[English] 日本語
Yorodumi
- PDB-8ws1: Crystal structure of human NEK7 D161N mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ws1
TitleCrystal structure of human NEK7 D161N mutant
ComponentsSerine/threonine-protein kinase Nek7
KeywordsCELL CYCLE / Kinase / Complex / autoinhibitory / human / inflammasomes
Function / homology
Function and homology information


NEK6-subfamily protein kinase / Activation of NIMA Kinases NEK9, NEK6, NEK7 / Nuclear Pore Complex (NPC) Disassembly / cellular response to potassium ion / positive regulation of NLRP3 inflammasome complex assembly / positive regulation of telomere maintenance / microtubule organizing center / spindle assembly / EML4 and NUDC in mitotic spindle formation / regulation of mitotic cell cycle ...NEK6-subfamily protein kinase / Activation of NIMA Kinases NEK9, NEK6, NEK7 / Nuclear Pore Complex (NPC) Disassembly / cellular response to potassium ion / positive regulation of NLRP3 inflammasome complex assembly / positive regulation of telomere maintenance / microtubule organizing center / spindle assembly / EML4 and NUDC in mitotic spindle formation / regulation of mitotic cell cycle / molecular function activator activity / spindle pole / microtubule / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / nucleoplasm / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Serine-threonine/tyrosine-protein kinase, catalytic domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / 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
Serine/threonine-protein kinase Nek7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBijpuria, S. / Kanavalli, M. / Subbiah, R. / Mollard, A. / Bearss, D.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To Be Published
Title: Crystal structure of human NEK7 D161N mutant
Authors: Bijpuria, S. / Kanavalli, M. / Subbiah, R. / Mollard, A. / Bearss, D.
History
DepositionOct 16, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine/threonine-protein kinase Nek7
B: Serine/threonine-protein kinase Nek7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6497
Polymers71,3382
Non-polymers3105
Water3,171176
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.894, 87.894, 155.319
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein Serine/threonine-protein kinase Nek7 / Never in mitosis A-related kinase 7 / NimA-related protein kinase 7


Mass: 35669.125 Da / Num. of mol.: 2 / Mutation: D161N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NEK7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TDX7, NEK6-subfamily protein kinase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.78 Å3/Da / Density % sol: 55.74 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris pH 8.4, PEG 8000 15%

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.4→43.99 Å / Num. obs: 27883 / % possible obs: 100 % / Redundancy: 10.1 % / CC1/2: 0.999 / Net I/σ(I): 14.9
Reflection shellResolution: 2.4→2.53 Å / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4011 / CC1/2: 0.794

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DE2

5de2


Resolution: 2.4→43.99 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.941 / SU B: 9.031 / SU ML: 0.2 / Cross valid method: THROUGHOUT / ESU R: 0.325 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23837 1365 4.9 %RANDOM
Rwork0.17929 ---
obs0.18234 26478 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.821 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20.32 Å20 Å2
2--0.65 Å2-0 Å2
3----2.11 Å2
Refinement stepCycle: 1 / Resolution: 2.4→43.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4347 0 20 176 4543
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0134478
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154305
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.6486037
X-RAY DIFFRACTIONr_angle_other_deg1.2441.5839919
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2185540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.00821.811243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.95715808
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2991532
X-RAY DIFFRACTIONr_chiral_restr0.0720.2561
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024989
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021039
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.5115.662154
X-RAY DIFFRACTIONr_mcbond_other4.5125.6592153
X-RAY DIFFRACTIONr_mcangle_it6.6518.4742687
X-RAY DIFFRACTIONr_mcangle_other6.658.4762688
X-RAY DIFFRACTIONr_scbond_it5.2626.2772324
X-RAY DIFFRACTIONr_scbond_other5.2616.2782325
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.0989.1463348
X-RAY DIFFRACTIONr_long_range_B_refined10.85364.6644879
X-RAY DIFFRACTIONr_long_range_B_other10.84964.6454871
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 99 -
Rwork0.262 1923 -
obs--100 %

+
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