[English] 日本語
Yorodumi
- PDB-6wjq: Crystal structure of WDR5 in complex with the WIN peptide of PDPK1 -

+
Open data


ID or keywords:

Loading...

-
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


intracellular signaling cassette / Activation of AKT2 / regulation of mast cell degranulation / type B pancreatic cell development / negative regulation of toll-like receptor signaling pathway / 3-phosphoinositide-dependent protein kinase activity / histone H3Q5ser reader activity / histone H3K4me1 reader activity / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / MLL3/4 complex ...intracellular signaling cassette / Activation of AKT2 / regulation of mast cell degranulation / type B pancreatic cell development / negative regulation of toll-like receptor signaling pathway / 3-phosphoinositide-dependent protein kinase activity / histone H3Q5ser reader activity / histone H3K4me1 reader activity / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / MLL3/4 complex / RSK activation / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / regulation of canonical NF-kappaB signal transduction / hyperosmotic response / Cardiogenesis / positive regulation of vascular endothelial cell proliferation / negative regulation of cardiac muscle cell apoptotic process / phospholipase activator activity / Formation of WDR5-containing histone-modifying complexes / positive regulation of sprouting angiogenesis / Constitutive Signaling by AKT1 E17K in Cancer / histone methyltransferase complex / regulation of cell division / MLL1 complex / regulation of embryonic development / histone acetyltransferase complex / CD28 dependent PI3K/Akt signaling / positive regulation of blood vessel endothelial cell migration / Role of LAT2/NTAL/LAB on calcium mobilization / negative regulation of endothelial cell apoptotic process / Estrogen-stimulated signaling through PRKCZ / vascular endothelial cell response to laminar fluid shear stress / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / phospholipase binding / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / GPVI-mediated activation cascade / RHO GTPases activate PKNs / T cell costimulation / extrinsic apoptotic signaling pathway / Integrin signaling / positive regulation of gluconeogenesis / insulin-like growth factor receptor signaling pathway / transcription initiation-coupled chromatin remodeling / cellular response to epidermal growth factor stimulus / positive regulation of release of sequestered calcium ion into cytosol / VEGFR2 mediated cell proliferation / VEGFR2 mediated vascular permeability / skeletal system development / gluconeogenesis / cell projection / positive regulation of protein localization to plasma membrane / phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of transforming growth factor beta receptor signaling pathway / calcium-mediated signaling / CLEC7A (Dectin-1) signaling / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / FCERI mediated NF-kB activation / PKMTs methylate histone lysines / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / epidermal growth factor receptor signaling pathway / cellular response to insulin stimulus / positive regulation of angiogenesis / Regulation of TP53 Degradation / mitotic spindle / Downstream TCR signaling / G beta:gamma signalling through PI3Kgamma / insulin receptor signaling pathway / cell migration / Neddylation / PIP3 activates AKT signaling / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / protein autophosphorylation / actin cytoskeleton organization / cytoplasmic vesicle / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / histone binding / protein phosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / non-specific serine/threonine protein kinase / regulation of cell cycle / postsynaptic density / intracellular signal transduction / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol
Similarity search - Function
PDK1-type, PH domain / PH domain / PDPK1 family / : / WDR5 beta-propeller 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. ...PDK1-type, PH domain / PH domain / PDPK1 family / : / WDR5 beta-propeller 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. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / WD40/YVTN repeat-like-containing domain superfamily / 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
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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
Has protein modificationY

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more