PDB-5yay: Crystal structure of KANK1/KIF21A complex

ID or keywords:

Entry

Database: PDB / ID: 5yay

Title

Crystal structure of KANK1/KIF21A complex

Components

KN motif and ankyrin repeat domains 1
Kinesin-like protein KIF21A

Keywords

PROTEIN BINDING /

Scaffold protein / ANK repeat

Function / homology

Function and homology information

negative regulation of lamellipodium morphogenesis / negative regulation of ruffle assembly / podocyte cell migration / negative regulation of substrate adhesion-dependent cell spreading / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / negative regulation of actin filament polymerization / MHC class II antigen presentation /

ankyrin repeat binding / regulation of Rho protein signal transduction ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.55 Å

Authors

Wei, Z. / Pan, W.

Funding support

China, 2items

Citation

Journal: J. Biol. Chem. / Year: 2018
Title: Structural insights into ankyrin repeat-mediated recognition of the kinesin motor protein KIF21A by KANK1, a scaffold protein in focal adhesion.
Authors: Pan, W. / Sun, K. / Tang, K. / Xiao, Q. / Ma, C. / Yu, C. / Wei, Z.

History

Deposition	Sep 2, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Dec 20, 2017	Provider: repository / Type: Initial release
Revision 1.1	Dec 27, 2017	Group: Database references / Category: citation Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed
Revision 1.2	Mar 7, 2018	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.3	Nov 22, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5yay.cif.gz	118.5 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ya/5yay ftp://data.pdbj.org/pub/pdb/validation_reports/ya/5yay	HTTPS FTP

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Related structure data

Related structure data	5yazC 4hbdS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6tlh-2 6tlh-1 4o8q-1 2p45-d 6tmd-d 4wt3-d 2fyx-d 4nkh-4 2p4a-1 1tr4-d Search similar-shape structures by Omokage search (details) 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	#64 - Apr 2005 Kinesin similarity (8) #88 - Apr 2007 Clathrin similarity (1) #175 - Jul 2014 Microtubules similarity (7) #176 - Aug 2014 Dynein similarity (1) #63 - Mar 2005 T-Cell Receptor similarity (1) #18 - Jun 2001 Myosin similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (7) #174 - Jun 2014 GFP-like Proteins similarity (1)

Deposited unit

A: KN motif and ankyrin repeat domains 1

B: Kinesin-like protein KIF21A

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	38.043, 52.080, 136.095
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	KN motif and ankyrin repeat domains 1 Mass: 27705.535 Da / Num. of mol.: 1 / Fragment: UNP residues 1088-1338 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kank1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(C plus) / References: UniProt: E9Q238
#2: Protein/peptide	Kinesin-like protein KIF21A Mass: 3301.966 Da / Num. of mol.: 1 / Fragment: UNP residues 1142-1169 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q9QXL2
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.17 Å³/Da / Density % sol: 43.42 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.2 M ammonium formate and 20% w/v polyethylene glycol 3350

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL17U1 / Wavelength: 0.98 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 2, 2016

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.98 Å / Relative weight: 1

Reflection

Resolution: 1.55→50 Å / Num. obs: 39577 / % possible obs: 98.2 % / Redundancy: 5.4 % / B_iso Wilson estimate: 22.36 Å² / R_merge(I) obs: 0.057 / R_pim(I) all: 0.028 / R_rim(I) all: 0.064 / Χ²: 1.957 / Net I/σ(I): 15.1

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.55-1.58	5.5	0.835	2005	0.688	0.397	0.929	1.439	100
1.58-1.61	5.5	0.674	1961	0.738	0.322	0.751	1.438	100
1.61-1.64	5.5	0.551	1957	0.819	0.263	0.613	1.432	100
1.64-1.67	5.5	0.443	1984	0.851	0.211	0.493	1.451	100
1.67-1.71	5.5	0.405	1979	0.89	0.192	0.45	1.449	99.9
1.71-1.75	5.5	0.322	1998	0.912	0.154	0.359	1.493	99.9
1.75-1.79	5.6	0.263	1986	0.948	0.125	0.293	1.48	100
1.79-1.84	5.5	0.214	1979	0.967	0.101	0.238	1.537	100
1.84-1.89	5.5	0.173	1997	0.977	0.082	0.192	1.638	99.9
1.89-1.95	5.5	0.138	1988	0.985	0.065	0.153	1.807	99.9
1.95-2.02	5.5	0.114	1993	0.988	0.054	0.127	2.064	99.6
2.02-2.1	5.4	0.093	1987	0.991	0.045	0.104	2.286	99.8
2.1-2.2	5.3	0.077	1992	0.993	0.037	0.086	2.421	99.6
2.2-2.32	5.3	0.069	2014	0.995	0.033	0.077	2.618	99.4
2.32-2.46	5.3	0.065	1977	0.994	0.031	0.073	2.819	99.1
2.46-2.65	5.4	0.053	2001	0.997	0.025	0.059	2.489	98.8
2.65-2.92	5.3	0.043	2015	0.998	0.02	0.047	2.234	97.9
2.92-3.34	5.5	0.039	1993	0.998	0.018	0.043	2.378	98.1
3.34-4.21	5.1	0.038	1973	0.996	0.019	0.043	2.553	94.1
4.21-50	4.5	0.039	1798	0.996	0.021	0.044	2.431	81

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
HKL-2000		data scaling
PHASER		phasing
PHENIX	1.8.4_1496	refinement
PDB_EXTRACT	3.22	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4HBD

4hbd

Resolution: 1.55→28.484 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.64 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1998	1976	5 %
R_work	0.1833	37542	-
obs	0.1841	39518	98.24 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 86.49 Å² / B_iso mean: 35.4218 Å² / B_iso min: 14.42 Å²

Refinement step

Cycle: final / Resolution: 1.55→28.484 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1960	0	0	121	2081
B_iso mean	-	-	-	35.8	-
Num. residues	-	-	-	-	259

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	2022
X-RAY DIFFRACTION	f_angle_d	1.353	2742
X-RAY DIFFRACTION	f_chiral_restr	0.06	321
X-RAY DIFFRACTION	f_plane_restr	0.006	357
X-RAY DIFFRACTION	f_dihedral_angle_d	13.481	748

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.5498-1.5886	0.2979	141	0.2458	2691	2832	99
1.5886-1.6315	0.2506	140	0.2296	2661	2801	100
1.6315-1.6795	0.2744	142	0.2133	2688	2830	100
1.6795-1.7337	0.2258	143	0.2052	2701	2844	100
1.7337-1.7957	0.2107	141	0.1933	2693	2834	100
1.7957-1.8676	0.2009	140	0.1946	2666	2806	100
1.8676-1.9525	0.2118	143	0.1877	2714	2857	100
1.9525-2.0555	0.203	142	0.1792	2693	2835	100
2.0555-2.1842	0.1884	142	0.1688	2698	2840	100
2.1842-2.3528	0.196	143	0.1795	2729	2872	99
2.3528-2.5894	0.2055	143	0.1812	2694	2837	99
2.5894-2.9637	0.2025	142	0.188	2713	2855	98
2.9637-3.7327	0.1931	143	0.1745	2712	2855	97
3.7327-28.4888	0.1816	131	0.1788	2489	2620	85

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	5.0489	2.0032	0.6431	5.0904	0.5131	4.5822	-0.332	-0.8767	0.1909	1.2242	0.2827	0.2312	-0.6551	-0.6273	0.0334	0.7803	0.1512	0.0389	0.4808	-0.0473	0.2586	-2.0133	1.4637	59.7579
2	0.5929	-0.5747	-0.3727	0.5418	-0.1976	0.7285	0.0311	-0.3848	0.3478	0.7235	-0.1331	-0.2404	-0.1437	0.3708	0.175	0.6021	-0.0142	-0.102	0.3674	-0.0371	0.3099	8.2468	-0.1132	55.8785
3	3.4753	0.527	-0.2249	2.5662	0.1378	3.7562	-0.1807	-0.3564	0.3241	0.6108	0.1449	0.1459	-0.3374	-0.1164	0.029	0.3448	0.0718	-0.0272	0.1888	0.0051	0.1803	-0.5439	0.3122	48.1089
4	3.53	-0.7148	-0.9096	3.6286	0.1694	3.6859	-0.0175	-0.0687	0.2482	0.3226	0.0714	-0.1521	-0.3655	-0.0468	-0.0623	0.1819	0.0185	-0.032	0.138	0.0339	0.1547	2.0987	-0.1631	37.7063
5	6.3887	-0.7428	-0.7883	6.2563	-0.222	4.4184	0.0703	0.4438	0.0809	-0.1804	0.1041	0.731	-0.1319	-0.7099	-0.1353	0.1177	0.0072	-0.0049	0.2451	0.0466	0.2065	-2.8298	0.2063	28.7897
6	2.1276	0.5299	-0.5283	4.4843	-1.2643	4.6077	-0.0544	0.27	-0.0705	-0.7376	-0.162	-0.6047	0.345	0.3667	0.1705	0.2384	0.0502	0.0913	0.2276	0.0404	0.2315	10.4547	-0.066	15.548
7	3.33	0.5284	-1.6232	3.9005	-2.2517	5.5371	-0.2232	0.0523	0.1114	-0.3601	0.2521	0.8236	0.096	0.1264	0.1114	0.9393	0.0128	0.1917	0.3986	0.018	0.3094	9.6476	-0.0135	0.4063
8	6.8943	4.5372	-8.2544	3.0394	-5.6306	2.0557	-0.2545	0.5735	-0.5952	-1.0967	-0.45	-1.249	0.6289	0.4412	0.5704	0.4512	0.0526	0.2103	0.4899	0.027	0.4936	15.5144	-9.538	19.8682
9	2.0554	1.642	-0.6223	7.7692	-1.746	9.1172	-0.1569	0.3333	-0.4946	0.3396	0.2886	-0.6397	0.6341	-0.0139	-0.1512	0.2459	0.0412	0.0156	0.2035	-0.0219	0.2915	9.345	-11.0657	33.6898

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1090 through 1107 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 1108 through 1134 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 1135 through 1172 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 1173 through 1206 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 1207 through 1231 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 1232 through 1321 )	A
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 1322 through 1333 )	A
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 1154 through 1161 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 1162 through 1168 )	B

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