PDB-6hyf: Crystal structure of the third FNIII domain from rat beta4 integr...

ID or keywords:

Entry

Database: PDB / ID: 6hyf

Title

Crystal structure of the third FNIII domain from rat beta4 integrin, a binding site for periaxin

Components

Integrin beta-4

Keywords

PROTEIN BINDING /

myelin /

integrin / periaxin

Function / homology

Function and homology information

Type I hemidesmosome assembly / Laminin interactions / Assembly of collagen fibrils and other multimeric structures / Syndecan interactions / trophoblast cell migration /

hemidesmosome assembly /

hemidesmosome / nail development /

peripheral nervous system myelin formation / skin morphogenesis ...
Similarity search - Function

Biological species

Rattus norvegicus (Norway rat)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Raasakka, A. / Kursula, P.

Citation

Journal: Front Mol Neurosci / Year: 2019
Title: Direct Binding of the Flexible C-Terminal Segment of Periaxin to beta 4 Integrin Suggests a Molecular Basis for CMT4F.
Authors: Raasakka, A. / Linxweiler, H. / Brophy, P.J. / Sherman, D.L. / Kursula, P.

History

Deposition	Oct 20, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 8, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jan 24, 2024	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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Download

PDBx/mmCIF format	6hyf.cif.gz	241.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6hyf.ent.gz	201.2 KB	Display	PDB format
PDBx/mmJSON format	6hyf.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/hy/6hyf ftp://data.pdbj.org/pub/pdb/validation_reports/hy/6hyf	HTTPS FTP

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Related structure data

Related structure data	4wtwS S: Starting model for refinement
Similar structure data	4qyl-2 1gcf-d 4omo-d 6dps-1 6bya-2 2pl7-d 4qyl-1 3fpn-2 1iu1-2 3m86-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

4wtwS

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#134 - Feb 2011 Integrin similarity (15) #196 - Apr 2016 Lead Poisoning similarity (1) #185 - May 2015 Titin similarity (1) #52 - Apr 2004 Growth Hormone similarity (1) #166 - Oct 2013 Proteasome similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #141 - Sep 2011 O-GlcNAc Transferase similarity (1)

Deposited unit

A: Integrin beta-4

B: Integrin beta-4

C: Integrin beta-4

D: Integrin beta-4

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

1

A: Integrin beta-4

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

2

B: Integrin beta-4

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

3

C: Integrin beta-4

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

4

D: Integrin beta-4

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

Unit cell

Length a, b, c (Å)	51.220, 52.840, 144.530
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Integrin beta-4 / GP150 Mass: 12775.204 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Itgb4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q64632
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 162 / 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: 1.91 Å³/Da / Density % sol: 36 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 3350, NH4NO3

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.996 Å
Detector	Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 23, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.996 Å / Relative weight: 1
Reflection	Resolution: 1.6→50 Å / Num. obs: 51757 / % possible obs: 98.3 % / Redundancy: 3.3 % / B_iso Wilson estimate: 39.2 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.061 / R_rim(I) all: 0.073 / Net I/σ(I): 8.8
Reflection shell	Resolution: 1.6→1.64 Å / Redundancy: 3.3 % / R_merge(I) obs: 2.392 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 3746 / CC_1/2: 0.166 / R_rim(I) all: 2.839 / % possible all: 98.6

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Processing

Software

Name	Version	Classification
PHENIX	(1.14_3260: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4wtw

4wtw

Resolution: 1.6→41.788 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.76

	R_factor	Num. reflection	% reflection
R_free	0.2391	3580	3.89 %
R_work	0.1896	-	-
obs	0.1915	92136	92.2 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.6→41.788 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3003	0	0	162	3165

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.013	3137
X-RAY DIFFRACTION	f_angle_d	1.051	4283
X-RAY DIFFRACTION	f_dihedral_angle_d	16.272	1865
X-RAY DIFFRACTION	f_chiral_restr	0.067	465
X-RAY DIFFRACTION	f_plane_restr	0.007	573

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 (%)
1.6-1.6211	0.473	99	0.4779	2431	X-RAY DIFFRACTION	67
1.6211-1.6433	0.4324	119	0.4361	2953	X-RAY DIFFRACTION	80
1.6433-1.6668	0.4619	121	0.4157	3038	X-RAY DIFFRACTION	82
1.6668-1.6917	0.4611	121	0.3935	3220	X-RAY DIFFRACTION	87
1.6917-1.7181	0.3582	130	0.3738	3497	X-RAY DIFFRACTION	93
1.7181-1.7463	0.3375	153	0.3494	3480	X-RAY DIFFRACTION	94
1.7463-1.7764	0.3764	151	0.3263	3528	X-RAY DIFFRACTION	96
1.7764-1.8087	0.3342	136	0.3226	3561	X-RAY DIFFRACTION	96
1.8087-1.8435	0.3148	151	0.2933	3533	X-RAY DIFFRACTION	95
1.8435-1.8811	0.2936	145	0.2889	3378	X-RAY DIFFRACTION	92
1.8811-1.922	0.3488	133	0.2784	3354	X-RAY DIFFRACTION	91
1.922-1.9667	0.3176	141	0.2664	3499	X-RAY DIFFRACTION	94
1.9667-2.0159	0.3016	140	0.2347	3521	X-RAY DIFFRACTION	96
2.0159-2.0704	0.2636	147	0.1973	3580	X-RAY DIFFRACTION	97
2.0704-2.1313	0.2527	158	0.2028	3569	X-RAY DIFFRACTION	96
2.1313-2.2001	0.2069	133	0.1922	3538	X-RAY DIFFRACTION	96
2.2001-2.2787	0.2776	128	0.2008	3296	X-RAY DIFFRACTION	89
2.2787-2.37	0.2459	154	0.1973	3583	X-RAY DIFFRACTION	96
2.37-2.4778	0.248	138	0.1949	3527	X-RAY DIFFRACTION	96
2.4778-2.6084	0.2614	150	0.1989	3481	X-RAY DIFFRACTION	94
2.6084-2.7718	0.241	121	0.1884	3495	X-RAY DIFFRACTION	94
2.7718-2.9858	0.2375	146	0.1772	3563	X-RAY DIFFRACTION	96
2.9858-3.2861	0.2114	139	0.1644	3525	X-RAY DIFFRACTION	95
3.2861-3.7614	0.2144	149	0.153	3438	X-RAY DIFFRACTION	93
3.7614-4.7379	0.2013	142	0.1393	3401	X-RAY DIFFRACTION	92
4.7379-41.8022	0.1893	135	0.1726	3567	X-RAY DIFFRACTION	96

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	2.0924	-0.3529	-0.8891	2.7317	0.0089	0.3965	0.1924	-0.1349	0.2747	0.1244	-0.0457	0.0808	-0.2561	-0.1015	-0.1119	0.4359	0.0004	-0.0212	0.3041	0.0068	0.4256	-0.0496	-22.8848	-10.2063
2	6.8912	-4.6959	3.4629	3.5911	-1.4215	3.2401	-0.0515	-0.0173	0.3845	0.1107	-0.0708	-0.064	-0.2336	-0.318	0.1037	0.3033	-0.0217	0.0007	0.2073	0.0141	0.4501	-3.2646	-23.7433	-11.0798
3	3.0442	-2.9088	2.0538	4.9409	-4.2733	3.8982	-0.7474	-0.2876	0.7333	1.727	0.3779	-0.5302	-1.1845	-0.4836	0.0734	0.6146	0.0316	-0.1537	0.3353	-0.0127	0.7227	7.9367	-26.6118	-2.0227
4	3.113	0.6741	0.1456	0.1393	-0.1889	2.6773	0.0946	0.6956	0.2972	-0.0129	-0.1671	-0.1319	-0.2415	0.2421	0.1048	0.3223	-0.0336	-0.0183	0.2166	0.0508	0.4542	9.9995	-27.9827	-11.9104
5	5.3791	-3.3896	1.3219	6.3005	-0.6363	2.0917	-0.131	-0.3704	0.0087	0.1471	0.1191	0.4561	-0.2431	-0.1915	-0.0067	0.3264	-0.0181	-0.019	0.1996	-0.0012	0.4034	-0.6526	-28.2985	-6.2166
6	6.4232	-2.9416	-3.1188	1.8147	1.0991	6.2494	0.1704	-0.6	-1.5014	-0.1879	1.4811	-0.4017	1.0919	0.4357	-0.2461	0.9559	0.1775	0.1241	0.7852	-0.0024	1.0073	-3.866	-33.5574	1.987
7	1.4886	1.3088	-1.0918	7.1221	-3.3584	2.7358	-0.0921	-0.3106	-0.4348	-0.2331	-0.157	-1.1368	0.0241	0.4004	0.1112	0.3635	-0.0252	-0.0266	0.2537	0.0248	0.4856	-13.2398	-29.3136	10.8973
8	8.3187	6.4944	6.2793	5.6502	4.3708	7.2373	0.3533	-2.0319	-0.7244	0.6547	-0.4668	0.4036	0.1017	-0.4402	-0.014	0.2551	-0.0296	0.0503	0.2781	0.069	0.4818	-26.7187	-29.5509	14.7293
9	3.3967	1.652	-0.7897	0.8451	-0.4524	2.0752	0.081	-0.427	-0.1808	-0.3132	0.0417	-1.6613	-0.5741	1.5797	-0.0856	0.6808	-0.213	0.0058	0.5566	-0.0603	0.8365	-6.1975	-19.6908	11.1852
10	3.2566	3.3491	2.5484	3.4647	2.1075	3.2057	-0.5842	0.1054	0.3123	-0.9157	0.2976	0.2056	-0.6883	-0.0111	0.1982	0.4765	-0.0007	-0.0742	0.1868	0.0146	0.4522	-23.0153	-25.0122	1.8535
11	3.715	3.0578	0.7838	3.6065	1.4722	1.2024	-0.4926	-0.5141	1.5137	-0.2056	-0.102	0.833	-0.7331	0.058	0.019	0.4112	0.0069	-0.0836	0.1255	-0.0662	0.5033	-19.0587	-19.3126	13.008
12	6.6528	3.7698	2.0964	8.2359	2.0346	3.3352	-0.3494	0.1963	0.3599	-0.4497	0.19	0.3861	-0.2638	-0.3041	0.0097	0.289	0.0313	-0.054	0.1355	0.0276	0.3404	-24.3885	-29.5056	5.4083
13	4.9969	0.6138	1.7278	1.8068	2.9279	4.8625	0.138	-0.223	0.5647	0.1324	0.1643	-1.3651	-1.8738	1.1498	0.0314	0.7279	-0.1403	0.0774	0.3542	0.0453	0.7433	-7.4725	-16.9792	0.6634
14	5.3942	4.6702	-1.0851	4.081	-0.5661	3.0931	-0.2499	0.4898	-0.3297	-0.3242	0.27	-0.2888	-0.0474	-0.0936	0.0071	0.3167	0.0395	0.0134	0.1696	0.0097	0.4455	-18.4613	-33.2494	6.1251
15	5.192	0.4651	-1.0139	5.6234	-2.3719	5.1685	-0.1587	-0.0919	-0.4044	-0.6989	-0.069	-0.157	0.4096	-0.2805	0.1571	0.3964	0.0281	-0.0226	0.2456	-0.0548	0.3384	-7.6055	-9.4216	23.1213
16	5.4938	4.2055	1.5123	3.4784	1.8933	2.0516	0.062	-0.1552	-0.0601	-0.2756	-0.3665	0.3937	0.2575	-0.5334	-0.0034	0.4529	-0.0459	-0.0129	0.3389	-0.0769	0.4099	-14.5933	-17.6174	21.2463
17	6.1212	5.3849	5.7017	4.7318	5.7703	9.4298	0.6942	-0.8181	-0.3896	1.0069	-0.4013	-0.0885	0.4175	-0.9442	-0.2092	0.4158	0.0106	0.0325	0.3189	-0.0741	0.4616	-15.5172	-10.6	29.8656
18	9.3749	-3.2264	0.1511	1.5953	0.8416	2.0217	-0.7141	-1.5326	0.5641	1.0806	0.1727	0.3464	-0.4441	-0.9398	0.5414	0.7545	-0.0158	0.0222	0.7579	-0.1923	0.6346	-8.0313	-2.6373	39.1685
19	1.651	2.7733	2.6224	7.1986	6.6831	6.1854	0.3809	-0.638	0.3702	0.1309	-0.4018	0.6736	0.3502	-0.8436	-0.2182	0.6073	0.1226	-0.0799	0.5193	-0.0937	0.6231	-19.4073	-7.5491	30.3722
20	2.2262	0.5069	0.9863	1.2136	1.6067	4.8466	-0.0026	0.111	0.0069	-0.0936	-0.0918	0.3363	-0.2985	-0.2215	0.0041	0.4764	0.0588	-0.0462	0.21	-0.0748	0.462	-11.1702	-2.5526	24.9956
21	3.6046	3.681	2.9448	5.1823	4.0472	4.9483	0.9369	-0.9234	-0.4602	1.3224	-0.8719	-0.3548	0.3367	-0.8921	-0.027	0.4144	-0.0694	0.0525	0.3177	-0.0203	0.3285	-11.9229	-11.6172	30.9
22	6.8829	3.4877	2.2357	4.1264	2.1876	2.7322	0.2773	-0.3467	-0.8616	0.2504	-0.1759	0.0352	0.5009	-0.4803	0.0187	0.5605	-0.044	-0.0564	0.2744	0.0444	0.5207	-11.3768	-15.7109	30.0165
23	6.1952	2.4394	1.1809	6.3537	4.9014	4.6494	0.2153	0.1947	1.2028	-1.037	-0.7537	0.6336	-1.1419	0.3356	0.0401	0.452	-0.0863	0.0121	0.2645	0.0468	0.529	6.8882	-3.6948	23.5049
24	6.8032	5.024	-2.8681	3.8154	-2.853	8.0888	-0.5235	0.2215	-1.0618	-0.9003	0.0083	-0.3835	0.9848	0.1829	0.3357	0.4841	-0.0156	0.0982	0.1844	0.0157	0.5371	10.1059	-13.8652	22.0767
25	0.743	-0.3677	1.1972	0.2377	-0.5877	1.902	0.2344	-0.2443	2.2347	0.5552	-0.2216	-0.3558	-0.5815	0.9644	0.1179	0.4793	-0.1837	0.0409	0.5577	-0.0493	0.7569	18.7092	3.8657	25.151
26	4.5818	5.533	-2.0343	6.5339	-2.2645	1.6718	0.563	-1.2798	-0.1724	0.5867	-0.5527	-0.2144	-0.2154	0.7311	0.1684	0.5031	-0.1117	-0.1374	0.5342	0.0826	0.495	14.3242	-6.7945	33.4418
27	2.4703	-0.1013	1.7701	3.2106	0.8644	2.543	-0.0539	-0.934	-2.5662	0.5802	-0.0846	-0.5286	1.5735	0.9412	0.0177	0.7958	-0.1274	0.0302	0.8492	0.1935	0.827	7.8586	-14.9329	38.1174
28	5.081	4.7074	-0.3453	6.0125	-2.7708	3.8116	0.2429	-1.409	-0.3558	0.5101	-0.3034	0.0473	-0.1532	0.9196	0.0511	0.404	-0.0343	0.0026	0.6759	0.1322	0.6816	19.21	-8.5489	33.7437
29	5.5724	-1.497	-0.1928	1.0077	0.5297	0.3622	-0.0392	-0.411	-0.64	-0.1975	-0.1199	-1.2642	0.2898	0.8263	0.1844	0.4479	-0.0838	0.0552	0.4087	0.0458	0.5942	20.1101	-4.8622	24.1021
30	2.7256	-3.6538	-2.5555	5.6843	1.7602	5.8743	0.044	-0.0988	0.0888	-0.6057	-0.2791	-1.0337	0.3291	0.6636	-0.0828	0.4947	-0.0183	0.0028	0.2219	0.1358	0.5359	6.9876	-19.3609	28.8398
31	5.4076	4.6483	-0.4417	3.9374	-0.438	3.1844	0.4599	-1.2816	-0.1977	0.3752	-0.7366	-0.4595	-0.2968	0.8884	0.1759	0.4959	-0.1067	-0.0803	0.3896	0.05	0.3807	11.6194	-4.774	33.1816
32	9.1823	-0.3689	8.8453	0.5315	-0.2688	8.5931	0.0627	0.2904	-0.6157	0.4921	0.9326	-0.5614	-0.0698	0.8537	-0.2805	0.8116	-0.2236	-0.1556	1.0082	-0.1901	1.097	19.2743	10.5357	34.8248
33	8.1053	1.6635	-1.4553	7.512	-0.6758	3.8087	-0.0677	-0.3233	0.2303	-0.3792	0.2171	-0.6061	-0.4421	0.6111	0.1336	0.4202	-0.0417	0.0667	0.2415	-0.0175	0.4417	6.0864	-5.334	30.1332

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1438 through 1477 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 1478 through 1496 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 1497 through 1507 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 1508 through 1524 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 1525 through 1548 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 1449 through 1458 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1459 through 1468 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 1469 through 1477 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 1478 through 1488 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 1489 through 1507 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 1508 through 1517 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 1518 through 1533 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 1534 through 1540 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 1541 through 1548 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 1458 through 1473 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 1474 through 1486 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 1487 through 1496 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 1497 through 1502 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 1503 through 1508 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 1509 through 1524 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 1525 through 1534 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 1535 through 1548 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 1462 through 1468 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 1469 through 1477 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 1478 through 1488 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 1489 through 1496 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 1497 through 1502 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 1503 through 1507 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 1508 through 1517 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 1518 through 1524 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 1525 through 1533 )
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 1534 through 1540 )
33	X-RAY DIFFRACTION	33	chain 'D' and (resid 1541 through 1548 )

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