[English] 日本語
Yorodumi
- PDB-4g3g: Crystal structure of murine NF-kappaB inducing kinase (NIK) V408L... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4g3g
TitleCrystal structure of murine NF-kappaB inducing kinase (NIK) V408L bound to a 2-(aminothiazolyl)phenol (cmp3)
ComponentsNF-kappa-beta-inducing kinase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / non-RD kinase / protein serine/threonine kinase / NF-kappaB / MAP3K14 / Structure-based drug design / transferase / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


CD28 dependent PI3K/Akt signaling / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / Dectin-1 mediated noncanonical NF-kB signaling / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / mitogen-activated protein kinase kinase kinase / non-canonical NF-kappaB signal transduction / MAP kinase kinase kinase activity / canonical NF-kappaB signal transduction / fibrillar center ...CD28 dependent PI3K/Akt signaling / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / Dectin-1 mediated noncanonical NF-kB signaling / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / mitogen-activated protein kinase kinase kinase / non-canonical NF-kappaB signal transduction / MAP kinase kinase kinase activity / canonical NF-kappaB signal transduction / fibrillar center / cellular response to mechanical stimulus / defense response to virus / protein kinase activity / immune response / protein serine kinase activity / protein serine/threonine kinase activity / nucleoplasm / ATP binding / cytosol
Similarity search - Function
Mitogen-activated protein (MAP) kinase kinase kinase 14 / M3K14, catalytic domain / : / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...Mitogen-activated protein (MAP) kinase kinase kinase 14 / M3K14, catalytic domain / : / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-0WA / Mitogen-activated protein kinase kinase kinase 14
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHymowitz, S.
CitationJournal: Structure / Year: 2012
Title: The crystal structure of the catalytic domain of the NF-kappaB inducing kinase reveals a narrow but flexible active site.
Authors: de Leon-Boenig, G. / Bowman, K.K. / Feng, J.A. / Crawford, T. / Everett, C. / Franke, Y. / Oh, A. / Stanley, M. / Staben, S.T. / Starovasnik, M.A. / Wallweber, H.J. / Wu, J. / Wu, L.C. / ...Authors: de Leon-Boenig, G. / Bowman, K.K. / Feng, J.A. / Crawford, T. / Everett, C. / Franke, Y. / Oh, A. / Stanley, M. / Staben, S.T. / Starovasnik, M.A. / Wallweber, H.J. / Wu, J. / Wu, L.C. / Johnson, A.R. / Hymowitz, S.G.
History
DepositionJul 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / software / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NF-kappa-beta-inducing kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0932
Polymers38,8061
Non-polymers2871
Water68538
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.423, 135.320, 64.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-822-

HOH

-
Components

#1: Protein NF-kappa-beta-inducing kinase / Serine/threonine-protein kinase NIK


Mass: 38805.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Map3k14, NF-kappaB inducing kinase (NIK), Nik / Plasmid: pAcGP67 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9
References: UniProt: Q9WUL6, mitogen-activated protein kinase kinase kinase
#2: Chemical ChemComp-0WA / 4-fluoro-2-{[4-(pyridin-4-yl)-1,3-thiazol-2-yl]amino}phenol


Mass: 287.312 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H10FN3OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 uL protein plus 0.2 uL of 0.5 mM Cmp3, 100 mM HEPES pH 7.0, 0.01 M zinc chloride, 20% PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 13, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.5→46.57 Å / Num. all: 11486 / Num. obs: 11486 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Rsym value: 0.119 / Net I/σ(I): 15.6
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 1051 / Rsym value: 0.619 / % possible all: 93.3

-
Processing

Software
NameVersionClassification
Web-Icedata collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→46.57 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.905 / SU B: 19.01 / SU ML: 0.209 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 1.69 / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2515 1143 10 %RANDOM
Rwork0.19589 ---
all0.20136 11472 --
obs0.20136 10329 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.35 Å2
Baniso -1Baniso -2Baniso -3
1-1.58 Å20 Å2-0 Å2
2---1.06 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 2.5→46.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2421 0 20 38 2479
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192554
X-RAY DIFFRACTIONr_angle_refined_deg1.1951.9813460
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4265321
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.57823.028109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.91815445
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7721521
X-RAY DIFFRACTIONr_chiral_restr0.0830.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211948
LS refinement shellResolution: 2.5→2.552 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.357 62 -
Rwork0.283 478 -
obs--86.96 %
Refinement TLS params.Method: refined / Origin x: 18.7916 Å / Origin y: 17.6438 Å / Origin z: 2.4961 Å
111213212223313233
T0.0143 Å2-0.0029 Å20.0083 Å2-0.0617 Å2-0.0133 Å2--0.0461 Å2
L0.6051 °20.2004 °20.0736 °2-2.2126 °2-0.4455 °2--1.5469 °2
S-0.0358 Å °-0.0242 Å °-0.0041 Å °-0.003 Å °0.0129 Å °0.1264 Å °0.125 Å °-0.0392 Å °0.0229 Å °

+
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