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- PDB-7bcy: X-ray structure of WDR5delta24 bound to the Kaposi's sarcoma herp... -

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Basic information

Entry
Database: PDB / ID: 7bcy
TitleX-ray structure of WDR5delta24 bound to the Kaposi's sarcoma herpesvirus LANA win motif peptide
Components
  • ORF 73
  • WD repeat-containing protein 5
KeywordsTRANSFERASE / WD repeat-containing protein 5 LANA Histone Methyltransferase H3K4 / TRANSCRIPTION
Function / homology
Function and homology information


histone H3Q5ser reader activity / histone H3K4me1 reader activity / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis ...histone H3Q5ser reader activity / histone H3K4me1 reader activity / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / Formation of WDR5-containing histone-modifying complexes / histone methyltransferase complex / regulation of cell division / MLL1 complex / regulation of embryonic development / histone acetyltransferase complex / positive regulation of gluconeogenesis / transcription initiation-coupled chromatin remodeling / gluconeogenesis / skeletal system development / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / PKMTs methylate histone lysines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / RMTs methylate histone arginines / mitotic spindle / HATs acetylate histones / Neddylation / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / histone binding / regulation of cell cycle / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / host cell nucleus / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus
Similarity search - Function
: / Protein LANA1-like, DNA-binding domain / Epstein Barr virus nuclear antigen-1, DNA-binding domain superfamily / WDR5 beta-propeller domain / 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 ...: / Protein LANA1-like, DNA-binding domain / Epstein Barr virus nuclear antigen-1, DNA-binding domain superfamily / WDR5 beta-propeller domain / 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
Similarity search - Domain/homology
WD repeat-containing protein 5 / ORF 73
Similarity search - Component
Biological speciesHomo sapiens (human)
Human herpesvirus 8 type M
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 21, 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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
P: ORF 73
Q: ORF 73


Theoretical massNumber of molelcules
Total (without water)71,6734
Polymers71,6734
Non-polymers00
Water12,466692
1
A: WD repeat-containing protein 5
Q: ORF 73


Theoretical massNumber of molelcules
Total (without water)35,8372
Polymers35,8372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-5 kcal/mol
Surface area11300 Å2
MethodPISA
2
B: WD repeat-containing protein 5
P: ORF 73


Theoretical massNumber of molelcules
Total (without water)35,8372
Polymers35,8372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-5 kcal/mol
Surface area11160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.313, 53.171, 65.124
Angle α, β, γ (deg.)72.579, 89.749, 73.156
Int Tables number1
Space group name H-MP1
Space group name HallP1

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Components

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


Mass: 34506.125 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): T7 Kan / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: P61964
#2: Protein/peptide ORF 73


Mass: 1330.568 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: N-terminal acetylation and C-terminal amidation of LANA peptide
Source: (synth.) Human herpesvirus 8 type M / References: UniProt: Q76SB0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 692 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 1.94 Å3/Da / Density % sol: 36.7 % / Description: Rod-shaped
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 100 mM Bis-Tris pH 5.5, 50 mM (NH4)2SO4, 25% PEG3350
PH range: 5.5 - 6.5

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Oxford cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 23, 2017 / Details: Vertical CRL / Horizontal Eliptical mirror
RadiationMonochromator: Standard ESRF channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.4996→61.9364 Å / Num. obs: 78054 / % possible obs: 86.35 % / Redundancy: 3.1 % / Biso Wilson estimate: 13.72 Å2 / CC1/2: 0.993 / R split: 0.069 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.046 / Rrim(I) all: 0.082 / Χ2: 4.3 / Net I/av σ(I): 5.3 / Net I/σ(I): 7.8
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3941 / CC1/2: 0.816 / R split: 0.381 / Rpim(I) all: 0.258 / Rrim(I) all: 0.461 / Χ2: 0.73 / % possible all: 87.4

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Processing

Software
NameVersionClassification
PHENIX1.19rc7_4070refinement
DIALS1.10.0-gf2f43cdc6data reduction
Aimless0.7.1data scaling
MOLREP11.6.04phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ery

4ery


Resolution: 1.5→39 Å / SU ML: 0.1829 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 25.2669
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2268 3891 4.99 %
Rwork0.1932 74131 -
obs0.1949 78022 86.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.1 Å2
Refinement stepCycle: LAST / Resolution: 1.5→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4713 0 0 692 5405
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01054860
X-RAY DIFFRACTIONf_angle_d1.15616612
X-RAY DIFFRACTIONf_chiral_restr0.0708755
X-RAY DIFFRACTIONf_plane_restr0.0089825
X-RAY DIFFRACTIONf_dihedral_angle_d7.5103659
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.30651310.25142704X-RAY DIFFRACTION87.12
1.52-1.540.30881390.24062698X-RAY DIFFRACTION87.24
1.54-1.560.25171670.23562588X-RAY DIFFRACTION86.17
1.56-1.580.31221390.22922578X-RAY DIFFRACTION84.3
1.58-1.60.31541230.2222612X-RAY DIFFRACTION83.74
1.6-1.630.25451360.22122480X-RAY DIFFRACTION80.94
1.63-1.650.24931190.20122283X-RAY DIFFRACTION73.86
1.65-1.680.25391420.19552557X-RAY DIFFRACTION84.87
1.68-1.710.24641570.20192792X-RAY DIFFRACTION89.28
1.71-1.740.23991390.20472698X-RAY DIFFRACTION89.5
1.74-1.770.29691340.21132763X-RAY DIFFRACTION88.38
1.77-1.810.29341330.21682680X-RAY DIFFRACTION87.41
1.81-1.850.2561460.21172683X-RAY DIFFRACTION87.15
1.85-1.890.25931540.19682553X-RAY DIFFRACTION84.86
1.89-1.940.23561290.18572479X-RAY DIFFRACTION80.62
1.94-1.990.21811220.17782371X-RAY DIFFRACTION76.85
1.99-2.050.2011380.18222819X-RAY DIFFRACTION91.58
2.05-2.110.24771470.18092804X-RAY DIFFRACTION90.88
2.11-2.190.2171490.18912754X-RAY DIFFRACTION90.27
2.19-2.280.22061370.18592725X-RAY DIFFRACTION88.72
2.28-2.380.22911370.18472679X-RAY DIFFRACTION87.1
2.38-2.510.21771300.18552418X-RAY DIFFRACTION78.14
2.51-2.660.23031320.19022708X-RAY DIFFRACTION88.03
2.66-2.870.20941260.18812852X-RAY DIFFRACTION92.83
2.87-3.160.21611560.19162766X-RAY DIFFRACTION90.44
3.16-3.610.19951220.17682561X-RAY DIFFRACTION83.04
3.61-4.550.18441550.1732782X-RAY DIFFRACTION90.82
4.55-390.22241520.21452744X-RAY DIFFRACTION89.38
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)
10.553041459881-0.0478517255462-0.06323580479720.3944562354850.07437059244520.450838301336-0.03476723607580.0672005185106-0.000602469377163-0.1200773191720.0344230939594-0.0892333315328-0.003135827171870.0295753112590.0001800314266240.118279632921-0.02173601501520.02130667516190.120582508465-0.008493709281160.1043357110920.5697639929-5.902035756-20.0752975902
20.7431015966220.173903149601-0.07253263502250.6349240915720.08292993057220.615099938959-0.04894106048380.01071842232730.131163289214-0.06146050635370.04019869260470.0155616651423-0.0769435526497-0.05793357755470.00250971520180.1033587363570.0015900387239-0.01092227927190.1062507450760.01086341351710.113686514625.801727590793.33307797802-15.7601409264
30.598542688543-0.3572385816610.02997243942490.689009725449-0.2971640193580.2007238002350.0074438639077-0.0696259976265-0.147551755323-0.05303857458210.06684347860960.146018677950.111366418564-0.113429934111-0.03048157896320.11009830255-0.0107566734635-0.001781349561660.1441183208730.01359601652260.132368858104-0.428161384201-14.2917142907-10.7914464644
40.4290508118420.132691789376-0.1637906809770.6327245148130.0541509940220.495975245071-0.00790870770877-0.0449645389593-0.111632831884-0.01924395888240.0392494929247-0.03574310235830.08307760071580.0311014622306-0.02277009639890.1411779106940.01315774396810.009007504217070.1046186337680.01393713152770.14278912716915.9634917915-22.4468701181-11.3436913366
51.05284291118-0.01702729099370.1451354002620.723255811414-0.05025194321611.27761838389-0.04649327024580.0383217549529-0.100076145406-0.04924597885910.0560388698326-0.04210856832460.04707666890580.0997040626101-0.01551671785460.150860678959-0.01152767855550.0221925711130.129062148447-0.006171135397260.11484366429622.1152502688-16.0597619231-17.8902257692
60.432199108640.1917897338310.05776961146120.4101563372590.1558431376350.566028046767-0.054440826925-0.01699855534890.08131734344770.03745145245640.0267044057452-0.0766214130443-0.0539875807840.05185228386650.009649840516710.1107733495750.0201162164632-0.02391051118190.101418074352-0.007150988808250.123888784355-0.73554657387912.167597517819.8274901591
70.744553182675-0.01994753944580.05242652916060.5786940230240.09288467221580.344178428074-0.0232130125905-0.0197572530908-0.07464934856890.04605403093260.01910391543580.01028524656290.0337266140972-0.02075762928550.008679479782840.09085150982990.0005549741616890.006469427407890.07936523695280.002406831543340.0821986416132-15.61381984180.96526722661915.7259303691
81.891682925440.00221424277795-0.7118823280051.29686082127-0.2004004323660.303361299107-0.06148554522070.1271051413250.1773400786910.003417516352330.04822874609790.1352136768-0.182868601119-0.1866989813160.01093634110690.1113906894470.011641871472-0.00782816421340.1208740279850.01439056725140.138358861368-21.538919293616.58222507510.7362671727
90.589850807574-0.06330030345620.3024671841540.848964608799-0.1851753460190.691778335567-0.07124735301060.04507402340740.1098880449720.05809239924080.04469347478230.0235956963154-0.09587573983350.0335561629010.008167348805450.124317849209-0.00635881208812-0.009441037094110.09957013487780.00668435927160.123612998903-7.9683070150320.593161133712.7665263109
102.577877943830.162271824647-0.8216562519582.354147838720.09210399418431.215494559090.02979605681780.524824800998-0.087144350618-0.4981212491490.08152083415550.06247289014830.0774266994405-0.00576847830153-0.02080438726830.2075685473750.01226450017830.009832656707350.227125175191-0.009368400667920.139610628437-8.05509510425.405194340840.441000985978
111.996329530340.1017896445220.8354163881072.406707765560.1796491472562.16492237592-0.100586995561-0.53323375396-0.02644977064830.602184928845-0.04814186753370.1214180926640.0347033985305-0.062976161412-0.01000037755110.2465665192970.0002716556600850.008531118969120.246755172466-0.0118501790030.13452634689515.2938263984-5.86737562405-0.878049124921
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 31 through 106 )AA31 - 1061 - 76
22chain 'A' and (resid 107 through 167 )AA107 - 16777 - 137
33chain 'A' and (resid 168 through 252 )AA168 - 252138 - 219
44chain 'A' and (resid 253 through 303 )AA253 - 303220 - 270
55chain 'A' and (resid 304 through 334 )AA304 - 334271 - 301
66chain 'B' and (resid 30 through 64 )BB30 - 641 - 35
77chain 'B' and (resid 65 through 206 )BB65 - 20636 - 177
88chain 'B' and (resid 207 through 233 )BB207 - 233178 - 202
99chain 'B' and (resid 234 through 334 )BB234 - 334203 - 303
1010chain 'P' and (resid 23 through 29 )PD23 - 292 - 8
1111chain 'Q' and (resid 23 through 29 )QF23 - 292 - 8

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