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- PDB-6wjq: Crystal structure of WDR5 in complex with the WIN peptide of PDPK1 -

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Basic information

Entry
Database: PDB / ID: 6wjq
TitleCrystal structure of WDR5 in complex with the WIN peptide of PDPK1
Components
  • 3-phosphoinositide-dependent protein kinase 1
  • WD repeat-containing protein 5
KeywordsTRANSCRIPTION / WDR5 / PDPK1 / chromatin / signaling / WIN / acetylation
Function / homology
Function and homology information


3-phosphoinositide-dependent protein kinase activity / Activation of AKT2 / regulation of mast cell degranulation / negative regulation of toll-like receptor signaling pathway / type B pancreatic cell development / positive regulation of phospholipase activity / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / RSK activation ...3-phosphoinositide-dependent protein kinase activity / Activation of AKT2 / regulation of mast cell degranulation / negative regulation of toll-like receptor signaling pathway / type B pancreatic cell development / positive regulation of phospholipase activity / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / RSK activation / hyperosmotic response / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / regulation of canonical NF-kappaB signal transduction / Cardiogenesis / positive regulation of vascular endothelial cell proliferation / negative regulation of cardiac muscle cell apoptotic process / histone methyltransferase complex / regulation of tubulin deacetylation / phospholipase activator activity / positive regulation of sprouting angiogenesis / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / Constitutive Signaling by AKT1 E17K in Cancer / CD28 dependent PI3K/Akt signaling / phospholipase binding / regulation of embryonic development / MLL1 complex / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / histone acetyltransferase complex / positive regulation of blood vessel endothelial cell migration / Role of LAT2/NTAL/LAB on calcium mobilization / Estrogen-stimulated signaling through PRKCZ / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / negative regulation of endothelial cell apoptotic process / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / extrinsic apoptotic signaling pathway / RHO GTPases activate PKNs / positive regulation of gluconeogenesis / transcription initiation-coupled chromatin remodeling / cellular response to epidermal growth factor stimulus / GPVI-mediated activation cascade / methylated histone binding / T cell costimulation / activation of protein kinase B activity / Integrin signaling / insulin-like growth factor receptor signaling pathway / positive regulation of release of sequestered calcium ion into cytosol / VEGFR2 mediated vascular permeability / VEGFR2 mediated cell proliferation / skeletal system development / cell projection / gluconeogenesis / calcium-mediated signaling / positive regulation of protein localization to plasma membrane / peptidyl-threonine phosphorylation / negative regulation of transforming growth factor beta receptor signaling pathway / negative regulation of protein kinase activity / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / epidermal growth factor receptor signaling pathway / mitotic spindle / CLEC7A (Dectin-1) signaling / PKMTs methylate histone lysines / RMTs methylate histone arginines / FCERI mediated NF-kB activation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / G beta:gamma signalling through PI3Kgamma / cellular response to insulin stimulus / positive regulation of angiogenesis / Regulation of TP53 Degradation / cell migration / Downstream TCR signaling / insulin receptor signaling pathway / PIP3 activates AKT signaling / Neddylation / HATs acetylate histones / histone binding / cytoplasmic vesicle / actin cytoskeleton organization / protein autophosphorylation / postsynaptic density / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / non-specific serine/threonine protein kinase / regulation of cell cycle / intracellular signal transduction / protein phosphorylation / focal adhesion / protein serine kinase activity / protein serine/threonine kinase activity / 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 / ATP binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
PDK1-type, PH domain / PDPK1 family / PH domain / PH-like domain superfamily / 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. / WD domain, G-beta repeat ...PDK1-type, PH domain / PDPK1 family / PH domain / PH-like domain superfamily / 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. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
3-phosphoinositide-dependent protein kinase 1 / WD repeat-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsZhao, B. / Fesik, S.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA200709 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)HHSN261200800001E United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA225065 United States
CitationJournal: Cell Rep / Year: 2021
Title: Crystal structure of WDR5 in complex with the WIN peptide of PDPK1
Authors: zhao, B. / Fesik, S.
History
DepositionApr 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
C: 3-phosphoinositide-dependent protein kinase 1
D: 3-phosphoinositide-dependent protein kinase 1


Theoretical massNumber of molelcules
Total (without water)72,1324
Polymers72,1324
Non-polymers00
Water88349
1
A: WD repeat-containing protein 5
C: 3-phosphoinositide-dependent protein kinase 1


Theoretical massNumber of molelcules
Total (without water)36,0662
Polymers36,0662
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-8 kcal/mol
Surface area11330 Å2
MethodPISA
2
B: WD repeat-containing protein 5
D: 3-phosphoinositide-dependent protein kinase 1


Theoretical massNumber of molelcules
Total (without water)36,0662
Polymers36,0662
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-8 kcal/mol
Surface area11450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.518, 47.228, 118.965
Angle α, β, γ (deg.)90.000, 90.920, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 30 or (resid 31 through 32...
21(chain B and (resid 30 through 37 or (resid 38...
12chain C
22chain D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PROPROPROPRO(chain A and (resid 30 or (resid 31 through 32...AA309
121VALVALLYSLYS(chain A and (resid 30 or (resid 31 through 32...AA31 - 3210 - 11
131PROPROSERSER(chain A and (resid 30 or (resid 31 through 32...AA30 - 3329 - 311
141PROPROSERSER(chain A and (resid 30 or (resid 31 through 32...AA30 - 3329 - 311
151PROPROSERSER(chain A and (resid 30 or (resid 31 through 32...AA30 - 3329 - 311
161PROPROSERSER(chain A and (resid 30 or (resid 31 through 32...AA30 - 3329 - 311
211PROPROLEULEU(chain B and (resid 30 through 37 or (resid 38...BB30 - 379 - 16
221LYSLYSLYSLYS(chain B and (resid 30 through 37 or (resid 38...BB3817
231PROPROCYSCYS(chain B and (resid 30 through 37 or (resid 38...BB30 - 3349 - 313
241PROPROCYSCYS(chain B and (resid 30 through 37 or (resid 38...BB30 - 3349 - 313
251PROPROCYSCYS(chain B and (resid 30 through 37 or (resid 38...BB30 - 3349 - 313
261PROPROCYSCYS(chain B and (resid 30 through 37 or (resid 38...BB30 - 3349 - 313
112ACEACEALAALAchain CCC1 - 111 - 11
212ACEACEALAALAchain DDD1 - 111 - 11

NCS ensembles :
ID
1
2

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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.: 2
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 3-phosphoinositide-dependent protein kinase 1 / hPDK1


Mass: 1674.854 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: O15530, non-specific serine/threonine protein kinase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.12 Å3/Da / Density % sol: 42.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG 3350, Ammonium Acetate, Bis-tris / PH range: 6.0-8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. obs: 15751 / % possible obs: 93.2 % / Redundancy: 2.9 % / CC1/2: 0.99 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.045 / Rrim(I) all: 0.085 / Rsym value: 0.063 / Net I/σ(I): 15.11
Reflection shellResolution: 2.7→2.75 Å / Rmerge(I) obs: 0.208 / Num. unique obs: 765 / CC1/2: 0.889 / Rpim(I) all: 0.154 / Rrim(I) all: 0.261 / Rsym value: 0.209 / % possible all: 86.2

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UCS

6ucs


Resolution: 2.71→29.74 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.48 / Phase error: 27.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2517 1583 10.09 %
Rwork0.2234 14101 -
obs0.2262 15684 92.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.71 Å2 / Biso mean: 40.8027 Å2 / Biso min: 28.43 Å2
Refinement stepCycle: final / Resolution: 2.71→29.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4703 0 0 49 4752
Biso mean---35.33 -
Num. residues----625
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1788X-RAY DIFFRACTION3.732TORSIONAL
12B1788X-RAY DIFFRACTION3.732TORSIONAL
21C54X-RAY DIFFRACTION3.732TORSIONAL
22D54X-RAY DIFFRACTION3.732TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.71-2.790.3861290.30591177130686
2.79-2.890.32181270.28171178130586
2.89-3.010.28261430.28851178132188
3.01-3.150.30321410.28091276141791
3.15-3.310.27751430.25071253139694
3.31-3.520.26891480.22121303145195
3.52-3.790.24311460.21481330147696
3.79-4.170.22751540.20261314146897
4.17-4.770.21211540.17851371152598
4.77-60.19961530.21375152898
6-29.740.2361450.20211346149193
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)
10.85690.5459-0.46982.4681-0.09581.93570.1793-0.0538-0.2520.8436-0.2379-0.40770.1507-0.045500.2921-0.0961-0.0410.36170.07970.2356-21.865.249-40.893
20.78210.11190.20181.68640.11670.92370.11730.09450.07460.0762-0.2149-0.3419-0.36690.139800.3225-0.0692-0.00140.37210.04770.2345-17.6822.114-48.91
30.28950.3130.01170.1343-0.28820.2920.79910.3932-0.07120.0127-0.9311-1.1514-1.99980.4317-0-1.2847-0.38290.21920.69060.25850.6396-4.15213.978-51.37
40.0276-0.3651-0.61940.4296-0.20130.6120.80430.8147-1.38971.4487-0.2724-1.54540.93390.5359-00.07660.0958-0.28730.4970.24920.8877-5.4131.31-46.974
50.7487-0.1785-0.14132.77470.00811.72580.00980.1177-0.0012-0.0544-0.0778-0.3191-0.0325-0.0219-00.3190.06270.01910.2122-0.00210.2341-3.80929.602-17.813
60.8073-0.2514-0.46220.64230.35590.2615-0.2646-0.59130.73120.3732-0.0530.2331-0.5942-1.4719-00.52220.0346-0.12050.1719-0.07460.4196-12.50344.557-9.525
71.20910.6423-0.71760.86290.13771.35670.1026-0.1090.1090.1791-0.14330.4078-0.0201-0.38900.389-0.01520.00440.3822-0.06490.3647-21.90528.321-10.686
80.0087-0.01990.0047-0.0024-0.0027-0.0013-0.22040.305-0.1967-0.1937-0.0818-0.4232-0.0390.396900.7169-0.00160.03650.5925-0.02690.687-19.7446.425-60.923
90.01320.0128-0.00140.0126-0.0184-0.0023-0.1139-0.7066-0.28490.44070.06320.3453-0.0218-0.1423-00.71760.03-0.10390.77890.0390.6557-6.62628.3831.682
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 30:148 )A30 - 148
2X-RAY DIFFRACTION2( CHAIN A AND RESID 149:233 )A149 - 233
3X-RAY DIFFRACTION3( CHAIN A AND RESID 234:272 )A234 - 272
4X-RAY DIFFRACTION4( CHAIN A AND RESID 273:332 )A273 - 332
5X-RAY DIFFRACTION5( CHAIN B AND RESID 30:167 )B30 - 167
6X-RAY DIFFRACTION6( CHAIN B AND RESID 168:233 )B168 - 233
7X-RAY DIFFRACTION7( CHAIN B AND RESID 234:334 )B234 - 334
8X-RAY DIFFRACTION8( CHAIN C AND RESID 11:11 )C11
9X-RAY DIFFRACTION9( CHAIN D AND RESID 11:11 )D11

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