[English] 日本語
Yorodumi
- PDB-9j20: Structure of WDR5 in complex with KIF2A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9j20
TitleStructure of WDR5 in complex with KIF2A
Components
  • Kinesin-like protein KIF2A
  • WD repeat-containing protein 5
KeywordsCYTOSOLIC PROTEIN / WDR5 / WIN motif / KIF2A
Function / homology
Function and homology information


centriolar subdistal appendage / 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 / Kinesins / kinesin complex ...centriolar subdistal appendage / 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 / Kinesins / kinesin complex / microtubule depolymerization / Cardiogenesis / microtubule motor activity / COPI-dependent Golgi-to-ER retrograde traffic / microtubule-based movement / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / cytoskeletal motor activity / regulation of cell division / regulation of embryonic development / MLL1 complex / histone acetyltransferase complex / mitotic spindle assembly / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / : / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / centriole / positive regulation of gluconeogenesis / MHC class II antigen presentation / Resolution of Sister Chromatid Cohesion / transcription initiation-coupled chromatin remodeling / regulation of cell migration / mitotic spindle organization / gluconeogenesis / skeletal system development / RHO GTPases Activate Formins / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / PKMTs methylate histone lysines / microtubule cytoskeleton organization / spindle / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / spindle pole / mitotic spindle / Separation of Sister Chromatids / nervous system development / HATs acetylate histones / Neddylation / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / microtubule binding / histone binding / microtubule / cell differentiation / regulation of cell cycle / nuclear body / ciliary basal body / cell division / centrosome / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / nucleolus / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / nucleoplasm / ATP binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
: / Kinesin-like protein KIF2A-like, N-terminal / Kinesin-like protein / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily ...: / Kinesin-like protein KIF2A-like, N-terminal / Kinesin-like protein / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Kinesin-like protein KIF2A / WD repeat-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsXu, L. / Yang, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Biochim.Biophys.Sin. / Year: 2025
Title: Crystal structures of Kif2A complexed with WDR5 reveal the structural plasticity of WIN-S7 sites.
Authors: Yang, Y. / Zhang, S. / Wu, Z. / Li, W. / Sun, X. / Xuan, Y. / Hang, T. / Xu, L. / Chen, X.
History
DepositionAug 6, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: WD repeat-containing protein 5
D: Kinesin-like protein KIF2A
A: WD repeat-containing protein 5
C: Kinesin-like protein KIF2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2796
Polymers71,1554
Non-polymers1242
Water5,459303
1
B: WD repeat-containing protein 5
D: Kinesin-like protein KIF2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7014
Polymers35,5772
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-4 kcal/mol
Surface area11650 Å2
MethodPISA
2
A: WD repeat-containing protein 5
C: Kinesin-like protein KIF2A


Theoretical massNumber of molelcules
Total (without water)35,5772
Polymers35,5772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-3 kcal/mol
Surface area11570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.874, 47.150, 104.309
Angle α, β, γ (deg.)90.00, 107.47, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 34646.309 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 Kinesin-like protein KIF2A / Kinesin-2 / hK2


Mass: 931.009 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIF2A, KIF2, KNS2 / Production host: Escherichia coli (E. coli) / References: UniProt: O00139
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES (pH 7.5) and 18% PEG 600

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.85→40 Å / Num. obs: 51828 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.048 / Rrim(I) all: 0.125 / Net I/σ(I): 10.2 / Num. measured all: 355002
Reflection shellResolution: 1.85→1.95 Å / % possible obs: 100 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.587 / Num. measured all: 51186 / Num. unique obs: 7523 / CC1/2: 0.895 / Rpim(I) all: 0.244 / Rrim(I) all: 0.637 / Net I/σ(I) obs: 3.4

-
Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
SCALAdata scaling
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→34.1 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2063 2534 4.9 %
Rwork0.171 --
obs0.1727 51689 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→34.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4785 0 8 303 5096
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134923
X-RAY DIFFRACTIONf_angle_d1.2686691
X-RAY DIFFRACTIONf_dihedral_angle_d7.792662
X-RAY DIFFRACTIONf_chiral_restr0.084759
X-RAY DIFFRACTIONf_plane_restr0.01836
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.890.25541410.23052689X-RAY DIFFRACTION99
1.89-1.920.23531620.20162659X-RAY DIFFRACTION99
1.92-1.970.21421590.18822718X-RAY DIFFRACTION99
1.97-2.010.23121610.1832662X-RAY DIFFRACTION100
2.01-2.060.22771140.18132735X-RAY DIFFRACTION100
2.06-2.120.27141420.18662703X-RAY DIFFRACTION99
2.12-2.180.21471620.18762664X-RAY DIFFRACTION100
2.18-2.250.22771320.18392769X-RAY DIFFRACTION100
2.25-2.330.22881240.18482693X-RAY DIFFRACTION100
2.33-2.420.22911270.18622758X-RAY DIFFRACTION100
2.42-2.530.24331080.19212733X-RAY DIFFRACTION100
2.53-2.670.21551300.19722764X-RAY DIFFRACTION100
2.67-2.830.24171470.18792726X-RAY DIFFRACTION100
2.84-3.050.2511500.18512728X-RAY DIFFRACTION100
3.05-3.360.22691540.16972756X-RAY DIFFRACTION100
3.36-3.850.15751190.14382771X-RAY DIFFRACTION100
3.85-4.840.13251390.1272774X-RAY DIFFRACTION100
4.84-34.10.17611630.1592853X-RAY DIFFRACTION100
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)
11.9170.44540.02111.6230.39281.69160.0089-0.0390.08950.08320.0275-0.07-0.00270.0596-0.03250.0940.0210.00210.0577-0.00380.144216.6533-11.46395.675
28.5341-2.91960.08655.5524.32944.2671-0.179-0.0180.15220.16910.05380.3009-0.4172-0.30480.12260.16040.0301-0.00990.0750.0150.21214.0201-5.66083.1483
30.86120.10660.0631.4720.42891.41830.0899-0.10520.0069-0.029-0.29310.1395-0.0187-0.60230.17110.14460.00710.00510.5397-0.080.1445-0.331-7.931744.5123
49.37066.06133.38967.63961.77325.8053-0.0126-0.3484-0.0381-0.11740.1388-0.43980.21490.7442-0.11540.15120.052-0.02040.3668-0.03660.234412.6884-2.624545.9841
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'B' and resid 31 through 334)
2X-RAY DIFFRACTION2(chain 'D' and resid 114 through 121)
3X-RAY DIFFRACTION3(chain 'A' and resid 31 through 334)
4X-RAY DIFFRACTION4(chain 'C' and resid 114 through 121)

+
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