PDB-8yhw: The Crystal Structure of NF-kB-inducing Kinase (NIK) from Biortus

ID or keywords:

Entry

Database: PDB / ID: 8yhw

Title

The Crystal Structure of NF-kB-inducing Kinase (NIK) from Biortus

Components

Mitogen-activated protein kinase kinase kinase 14

Keywords

TRANSFERASE / Serine/threonine-protein kinase / ATP-binding / Nucleotide-binding

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 ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.9 Å

Authors

Wang, F. / Cheng, W. / Lv, Z. / Meng, Q. / Xu, Y.

Funding support

China, 1items

Citation

Journal: To Be Published
Title: The Crystal Structure of NF-kB-inducing Kinase (NIK) from Biortus
Authors: Wang, F. / Cheng, W. / Lv, Z. / Meng, Q. / Xu, Y.

History

Deposition	Feb 28, 2024	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Mar 13, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8yhw.cif.gz	283.2 KB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	8yhw.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8yhw_validation.pdf.gz	3.9 MB	Display	wwPDB validaton report
Full document	8yhw_full_validation.pdf.gz	4 MB	Display
Data in XML	8yhw_validation.xml.gz	48.2 KB	Display
Data in CIF	8yhw_validation.cif.gz	66 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yh/8yhw ftp://data.pdbj.org/pub/pdb/validation_reports/yh/8yhw	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#60 - Dec 2004 Ubiquitin similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1)

Deposited unit

A: Mitogen-activated protein kinase kinase kinase 14

B: Mitogen-activated protein kinase kinase kinase 14

C: Mitogen-activated protein kinase kinase kinase 14

D: Mitogen-activated protein kinase kinase kinase 14

hetero molecules

158 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Mitogen-activated protein kinase kinase kinase 14

hetero molecules

defined by author&software
Evidence: gel filtration
39.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Mitogen-activated protein kinase kinase kinase 14

hetero molecules

defined by author&software
39.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Mitogen-activated protein kinase kinase kinase 14

hetero molecules

defined by author&software
39.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Mitogen-activated protein kinase kinase kinase 14

hetero molecules

defined by author&software
39.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	119.652, 119.652, 115.586
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	76
Space group name H-M	P4₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A
3	2	A
4	2	A
5	3	A
6	3	A
7	4	A
8	4	A
9	5	A
10	5	A
11	6	A
12	6	A

NCS domain segments:

Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: PRO / End label comp-ID: PRO / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 334 - 675 / Label seq-ID: 6 - 347

Dom-ID	Component-ID	Ens-ID
1	1	1
2	1	1
3	2	2
4	2	2
5	3	3
6	3	3
7	4	4
8	4	4
9	5	5
10	5	5
11	6	6
12	6	6

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Mitogen-activated protein kinase kinase kinase 14 / NF-kappa-beta-inducing kinase / HsNIK / Serine/threonine-protein kinase NIK Mass: 38728.227 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAP3K14, NIK / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q99558, mitogen-activated protein kinase kinase kinase

#1: Protein

Mitogen-activated protein kinase kinase kinase 14 / NF-kappa-beta-inducing kinase / HsNIK / Serine/threonine-protein kinase NIK

Mass: 38728.227 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: MAP3K14, NIK / Production host:

Spodoptera frugiperda (fall armyworm)
References: UniProt: Q99558, mitogen-activated protein kinase kinase kinase

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Non-polymers , 5 types, 161 molecules

#2: Chemical	ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE Mass: 523.247 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₂P₃S / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₆O₂ / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL Mass: 370.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₆H₃₄O₉ / Feature type: SUBJECT OF INVESTIGATION
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.67 Å³/Da / Density % sol: 53.94 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M MMT pH9.0, 25% PEG1500

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.18079 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 28, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.18079 Å / Relative weight: 1
Reflection	Resolution: 2.9→48.56 Å / Num. obs: 36217 / % possible obs: 100 % / Redundancy: 9.4 % / CC_1/2: 0.992 / Net I/σ(I): 11.2
Reflection shell	Resolution: 2.9→3.03 Å / Num. unique obs: 4398 / CC_1/2: 0.709

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0419	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.9→48.56 Å / Cor.coef. F_o:F_c: 0.927 / Cor.coef. F_o:F_c free: 0.889 / SU B: 15.609 / SU ML: 0.292 / Cross valid method: FREE R-VALUE / ESU R Free: 0.395
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2412	1628	4.499 %
R_work	0.194	34558	-
all	0.196	-	-
obs	-	36186	99.967 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 49.624 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.255 Å²	-0 Å²	-0 Å²
2-	-	0.255 Å²	-0 Å²
3-	-	-	-0.509 Å²

Refinement step

Cycle: LAST / Resolution: 2.9→48.56 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10356	0	173	147	10676

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.004	0.012	10798
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	10078
X-RAY DIFFRACTION	r_angle_refined_deg	1.179	1.856	14596
X-RAY DIFFRACTION	r_angle_other_deg	0.398	1.756	23301
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.144	5	1327
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	5.004	5	88
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	0.319	5	4
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.249	10	1792
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	12.801	10	471
X-RAY DIFFRACTION	r_chiral_restr	0.057	0.2	1564
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	12694
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2382
X-RAY DIFFRACTION	r_nbd_refined	0.216	0.2	2273
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.185	0.2	9472
X-RAY DIFFRACTION	r_nbtor_refined	0.171	0.2	5161
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.079	0.2	5366
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.126	0.2	235
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.065	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.153	0.2	18
X-RAY DIFFRACTION	r_nbd_other	0.199	0.2	81
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.174	0.2	4
X-RAY DIFFRACTION	r_mcbond_it	2.891	4.926	5332
X-RAY DIFFRACTION	r_mcbond_other	2.878	4.926	5332
X-RAY DIFFRACTION	r_mcangle_it	4.828	8.846	6651
X-RAY DIFFRACTION	r_mcangle_other	4.829	8.848	6652
X-RAY DIFFRACTION	r_scbond_it	2.877	5.253	5466
X-RAY DIFFRACTION	r_scbond_other	2.877	5.253	5467
X-RAY DIFFRACTION	r_scangle_it	4.861	9.527	7945
X-RAY DIFFRACTION	r_scangle_other	4.86	9.527	7946
X-RAY DIFFRACTION	r_lrange_it	7.652	47.034	11731
X-RAY DIFFRACTION	r_lrange_other	7.65	47.047	11725
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.06	0.05	10656
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.066	0.05	10586
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.061	0.05	10520
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.063	0.05	10615
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.059	0.05	10535
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.062	0.05	10439

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.06013	0.0501
1	2	A	X-RAY DIFFRACTION	Local ncs	0.06013	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.06614	0.0501
2	4	A	X-RAY DIFFRACTION	Local ncs	0.06614	0.0501
3	5	A	X-RAY DIFFRACTION	Local ncs	0.06075	0.0501
3	6	A	X-RAY DIFFRACTION	Local ncs	0.06075	0.0501
4	7	A	X-RAY DIFFRACTION	Local ncs	0.06297	0.0501
4	8	A	X-RAY DIFFRACTION	Local ncs	0.06297	0.0501
5	9	A	X-RAY DIFFRACTION	Local ncs	0.05881	0.0501
5	10	A	X-RAY DIFFRACTION	Local ncs	0.05881	0.0501
6	11	A	X-RAY DIFFRACTION	Local ncs	0.06213	0.0501
6	12	A	X-RAY DIFFRACTION	Local ncs	0.06213	0.0501

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.9-2.975	0.342	110	0.283	2568	X-RAY DIFFRACTION	99.9627
2.975-3.056	0.275	96	0.255	2467	X-RAY DIFFRACTION	100
3.056-3.145	0.281	105	0.252	2429	X-RAY DIFFRACTION	100
3.145-3.241	0.328	118	0.235	2331	X-RAY DIFFRACTION	100
3.241-3.347	0.289	124	0.231	2225	X-RAY DIFFRACTION	100
3.347-3.464	0.251	133	0.217	2177	X-RAY DIFFRACTION	99.9567
3.464-3.594	0.228	116	0.192	2100	X-RAY DIFFRACTION	100
3.594-3.739	0.214	116	0.176	2013	X-RAY DIFFRACTION	100
3.739-3.905	0.237	62	0.184	1969	X-RAY DIFFRACTION	100
3.905-4.094	0.221	85	0.174	1889	X-RAY DIFFRACTION	100
4.094-4.314	0.237	76	0.173	1781	X-RAY DIFFRACTION	100
4.314-4.573	0.203	82	0.156	1697	X-RAY DIFFRACTION	100
4.573-4.886	0.23	96	0.156	1560	X-RAY DIFFRACTION	100
4.886-5.273	0.221	89	0.176	1474	X-RAY DIFFRACTION	100
5.273-5.769	0.342	47	0.198	1382	X-RAY DIFFRACTION	100
5.769-6.439	0.206	51	0.193	1247	X-RAY DIFFRACTION	100
6.439-7.413	0.207	18	0.173	1132	X-RAY DIFFRACTION	100
7.413-9.027	0.181	36	0.159	943	X-RAY DIFFRACTION	100
9.027-12.552	0.189	51	0.163	725	X-RAY DIFFRACTION	100
12.552-48.56	0.315	18	0.308	449	X-RAY DIFFRACTION	99.7863

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