[English] 日本語
Yorodumi
- PDB-4g3d: Crystal structure of human NF-kappaB inducing kinase (NIK) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4g3d
TitleCrystal structure of human NF-kappaB inducing kinase (NIK)
ComponentsNF-kappa-beta-inducing kinase
KeywordsTRANSFERASE / non-RD kinase / protein serine/threonine kinase / NF-kappaB / MAP3K14
Function / homology
Function and homology information


TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / mitogen-activated protein kinase kinase kinase / non-canonical NF-kappaB signal transduction / CD28 dependent PI3K/Akt signaling / MAP kinase kinase kinase activity / canonical NF-kappaB signal transduction / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / Dectin-1 mediated noncanonical NF-kB signaling / fibrillar center ...TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / mitogen-activated protein kinase kinase kinase / non-canonical NF-kappaB signal transduction / CD28 dependent PI3K/Akt signaling / MAP kinase kinase kinase activity / canonical NF-kappaB signal transduction / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / Dectin-1 mediated noncanonical NF-kB signaling / fibrillar center / cellular response to mechanical stimulus / defense response to virus / protein kinase activity / immune response / phosphorylation / protein serine kinase activity / intracellular membrane-bounded organelle / 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 / Serine/Threonine protein kinases, catalytic 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
Mitogen-activated protein kinase kinase kinase 14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsHymowitz, S.G. / de Leon-Boenig, G.
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 15, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Jan 24, 2018Group: Refinement description / Structure summary / Category: audit_author / software / Item: _audit_author.name / _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _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
B: NF-kappa-beta-inducing kinase
D: NF-kappa-beta-inducing kinase
E: NF-kappa-beta-inducing kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,9227
Polymers162,8504
Non-polymers733
Water32418
1
A: NF-kappa-beta-inducing kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7372
Polymers40,7121
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NF-kappa-beta-inducing kinase


Theoretical massNumber of molelcules
Total (without water)40,7121
Polymers40,7121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
D: NF-kappa-beta-inducing kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7372
Polymers40,7121
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
E: NF-kappa-beta-inducing kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7372
Polymers40,7121
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.746, 145.851, 230.818
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.998665, 0.04522, 0.024954), (-0.017572, 0.751816, -0.659138), (-0.048567, 0.65782, 0.751608)-8.16074, 5.4088, -23.18439
3given(-0.988703, 0.130267, -0.074143), (-0.065251, 0.071258, 0.995321), (0.134941, 0.988915, -0.061953)43.4327, -78.60721, 38.17986
4given(-0.993738, 0.07328, 0.084353), (-0.007207, 0.711314, -0.702838), (-0.111505, -0.699044, -0.706331)37.34609, 40.64146, 160.30974

-
Components

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


Mass: 40712.395 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP3K14, NF-kappaB inducing kinase (NIK), NIK / Plasmid: pAcGP67 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9
References: UniProt: Q99558, mitogen-activated protein kinase kinase kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.36 Å3/Da / Density % sol: 47.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1:1 protein and well solution of 100 mM imidazole (pH 6.5), 1 M sodium acetate tri-hydrate, 7.5% 1,6-hexanediol, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 28, 2008
RadiationMonochromator: 0.97945 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 35489 / Num. obs: 35489 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Net I/σ(I): 21.8
Reflection shellResolution: 2.9→3 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 3.6 / Rsym value: 0.611 / % possible all: 100

-
Processing

Software
NameVersionClassification
Web-Icedata collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→47.57 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.887 / SU B: 35.575 / SU ML: 0.314 / Cross valid method: THROUGHOUT / ESU R Free: 0.443 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26646 2687 8 %RANDOM
Rwork0.20071 ---
obs0.20601 31030 95.22 %-
all-33717 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 80.574 Å2
Baniso -1Baniso -2Baniso -3
1-4.77 Å2-0 Å2-0 Å2
2---3.53 Å20 Å2
3----1.24 Å2
Refinement stepCycle: LAST / Resolution: 2.9→47.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9325 0 3 18 9346
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0199527
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0391.96512889
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.15451199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.89423.698411
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.73151601
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.031565
X-RAY DIFFRACTIONr_chiral_restr0.0640.21413
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217193
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.96 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rwork0.256 1625 -
Rfree-0 -
obs--85.8 %
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)
10.98390.59040.07092.7521-0.78550.32040.1485-0.16350.0389-0.2912-0.10380.00390.0720.0364-0.04480.375-0.02980.00050.3781-0.00980.456910.137330.503439.3384
21.04520.0519-0.06521.9936-0.870.91460.14260.10080.10430.1758-0.17170.020.02090.07920.0290.2848-0.03080.00240.47450.06890.41458.71486.234953.3823
30.94250.648-0.19571.0184-0.43112.76630.00350.0218-0.0901-0.22150.0532-0.0359-0.2037-0.0375-0.05670.4410.02040.04710.3374-0.04580.418514.683560.78630.8365
42.46570.47820.0050.56550.3291.23140.2758-0.1189-0.24760.1237-0.1548-0.02690.00480.0175-0.1210.2782-0.0095-0.05140.43670.01290.473412.576252.149357.3259
50.62690.4678-1.50492.3124-0.93033.86640.1784-0.0067-0.00730.3785-0.22960.2159-0.2890.25110.05120.70450.00360.1020.3211-0.03340.188425.09124.204110.331
61.15490.0605-0.49831.5099-1.05313.19460.13060.16850.0637-0.03990.1295-0.131-0.8046-0.1557-0.26020.8244-0.09310.1240.15080.04620.259931.220216.808885.9221
71.61130.2929-0.55062.5195-0.18362.44380.04930.13370.08270.21690.0141-0.00330.33870.0196-0.06340.64840-0.10670.26540.01190.24340.714875.508890.2764
82.45580.5521-1.11534.2014-1.07150.7401-0.12560.152-0.16760.41730.0531-0.04260.2472-0.03410.07251.26970.0573-0.08780.0684-0.01140.103838.87347.853395.7349
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A332 - 470
2X-RAY DIFFRACTION2A471 - 671
3X-RAY DIFFRACTION3B332 - 470
4X-RAY DIFFRACTION4B471 - 666
5X-RAY DIFFRACTION5D338 - 470
6X-RAY DIFFRACTION6D471 - 657
7X-RAY DIFFRACTION7E332 - 470
8X-RAY DIFFRACTION8E471 - 663

+
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