PDB-8ivz: Crystal structure of talin R7 in complex with KANK1 KN motif

ID or keywords:

Entry

Database: PDB / ID: 8ivz

Title

Crystal structure of talin R7 in complex with KANK1 KN motif

Components

KN motif and ankyrin repeat domains 1
Talin-1

Keywords

PROTEIN BINDING / Focal adhesion

Function / homology

Function and homology information

GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin signaling / Smooth Muscle Contraction / p130Cas linkage to MAPK signaling for integrins / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / MAP2K and MAPK activation / LIM domain binding / Platelet degranulation / negative regulation of actin filament polymerization / vinculin binding ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

Xu, Y. / Li, K. / Wei, Z. / Cong, Y.

Funding support

China, 2items

Citation

Journal: Cell Rep / Year: 2023
Title: KANK1 shapes focal adhesions by orchestrating protein binding, mechanical force sensing, and phase separation.
Authors: Guo, K. / Zhang, J. / Huang, P. / Xu, Y. / Pan, W. / Li, K. / Chen, L. / Luo, L. / Yu, W. / Chen, S. / He, S. / Wei, Z. / Yu, C.

History

Deposition	Mar 29, 2023	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Nov 8, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8ivz.cif.gz	163 KB	Display	PDBx/mmCIF format
PDB format	pdb8ivz.ent.gz	128.2 KB	Display	PDB format
PDBx/mmJSON format	8ivz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8ivz_validation.pdf.gz	461.4 KB	Display	wwPDB validaton report
Full document	8ivz_full_validation.pdf.gz	462.1 KB	Display
Data in XML	8ivz_validation.xml.gz	14.1 KB	Display
Data in CIF	8ivz_validation.cif.gz	18.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/iv/8ivz ftp://data.pdbj.org/pub/pdb/validation_reports/iv/8ivz	HTTPS FTP

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Related structure data

Related structure data	8iw0C 8iw5C 4w8pS S: Starting model for refinement C: citing same article (ref.)
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	#134 - Feb 2011 Integrin similarity (26) #126 - Jun 2010 Epidermal Growth Factor similarity (1)

Deposited unit

A: Talin-1

B: Talin-1

C: KN motif and ankyrin repeat domains 1

D: KN motif and ankyrin repeat domains 1

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

1

A: Talin-1

C: KN motif and ankyrin repeat domains 1

A: Talin-1

C: KN motif and ankyrin repeat domains 1

defined by author&software
Evidence: gel filtration
42.5 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Talin-1

D: KN motif and ankyrin repeat domains 1

B: Talin-1

D: KN motif and ankyrin repeat domains 1

defined by author&software
42.5 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	40.544, 46.898, 261.610
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	17
Space group name H-M	P222₁

#1: Protein	Talin-1 Mass: 18103.461 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tln1, Tln / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P26039
#2: Protein/peptide	KN motif and ankyrin repeat domains 1 Mass: 3129.470 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KANK1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A8J9BYE6
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.93 Å³/Da / Density % sol: 58 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 25% w/v pentaerythritol ethoxylate, 50 mM Magnesium chloride, 10 mM Tris pH8.5

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL17U1 / Wavelength: 0.98 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 15, 2020

Radiation

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

Radiation wavelength

Wavelength: 0.98 Å / Relative weight: 1

Reflection

Resolution: 2.8→50 Å / Num. obs: 12938 / % possible obs: 97.7 % / Redundancy: 9.8 % / CC_1/2: 0.993 / CC star: 0.998 / R_merge(I) obs: 0.21 / R_pim(I) all: 0.067 / R_rim(I) all: 0.221 / Χ²: 0.462 / Net I/σ(I): 2.2 / Num. measured all: 126666

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.8-2.85	6.5	1.524	623	0.464	0.796	0.59	1.642	0.399	96
2.85-2.9	7.6	1.244	588	0.643	0.885	0.453	1.328	0.416	92
2.9-2.96	7.6	1.158	644	0.699	0.907	0.416	1.235	0.415	97.4
2.96-3.02	8.4	0.992	602	0.738	0.921	0.342	1.052	0.421	98
3.02-3.08	8.3	0.835	636	0.788	0.939	0.291	0.888	0.426	97.1
3.08-3.15	8.6	0.755	619	0.828	0.952	0.263	0.801	0.402	93.8
3.15-3.23	10.2	0.687	601	0.901	0.974	0.22	0.723	0.441	98
3.23-3.32	10.6	0.627	652	0.923	0.98	0.195	0.658	0.433	97.6
3.32-3.42	10.7	0.53	620	0.919	0.979	0.164	0.556	0.442	94.5
3.42-3.53	10.9	0.478	625	0.932	0.982	0.148	0.501	0.44	99.7
3.53-3.65	10.5	0.486	672	0.959	0.99	0.151	0.51	0.448	97.8
3.65-3.8	11	0.403	603	0.956	0.989	0.124	0.422	0.512	96.6
3.8-3.97	10.3	0.273	651	0.978	0.994	0.087	0.287	0.463	98.6
3.97-4.18	9.5	0.194	648	0.988	0.997	0.065	0.206	0.471	98.6
4.18-4.44	10.9	0.168	667	0.992	0.998	0.052	0.176	0.475	99.7
4.44-4.79	11.2	0.145	662	0.993	0.998	0.044	0.152	0.478	99.4
4.79-5.27	10.9	0.145	679	0.993	0.998	0.045	0.152	0.469	99.9
5.27-6.03	10.2	0.152	676	0.993	0.998	0.049	0.16	0.447	99.3
6.03-7.59	11.1	0.102	685	0.998	0.999	0.032	0.107	0.45	100
7.59-50	10.2	0.073	785	0.997	0.999	0.023	0.076	0.661	99.9

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Processing

Software

Name	Version	Classification
PHENIX	(1.18.2_3874: ???)	refinement
HKL-2000		data scaling
HKL-3000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4W8P

4w8p

Resolution: 2.8→46.9 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.47 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2637	637	5 %
R_work	0.2376	-	-
obs	0.239	12745	97.33 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.8→46.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2847	0	0	5	2852

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	2914
X-RAY DIFFRACTION	f_angle_d	0.425	3956
X-RAY DIFFRACTION	f_dihedral_angle_d	18.211	1091
X-RAY DIFFRACTION	f_chiral_restr	0.035	451
X-RAY DIFFRACTION	f_plane_restr	0.005	525

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 (%)
2.8-3.02	0.3595	121	0.312	2310	X-RAY DIFFRACTION	96
3.02-3.32	0.32	124	0.2956	2350	X-RAY DIFFRACTION	97
3.32-3.8	0.3258	125	0.2831	2377	X-RAY DIFFRACTION	97
3.8-4.79	0.2203	130	0.2134	2473	X-RAY DIFFRACTION	99
4.79-46.9	0.2285	137	0.2009	2598	X-RAY DIFFRACTION	98

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	3.8711	-1.4187	3.4389	4.1564	2.8653	7.5032	-0.7493	0.528	0.1986	-0.0286	0.2705	0.8659	-0.3416	0.3565	0.5328	0.4609	0.0315	-0.0308	0.5403	0.0162	0.5879	-3.803	8.0196	49.8035
2	9.103	6.3529	5.6344	6.4769	4.3859	6.166	0.048	-0.5006	-0.1093	0.2506	0.0355	0.1402	0.1332	0.0712	-0.1162	0.4417	0.0451	-0.0242	0.4079	0.1241	0.413	4.4753	0.7335	56.2843
3	5.1317	-1.2753	4.0702	1.997	-2.2096	6.3706	-0.2556	-0.1945	-0.1149	0.1019	0.1076	0.3641	-0.612	-0.4724	0.5	0.6074	-0.0547	-0.0671	0.2992	-0.1459	0.4504	30.6674	9.287	80.1433
4	4.2894	-4.031	5.2821	5.2355	-2.5117	7.5013	-0.0169	-0.9477	-0.6411	-0.0419	0.5755	0.1394	-0.0348	-1.3005	-0.5861	0.415	0.0122	0.023	0.4136	0.0628	0.5726	33.3013	-3.8495	87.5885
5	7.1135	-0.5905	2.3109	6.1076	2.0215	5.9572	-0.322	0.0755	1.0907	-0.3131	-0.5936	-0.1937	-0.1607	-2.9255	0.3207	0.6516	-0.081	0.0707	1.091	-0.0706	0.6593	16.1198	24.9094	27.2363
6	2.196	-0.5918	-1.5309	1.965	-0.7733	9.0821	0.118	0.4222	0.0201	-0.1365	0.0382	-0.0627	0.441	-1.1018	-0.1272	0.4414	-0.1215	0.0016	0.418	0.0458	0.4045	24.7251	21.5398	18.4002
7	2.3818	-0.2588	-0.1037	1.4428	0.9449	6.9944	0.2082	0.006	0.3935	0.4932	0.024	0.1091	-0.5555	-3.8752	-0.2762	0.9888	0.2751	-0.0164	1.3854	0.0516	0.6944	13.7258	30.2509	-17.5578
8	3.4455	0.2601	2.0472	2.5144	-2.6858	5.7536	-0.0462	-0.3292	-0.027	0.6973	0.2445	0.473	-0.8516	-0.6659	-0.0334	1.0329	0.1868	0.3774	0.4434	0.17	0.6683	25.2644	36.5802	-27.7384
9	7.4103	4.338	1.6733	4.9295	3.4718	5.46	0.1203	0.43	-2.1945	0.4492	0.6062	-1.4983	1.2284	0.5116	-1.011	0.6785	0.0482	-0.0355	0.3355	-0.0088	1.0842	5.2316	-14.0309	41.9311
10	7.4025	-5.1412	4.0745	3.5951	-2.8617	5.1187	0.6858	-1.6861	-0.8163	0.6789	-0.0586	-2.4402	1.1827	1.9696	-0.0156	0.7259	-0.0988	-0.5802	1.0399	0.1904	1.3986	15.4487	-9.4488	54.3173
11	4.962	-1.098	4.8977	8.8034	-3.67	5.5973	-0.0986	0.6937	-1.2252	-0.6606	-0.3556	-0.1943	0.634	1.8535	0.2593	1.1406	0.0267	0.1829	1.1232	0.1332	1.2332	37.6797	9.6123	26.6182
12	7.4844	2.4028	-3.8823	7.1469	-4.4446	3.622	0.0243	0.1288	-0.6057	-0.2604	-0.5657	-0.4103	1.1647	0.5373	0.3887	0.5769	-0.0782	-0.0994	0.3941	0.1113	0.5446	32.8756	8.8874	33.8928
13	4.9531	-2.1522	2.2913	0.9876	-1.3102	3.2968	1.7859	2.9888	-1.4793	-1.5859	-1.9349	-0.8618	3.4175	0.6369	0.7282	1.5422	0.3389	0.0262	1.1058	-0.0633	0.7849	32.9672	10.0201	14.3727

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1359 through 1378 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 1379 through 1449 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 1450 through 1622 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 1623 through 1653 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 1358 through 1378 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 1379 through 1449 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1450 through 1622 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 1623 through 1652 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 30 through 43 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 44 through 53 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 30 through 34 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 35 through 43 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 44 through 53 )

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