PDB-5d68: Crystal structure of KRIT1 ARD-FERM

ID or keywords:

Entry

Database: PDB / ID: 5d68

Title

Crystal structure of KRIT1 ARD-FERM

Components

Krev interaction trapped protein 1

Keywords

SIGNALING PROTEIN / Ankyrin Repeat Domain / FERM domain / Cerebral Cavernous Malformations

Function / homology

Function and homology information

GTPase regulator activity / endothelium development / integrin activation / negative regulation of endothelial cell migration / regulation of establishment of cell polarity / small GTPase-mediated signal transduction / negative regulation of endothelial cell proliferation / regulation of angiogenesis / negative regulation of endothelial cell apoptotic process / phosphatidylinositol-4,5-bisphosphate binding ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.908 Å

Authors

Zhang, R. / Li, X. / Boggon, T.J.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	R01NS085078	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	P41GM103403	United States

Citation

Journal: J.Struct.Biol. / Year: 2015
Title: Structural analysis of the KRIT1 ankyrin repeat and FERM domains reveals a conformationally stable ARD-FERM interface.
Authors: Zhang, R. / Li, X. / Boggon, T.J.

History

Deposition	Aug 11, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 21, 2015	Provider: repository / Type: Initial release
Revision 1.1	Oct 28, 2015	Group: Database references
Revision 1.2	Dec 2, 2015	Group: Database references
Revision 1.3	Sep 13, 2017	Group: Author supporting evidence / Database references / Derived calculations Category: citation / pdbx_audit_support / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4	Dec 18, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5	Sep 27, 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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Download

PDBx/mmCIF format	5d68.cif.gz	538.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5d68.ent.gz	446.1 KB	Display	PDB format
PDBx/mmJSON format	5d68.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/d6/5d68 ftp://data.pdbj.org/pub/pdb/validation_reports/d6/5d68	HTTPS FTP

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Related structure data

Related structure data	4dxaS 4hb5S S: Starting model for refinement
Similar structure data	1thn-d 1th8-1 7jzj-1 4htf-d 5h1a-2 2le9-d 6d6y-d 4pok-5 5do9-4 4yiq-d 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

4dxaS

4hb5S

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 (8) #250 - Oct 2020 Capsaicin Receptor TRPV1 similarity (1) #223 - Jul 2018 Piezo1 Mechanosensitive Channel similarity (1)

Deposited unit

A: Krev interaction trapped protein 1

B: Krev interaction trapped protein 1

C: Krev interaction trapped protein 1

168 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Krev interaction trapped protein 1

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

2

B: Krev interaction trapped protein 1

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

3

C: Krev interaction trapped protein 1

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

Unit cell

Length a, b, c (Å)	125.734, 80.242, 213.145
Angle α, β, γ (deg.)	90.00, 91.69, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Krev interaction trapped protein 1 / Krev interaction trapped 1 / Cerebral cavernous malformations 1 protein Mass: 56154.168 Da / Num. of mol.: 3 / Fragment: ARD-FERM domain (UNP residues 52-529) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KRIT1, CCM1 / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / References: UniProt: O00522
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Krev interaction trapped protein 1 / Krev interaction trapped 1 / Cerebral cavernous malformations 1 protein

Mass: 56154.168 Da / Num. of mol.: 3 / Fragment: ARD-FERM domain (UNP residues 52-529)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: KRIT1, CCM1 / Plasmid: pET32 / Production host:

Escherichia coli (E. coli) / References: UniProt: O00522

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 3.19 Å³/Da / Density % sol: 61.44 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 0.05 M HEPES, pH 7.3, 8% ethylene glycol, 8% PEG8000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 19, 2012
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 2.9→50 Å / Num. obs: 46892 / % possible obs: 100 % / Redundancy: 3.7 % / R_merge(I) obs: 0.192 / Net I/σ(I): 7.5
Reflection shell	Resolution: 2.9→3 Å / Redundancy: 3.8 % / R_merge(I) obs: 0.899 / Mean I/σ(I) obs: 1.7 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	dev_1760	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entries 4DXA & 4HB5

4dxa

4hb5

Resolution: 2.908→49.369 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.85 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2464	2376	5.07 %	5.07
R_work	0.2066	-	-	-
obs	0.2086	46862	99.61 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.908→49.369 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10586	0	0	66	10652

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	10827
X-RAY DIFFRACTION	f_angle_d	0.788	14642
X-RAY DIFFRACTION	f_dihedral_angle_d	14.225	4080
X-RAY DIFFRACTION	f_chiral_restr	0.035	1611
X-RAY DIFFRACTION	f_plane_restr	0.004	1870

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 (%)
2.9077-2.9671	0.2985	127	0.2987	2517	X-RAY DIFFRACTION	95
2.9671-3.0316	0.3239	124	0.2922	2583	X-RAY DIFFRACTION	100
3.0316-3.1021	0.358	118	0.2832	2678	X-RAY DIFFRACTION	100
3.1021-3.1797	0.3446	161	0.2934	2533	X-RAY DIFFRACTION	100
3.1797-3.2656	0.3141	141	0.273	2607	X-RAY DIFFRACTION	100
3.2656-3.3617	0.2651	131	0.2593	2613	X-RAY DIFFRACTION	100
3.3617-3.4702	0.3215	136	0.2474	2607	X-RAY DIFFRACTION	100
3.4702-3.5942	0.288	152	0.2388	2608	X-RAY DIFFRACTION	100
3.5942-3.738	0.2543	140	0.2314	2646	X-RAY DIFFRACTION	100
3.738-3.9081	0.2662	147	0.212	2592	X-RAY DIFFRACTION	100
3.9081-4.114	0.244	149	0.198	2609	X-RAY DIFFRACTION	100
4.114-4.3716	0.2159	142	0.1658	2628	X-RAY DIFFRACTION	100
4.3716-4.7089	0.1848	134	0.1456	2629	X-RAY DIFFRACTION	100
4.7089-5.1824	0.2092	147	0.1504	2605	X-RAY DIFFRACTION	100
5.1824-5.9312	0.2085	144	0.1701	2640	X-RAY DIFFRACTION	100
5.9312-7.4685	0.2112	143	0.181	2688	X-RAY DIFFRACTION	100
7.4685-49.3761	0.1752	140	0.1632	2703	X-RAY DIFFRACTION	99

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	3.2417	-0.0275	0.0773	2.1593	1.3567	6.1756	-0.2953	-0.1726	-0.0124	0.0232	0.245	-0.175	-0.241	0.477	-0.0342	0.2678	-0.0664	-0.0196	0.3064	0.0446	0.3629	126.0699	-16.4298	-22.13
2	3.8896	0.7786	-1.1387	3.3369	0.3592	4.606	-0.3275	0.5411	-0.3658	-0.1051	0.0127	0.2289	0.852	-0.623	0.339	0.4403	-0.1682	0.0833	0.3385	-0.0575	0.3363	114.1401	-28.6149	-26.3664
3	3.2524	0.283	-0.6711	1.8933	1.0437	3.0551	-0.4124	-0.0935	-0.5708	0.5178	0.3353	0.0762	1.1826	-0.1932	0.6047	0.6778	-0.0195	0.1415	0.3087	0.0228	0.4627	106.3121	-32.8934	-5.5655
4	3.7249	1.373	-1.6918	3.734	0.651	4.3933	-0.2037	0.1351	-0.0958	-0.0816	-0.1697	0.4886	0.4833	-1.0671	0.28	0.3727	-0.088	-0.0019	0.3666	-0.0383	0.364	98.8254	-24.2321	-1.0725
5	2.8061	0.281	-0.4955	2.6657	0.0887	4.4014	-0.0221	0.2004	0.0946	-0.4046	0.0425	-0.4911	-0.4243	0.7671	0.0458	0.3482	-0.096	0.0456	0.3788	0.0073	0.3413	115.0784	-15.8043	0.0776
6	0.4602	0.1658	-1.2878	0.4576	-0.4408	3.5211	-0.3205	0.2538	-0.1426	-0.0234	-0.1867	0.1903	0.607	-0.812	0.1624	0.3388	-0.1644	0.0527	0.395	-0.08	0.4698	94.5033	-25.2897	10.3881
7	3.1948	1.0541	-0.9882	1.7109	0.8565	3.6093	-0.2645	-0.2405	-0.3951	0.2748	-0.002	-0.4327	0.855	0.371	0.3517	0.6323	0.0068	0.0812	0.297	0.0158	0.4321	100.5273	-29.6927	30.1289
8	1.255	0.3468	-0.0736	3.1127	-0.8777	5.3373	-0.2734	0.2515	-0.4634	0.5098	0.2391	0.6928	1.6842	-1.299	0.1554	0.6993	-0.208	0.2004	0.521	-0.0672	0.5018	89.9881	-31.9624	25.7943
9	2.013	2.0893	-1.0946	6.9367	-1.3576	2.3885	0.7039	-0.6994	0.0479	1.1039	-0.7624	-0.4615	-0.434	-0.0707	0.1822	0.4031	-0.0031	-0.0207	0.3907	-0.0029	0.3769	103.8056	-7.6371	16.1512
10	2.5924	0.4472	-0.9923	5.345	-1.4731	6.1467	0.2164	0.2571	0.6214	0.4125	-0.2735	0.2719	-1.0998	-0.1316	-0.0037	0.5039	0.0414	0.0177	0.3163	0.0544	0.3892	98.9168	-3.3331	13.5948
11	3.1197	0.5571	0.4805	5.9406	0.0165	6.3314	0.2762	-0.1413	0.3061	0.1606	-0.3894	0.4899	-0.8856	-1.0768	-0.1083	0.5276	0.1064	-0.0127	0.4433	0.0994	0.4806	96.5534	-2.5103	9.009
12	2.9131	0.4263	-1.9308	4.2451	-0.2509	7.7369	0.3802	-0.5375	0.2166	0.2708	-0.1945	-0.6323	-0.3943	0.8493	-0.154	0.3532	-0.1498	-0.0479	0.3758	0.0021	0.3891	154.1506	10.8491	93.7744
13	0.9604	0.9948	0.4713	3.32	2.1243	3.8236	0.1669	-0.4786	0.0667	0.4566	-0.7133	0.5493	0.2468	-0.9485	0.4092	0.3311	-0.1008	0.0696	0.6466	-0.0652	0.4045	134.8931	1.19	86.2952
14	2.3352	0.1647	-1.2031	0.8501	-0.3368	4.2277	0.1612	-0.1295	-0.1817	0.0674	-0.2192	-0.0553	-0.2012	-0.037	0.0446	0.2396	-0.0703	-0.0327	0.2358	0.0001	0.3225	137.9433	-7.4702	64.9732
15	5.9329	2.2061	-0.9558	2.3551	0.5548	2.0418	0.191	0.4004	0.7474	-0.6102	-0.2238	0.3352	-0.7273	-0.4673	-0.0122	0.4266	0.2323	-0.1022	0.4492	-0.0371	0.41	129.7363	-6.4612	41.0357
16	1.7975	-0.0818	1.1305	2.3647	0.0626	5.4158	0.2542	-0.1075	-0.3917	-0.108	-0.2068	0.3379	0.1719	-0.8821	-0.0512	0.2842	0.0305	-0.0268	0.3569	-0.0631	0.3433	129.6282	-14.7048	48.7047
17	4.3458	0.2125	1.489	3.1143	0.0684	4.2042	0.1777	0.2029	-0.4499	0.022	-0.557	-0.832	0.3882	1.0477	0.1725	0.3151	0.051	-0.0856	0.4697	0.142	0.5613	153.3134	-17.1727	57.3364
18	3.4324	3.1092	-2.0438	6.8829	-1.22	4.7098	0.004	-0.1028	-0.2958	-0.021	-0.4457	-0.5745	1.0523	0.5182	0.2972	0.3762	0.1183	-0.104	0.461	0.1258	0.5033	150.4656	-24.3202	64.8291
19	2.8246	-0.5192	1.0131	4.0895	-0.9233	6.2766	-0.0992	0.0688	-0.0415	-0.2898	-0.1053	0.0488	-0.1351	-0.4007	0.1789	0.3479	-0.0044	0.0046	0.2967	-0.0499	0.2842	87.3558	-21.5197	47.0409
20	1.9827	-0.7115	0.9896	1.907	1.3696	4.7289	-0.1106	0.2475	0.2127	-0.3315	-0.1565	0.3007	-0.7769	-0.2034	0.3568	0.4331	0.0354	-0.0477	0.3015	0.0312	0.4059	87.2323	-3.3543	63.6919
21	0.8429	-0.6653	-0.5944	2.6073	0.2395	5.1781	-0.052	-0.0151	-0.0135	0.0241	-0.1412	0.0479	-0.3983	0.0998	0.1349	0.229	-0.0542	-0.0469	0.2191	0.0142	0.3377	94.7653	-5.1966	76.9138
22	3.0751	-0.1939	-0.558	7.4193	1.5018	6.7764	-0.2661	-0.2951	0.2264	0.3104	0.2417	0.4387	-0.6647	-1.0042	-0.0397	0.4539	0.1189	-0.0656	0.4717	-0.0697	0.3356	88.6836	5.6731	98.577
23	1.8399	-0.7678	-1.1199	2.0983	0.0326	6.1184	-0.4574	-0.5092	-0.2575	0.1568	0.4734	-0.0712	0.794	0.1265	0.111	0.2947	0.0057	-0.0287	0.4054	0.0397	0.506	105.9334	-11.1103	87.2033
24	4.2272	-0.2978	-1.071	4.2848	1.6754	6.4839	-0.2591	-0.284	-0.0909	0.3596	0.0699	-0.5724	0.221	1.0293	0.2047	0.2596	-0.012	-0.0137	0.4863	-0.0083	0.4889	112.5068	-9.5403	84.9613
25	3.7606	-0.6807	-0.1237	7.8007	-1.5923	4.2505	-0.203	-0.5669	0.3746	0.6273	0.2181	-0.7119	-0.2399	1.0095	0.0301	0.3041	-0.0254	0.0581	0.6423	-0.0779	0.5058	114.2651	-8.7633	80.6422

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 288 through 342 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 343 through 414 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 415 through 443 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 444 through 479 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 480 through 504 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 505 through 541 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 542 through 597 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 598 through 630 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 631 through 662 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 663 through 701 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 702 through 730 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 288 through 333 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 334 through 479 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 480 through 541 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 542 through 597 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 598 through 644 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 645 through 701 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 702 through 736 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 288 through 403 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 404 through 479 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 480 through 541 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 542 through 630 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 631 through 662 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 663 through 701 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 702 through 729 )

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