflection shellResolution: 1.26→1.28 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4018 / CC1/2: 0.502 / R split: 0.619 / Rpim(I) all: 0.424 / Rrim(I) all: 0.831 / Χ2: 0.55 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX1.19rc7_4070refinement
REFMAC5.8.0238refinement
PDB_EXTRACT3.22data extraction
xia20.4.0.0data reduction
Aimless0.7.2data scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ERY

4ery


Resolution: 1.26→27.23 Å / SU ML: 0.1353 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 17.5211
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1713 7538 4.78 %RANDOM
Rwork0.159 150170 --
obs0.1596 157708 96.07 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.04 Å2
Refinement stepCycle: LAST / Resolution: 1.26→27.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2446 0 5 362 2813
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00632600
X-RAY DIFFRACTIONf_angle_d0.99713543
X-RAY DIFFRACTIONf_chiral_restr0.0902398
X-RAY DIFFRACTIONf_plane_restr0.0068442
X-RAY DIFFRACTIONf_dihedral_angle_d7.3814353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.26-1.270.29632510.30224641X-RAY DIFFRACTION90.84
1.27-1.290.29912350.29074935X-RAY DIFFRACTION92.95
1.29-1.30.28692300.28024894X-RAY DIFFRACTION93.76
1.3-1.320.28112610.28294912X-RAY DIFFRACTION95.2
1.32-1.340.28542220.26674995X-RAY DIFFRACTION95.08
1.34-1.360.25372260.26464982X-RAY DIFFRACTION94.54
1.36-1.380.272640.26074951X-RAY DIFFRACTION96.16
1.38-1.40.29282500.24575095X-RAY DIFFRACTION97.01
1.4-1.420.22552710.24224994X-RAY DIFFRACTION97.32
1.42-1.440.24522450.23315159X-RAY DIFFRACTION96.69
1.44-1.470.24132530.21994982X-RAY DIFFRACTION96.5
1.47-1.490.21212640.2184986X-RAY DIFFRACTION96.15
1.49-1.520.21662780.19934991X-RAY DIFFRACTION96.1
1.52-1.550.2062520.19285000X-RAY DIFFRACTION96.03
1.55-1.590.18032620.18464971X-RAY DIFFRACTION95.75
1.59-1.620.21712270.17575066X-RAY DIFFRACTION96.91
1.62-1.660.19262620.16245034X-RAY DIFFRACTION97.01
1.66-1.710.1732700.15645095X-RAY DIFFRACTION97.1
1.71-1.760.14442610.14784991X-RAY DIFFRACTION96.85
1.76-1.820.17432190.14625121X-RAY DIFFRACTION96.58
1.82-1.880.16072300.13685060X-RAY DIFFRACTION96.71
1.88-1.960.13372290.12314973X-RAY DIFFRACTION95.34
1.96-2.040.13332620.12624975X-RAY DIFFRACTION95.76
2.04-2.150.13642700.12145089X-RAY DIFFRACTION98.06
2.15-2.290.1362460.12155107X-RAY DIFFRACTION97.83
2.29-2.460.15222580.13085018X-RAY DIFFRACTION96.56
2.46-2.710.15092330.13055058X-RAY DIFFRACTION96.04
2.71-3.10.15422650.13284944X-RAY DIFFRACTION95.97
3.1-3.910.13262470.12195109X-RAY DIFFRACTION97.58
3.91-27.230.13972950.14165042X-RAY DIFFRACTION97.55
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)
12.9478219546-2.23160259173-1.271423266923.45706897660.8278096424461.878053071170.09122103035070.1357481952890.149179183088-0.0550909310089-0.06973186256340.117489461828-0.18692074632-0.153845217518-0.009838768814420.0603010198487-0.0148515520518-0.02167795519980.07723150157390.001576363363780.072014375641110.61554962221.0715490314123.648902719
21.61342421975-0.268129615932-0.5696546620352.452388412190.7624734062642.30446806460.01923634857410.02334493963690.0377889129292-0.109724044741-0.0117753664377-0.164010997843-0.09890846100520.129145256669-0.01565981140130.05765468344369.77595574378E-5-0.0006887279850320.07832387359010.006029777217770.057989307588724.813708358913.391913138127.512109787
31.345475334921.092299151070.5070914384564.778677442612.824902672853.7950584758-0.006740714109750.0311427671689-0.05748515027480.07313609802580.0781066258201-0.2760887883870.01983436045120.184750543715-0.05429671357450.04879765103460.00998943781537-0.007502046848750.05986820957970.01642933342970.072872806160825.49596460847.27140352963135.251201661
43.066243023641.730920291860.334851013785.79137668204-0.5686591296043.181510344070.04023007250060.0305853411708-0.172107747919-0.0506187442873-0.137209234711-0.4792917020770.01917683639860.3160000935490.1100951037860.05695469226430.02283440654740.009475459608820.08701454954240.01627569163890.099997645675430.44178639922.6695561392136.843448676
51.553432715690.2466572474560.3991136349411.03106280881-0.1647017754541.181276723580.0236333612214-0.0233788444534-0.0755352097990.081053167529-0.0057127150168-0.04129322482960.0272597353880.0442905107088-0.02081628381080.0647602439229-0.00265768183955-0.001354638032010.05627245293760.01316789213210.062804431974720.82959076573.83974040673142.764160901
63.298120081121.8861284192-0.4899111459273.880334414240.0188798859512.856176274610.131968243955-0.265855130514-0.2604236448620.218508072031-0.0992190853025-0.2343462014890.1044272371780.132188865988-0.04614947765210.08174336765830.0133097971343-0.01557241845480.06463616705830.02156209828330.091215420933322.6163463387-0.557943658588147.559890118
73.076665857061.59500001880.7098300150172.888156431170.769247744373.011038326540.0828411298966-0.215112223386-0.05048321139120.131214959767-0.1152561261140.008273475209210.00672002332404-0.1270568967940.03534263524750.04552916506210.0002977821644960.00371858817080.061653002510.01643749368210.046686314267611.77126581874.72710358269146.081517862
84.556161371212.840640529843.374805740633.398578457013.17022804996.141708272340.115038997151-0.306023383784-0.07691785465690.147976787281-0.08180443705150.0297924588090.0519191455236-0.28262576568-0.05989935595840.0822793222733-0.008472433397970.01228218165470.07604438134230.02419127489970.0759252993988.119220159882.42534695032149.92643042
93.595337294580.02530367017450.8126068430694.740240481921.735108082254.97985476744-0.0817680829989-0.3217264436070.05670879566890.202159994378-0.09132213617160.420090343584-0.0924225577244-0.4941999836330.0927197974990.06679769192150.03082025960820.01307496458910.1379206682640.01009737272990.09127576549633.542670361838.881894584142.669946781
101.52296562212-0.4727536210530.01825728108521.67698933221-0.1860530152581.15699785621-0.0388540670309-0.140214362889-0.0304867567330.1192489839870.06323220307470.13947597914-0.0404761579019-0.184457674918-0.02068334435550.06651999251060.01567093028930.001172989702480.1012694996920.007433871715280.06788047335371.981046555712.7829703018134.590979485
111.5682426635-0.251808085736-0.02609468703220.757168184166-0.02902565883661.11543499135-0.01721375037890.02352195411930.0890981101545-0.01967741775720.005966942208050.0388549519927-0.0791752512222-0.06997082491840.008873796869350.06616823815170.00608730916661-0.01043337724130.06274349214870.007099459813730.05310848003939.4535155324717.4915992386125.689889459
128.894636627261.96550541081-1.019019663437.52729841-1.72918015667.32587471718-0.2503102573480.79488498416-0.838813519527-0.5575166184240.193060811655-0.2019709500390.704168225240.1211007936140.1027380560870.1699133836610.01053573589670.004480474990530.144707472277-0.05189210248010.15094665312213.8944600661-2.50582055361127.105659147
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 27 through 47 )AA27 - 471 - 21
22chain 'A' and (resid 48 through 84 )AA48 - 8422 - 58
33chain 'A' and (resid 85 through 106 )AA85 - 10659 - 80
44chain 'A' and (resid 107 through 126 )AA107 - 12681 - 100
55chain 'A' and (resid 127 through 148 )AA127 - 148101 - 122
66chain 'A' and (resid 149 through 167 )AA149 - 167123 - 141
77chain 'A' and (resid 168 through 190 )AA168 - 190142 - 164
88chain 'A' and (resid 191 through 209 )AA191 - 209165 - 183
99chain 'A' and (resid 210 through 233 )AA210 - 233184 - 207
1010chain 'A' and (resid 234 through 287 )AA234 - 287208 - 261
1111chain 'A' and (resid 288 through 334 )AA288 - 334262 - 308
1212chain 'B' and (resid 10 through 19 )BC10 - 181 - 9

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