PDB-9esa: Aurora-C with SER mutation in complex with INCENP peptide

ID or keywords:

Entry

Database: PDB / ID: 9esa

Title

Aurora-C with SER mutation in complex with INCENP peptide

Components

Aurora kinase C
Inner centromere protein

Keywords

TRANSCRIPTION / surface entropy reduction / SER / KINASE / TRANSFERASE

Function / homology

Function and homology information

central element / meiotic spindle midzone / meiotic spindle midzone assembly / positive regulation of mitotic sister chromatid separation / positive regulation of mitotic cytokinesis / metaphase chromosome alignment / positive regulation of mitotic cell cycle spindle assembly checkpoint / mitotic spindle midzone assembly / positive regulation of attachment of mitotic spindle microtubules to kinetochore / attachment of spindle microtubules to kinetochore ...central element / meiotic spindle midzone / meiotic spindle midzone assembly / positive regulation of mitotic sister chromatid separation / positive regulation of mitotic cytokinesis / metaphase chromosome alignment / positive regulation of mitotic cell cycle spindle assembly checkpoint / mitotic spindle midzone assembly / positive regulation of attachment of mitotic spindle microtubules to kinetochore / attachment of spindle microtubules to kinetochore / chromocenter / lateral element / chromosome passenger complex / positive regulation of cytokinesis / mitotic cytokinesis / SUMOylation of DNA replication proteins / chromosome, centromeric region / mitotic spindle assembly / spindle midzone / pericentric heterochromatin / condensed chromosome / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / protein serine/threonine/tyrosine kinase activity / Resolution of Sister Chromatid Cohesion / molecular function activator activity / regulation of cytokinesis / mitotic spindle organization / meiotic cell cycle / spindle microtubule / chromosome segregation / RHO GTPases Activate Formins / kinetochore / spindle / spindle pole / Separation of Sister Chromatids / mitotic cell cycle / microtubule cytoskeleton / midbody / 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 / non-specific serine/threonine protein kinase / protein kinase activity / nuclear body / protein phosphorylation / cell division / protein serine kinase activity / centrosome / protein-containing complex / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

Hillig, R.C.

Funding support

1items

Citation

Journal: Acta Crystallogr D Struct Biol / Year: 2024
Title: Surface-mutagenesis strategies to enable structural biology crystallization platforms.
Authors: Schaefer, M. / Putter, V. / Hilpmann, A. / Egner, U. / Holton, S.J. / Hillig, R.C.

History

Deposition	Mar 26, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 11, 2024	Provider: repository / Type: Initial release
Revision 1.1	Sep 25, 2024	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9esa.cif.gz	263.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9esa.ent.gz		Display	PDB format
PDBx/mmJSON format	9esa.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/es/9esa ftp://data.pdbj.org/pub/pdb/validation_reports/es/9esa	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	#205 - Jan 2017 Nuclear Pore Complex similarity (6) #150 - Jun 2012 Sliding Clamps similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #245 - May 2020 Spliceosomes similarity (1) #43 - Jul 2003 Src Tyrosine Kinase similarity (1) #60 - Dec 2004 Ubiquitin similarity (1)

Deposited unit

AAA: Aurora kinase C

BBB: Aurora kinase C

CCC: Inner centromere protein

DDD: Inner centromere protein

hetero molecules

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

1

AAA: Aurora kinase C

CCC: Inner centromere protein

defined by author
Evidence: gel filtration
41.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

BBB: Aurora kinase C

DDD: Inner centromere protein

hetero molecules

defined by author
41.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	79.280, 79.490, 265.240
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	AAA
2	1	BBB
3	2	CCC
4	2	DDD

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	SER	SER	GLN	GLN	AAA	A	32 - 306	26 - 300
2	2	1	SER	SER	GLN	GLN	BBB	B	32 - 306	26 - 300
3	3	2	PRO	PRO	LYS	LYS	CCC	C	841 - 882	8 - 49
4	4	2	PRO	PRO	LYS	LYS	DDD	D	841 - 882	8 - 49

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4

#1: Protein	Aurora kinase C / Aurora 3 / Aurora/IPL1-related kinase 3 / ARK-3 / Aurora-related kinase 3 / Aurora/IPL1/Eg2 protein ...Aurora 3 / Aurora/IPL1-related kinase 3 / ARK-3 / Aurora-related kinase 3 / Aurora/IPL1/Eg2 protein 2 / Serine/threonine-protein kinase 13 / Serine/threonine-protein kinase aurora-C Mass: 34988.336 Da / Num. of mol.: 2 / Mutation: R195A, R196A, K197A Source method: isolated from a genetically manipulated source Details: TRIPPLE SURFACE ENTROPY REDUCTION (SER) MUTATION R195A/R196A/K197A INTRODUCED TO FACILITATE CRYSTALLIZATION. Source: (gene. exp.) Homo sapiens (human) / Gene: AURKC, AIE2, AIK3, AIRK3, ARK3, STK13 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q9UQB9, non-specific serine/threonine protein kinase
#2: Protein	Inner centromere protein Mass: 6857.935 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: INCENP / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9NQS7
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.5 Å³/Da / Density % sol: 50.73 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M Bis-Tris pH5.5, 0.025-0.05 M ammonium sulphate, 9-12% PEG3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5405 Å
Detector	Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 20, 2006
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5405 Å / Relative weight: 1
Reflection	Resolution: 2.8→19.87 Å / Num. obs: 21012 / % possible obs: 99.6 % / Redundancy: 4.8 % / R_merge(I) obs: 0.126 / Net I/σ(I): 6.1
Reflection shell	Resolution: 2.8→2.9 Å / Redundancy: 5.1 % / R_merge(I) obs: 0.35 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2057 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
CrystalClear	1.3.6sp3	data reduction
CrystalClear	1.3.6sp3	data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.8→19.87 Å / Cor.coef. F_o:F_c: 0.94 / Cor.coef. F_o:F_c free: 0.886 / SU B: 43.446 / SU ML: 0.39 / Cross valid method: FREE R-VALUE / ESU R Free: 0.433
Details: Hydrogens have been added in their riding positions.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.294	1075	5.127 %	Random selection
R_work	0.2279	19891	-	-
all	0.231	-	-	-
obs	0.2313	20966	99.252 %	-

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: 69.968 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.348 Å²	-0 Å²	0 Å²
2-	-	-4.312 Å²	-0 Å²
3-	-	-	4.659 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→19.87 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5214	0	4	56	5274

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.004	0.013	5379
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	5222
X-RAY DIFFRACTION	r_angle_refined_deg	1.279	1.65	7293
X-RAY DIFFRACTION	r_angle_other_deg	1.052	1.575	12041
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.453	5	639
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.31	20.6	300
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.002	15	956
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.167	15	49
X-RAY DIFFRACTION	r_chiral_restr	0.048	0.2	676
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	5912
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1238
X-RAY DIFFRACTION	r_nbd_refined	0.19	0.2	1065
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.172	0.2	4664
X-RAY DIFFRACTION	r_nbtor_refined	0.156	0.2	2476
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.074	0.2	2606
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.134	0.2	93
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.276	0.2	15
X-RAY DIFFRACTION	r_nbd_other	0.21	0.2	60
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.055	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	3.087	3.604	2553
X-RAY DIFFRACTION	r_mcbond_other	3.081	3.604	2552
X-RAY DIFFRACTION	r_mcangle_it	5.054	8.095	3187
X-RAY DIFFRACTION	r_mcangle_other	5.055	8.097	3188
X-RAY DIFFRACTION	r_scbond_it	3.202	3.927	2826
X-RAY DIFFRACTION	r_scbond_other	3.201	3.927	2826
X-RAY DIFFRACTION	r_scangle_it	5.297	8.619	4104
X-RAY DIFFRACTION	r_scangle_other	5.297	8.62	4105
X-RAY DIFFRACTION	r_lrange_it	7.902	43.238	5774
X-RAY DIFFRACTION	r_lrange_other	7.897	43.222	5772
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.099	0.05	8489
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.097	0.05	1139

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	AAA	X-RAY DIFFRACTION	Local ncs	0.09864	0.05009
1	2	BBB	X-RAY DIFFRACTION	Local ncs	0.09864	0.05009
2	3	CCC	X-RAY DIFFRACTION	Local ncs	0.09734	0.05007
2	4	DDD	X-RAY DIFFRACTION	Local ncs	0.09734	0.05007

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 (%)
2.8-2.871	0.395	63	0.364	1415	X-RAY DIFFRACTION	99.8649
2.871-2.948	0.402	79	0.318	1435	X-RAY DIFFRACTION	100
2.948-3.032	0.332	69	0.294	1314	X-RAY DIFFRACTION	100
3.032-3.123	0.331	80	0.289	1374	X-RAY DIFFRACTION	100
3.123-3.223	0.221	64	0.238	1254	X-RAY DIFFRACTION	99.9242
3.223-3.333	0.313	70	0.241	1245	X-RAY DIFFRACTION	99.924
3.333-3.455	0.324	70	0.25	1195	X-RAY DIFFRACTION	100
3.455-3.591	0.255	60	0.228	1162	X-RAY DIFFRACTION	99.8366
3.591-3.745	0.315	59	0.244	1126	X-RAY DIFFRACTION	99.4962
3.745-3.921	0.318	63	0.216	1050	X-RAY DIFFRACTION	99.9102
3.921-4.124	0.334	51	0.221	1020	X-RAY DIFFRACTION	99.6279
4.124-4.363	0.22	55	0.204	970	X-RAY DIFFRACTION	99.7082
4.363-4.648	0.231	43	0.182	944	X-RAY DIFFRACTION	99.697
4.648-4.998	0.302	48	0.209	847	X-RAY DIFFRACTION	99.8884
4.998-5.441	0.392	49	0.238	788	X-RAY DIFFRACTION	99.4062
5.441-6.027	0.266	46	0.232	723	X-RAY DIFFRACTION	99.354
6.027-6.855	0.315	41	0.216	651	X-RAY DIFFRACTION	98.8571
6.855-8.156	0.24	32	0.19	579	X-RAY DIFFRACTION	98.3897
8.156-10.671	0.199	16	0.175	466	X-RAY DIFFRACTION	96.7871
10.671-19.87	0.239	17	0.209	333	X-RAY DIFFRACTION	94.851

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	4.4097	1.2033	-0.2203	3.8749	1.0157	6.9037	-0.0415	-0.2747	0.3991	0.5175	0.0861	-0.0891	-0.1369	-0.0793	-0.0447	0.2244	0.0957	-0.0438	0.382	-0.0467	0.0482	-0.745	-18.635	-39.87
2	3.9912	-0.2158	1.0078	1.8599	0.211	3.6092	0.0838	0.1595	0.2166	0.1379	-0.0089	-0.2995	0.0759	0.5806	-0.0749	0.2807	0.0308	-0.0192	0.6014	0.0049	0.0591	20.248	-27.627	-53.598
3	3.9198	0.9346	0.7264	4.7184	-0.4094	5.8812	0.0507	0.5819	-0.062	-0.2934	-0.0206	0.4619	-0.1663	-0.1971	-0.0301	0.2219	0.087	-0.0493	0.4968	-0.0499	0.0537	-21.096	0.728	-26.45
4	1.3962	-0.3475	0.5342	4.4769	0.9596	3.5035	0.0058	0.0427	-0.2734	0.2187	0.0415	0.2146	0.6394	0.1032	-0.0473	0.4098	0.0312	0.0206	0.5392	0.0027	0.0591	-12.03	-20.396	-12.616
5	3.2704	0.6544	1.8035	1.187	1.2427	6.9676	-0.2187	-0.0414	0.4486	0.2174	0.0818	0.252	0.0587	-0.2482	0.1369	0.1724	0.061	-0.0006	0.5407	-0.0251	0.1033	-6.191	-20.891	-45.255
6	2.3197	1.2351	2.1927	4.943	0.9365	6.0555	-0.0708	0.2452	0.065	-0.0734	-0.1054	0.365	-0.5992	0.0113	0.1762	0.2412	0.1247	-0.0162	0.439	-0.0242	0.0322	-19.054	6.036	-21.277

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	32 - 123
2	X-RAY DIFFRACTION	2	ALL	AAA	124 - 306
3	X-RAY DIFFRACTION	3	ALL	BBB	32 - 123
4	X-RAY DIFFRACTION	4	ALL	BBB	124 - 306
5	X-RAY DIFFRACTION	5	ALL	CCC	841 - 883
6	X-RAY DIFFRACTION	6	ALL	DDD	841 - 884

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