PDB-4fqn: Crystal structure of the CCM2 C-terminal Harmonin Homology Domain...

ID or keywords:

Entry

Database: PDB / ID: 4fqn

Title

Crystal structure of the CCM2 C-terminal Harmonin Homology Domain (HHD)

Components

Malcavernin

Keywords

PROTEIN BINDING / helical domain / Harmonin-homology domain / Protein-protein interaction / homo-dimer

Function / homology

Function and homology information

endothelial cell development / venous blood vessel morphogenesis / blood vessel endothelial cell differentiation / pericardium development / endothelium development / endothelial tube morphogenesis / cell-cell junction organization / inner ear development / regulation of angiogenesis / vasculogenesis ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.9 Å

Authors

Fisher, O.S. / Zhang, R. / Li, X. / Murphy, J.W. / Boggon, T.J.

Citation

Journal: Febs Lett. / Year: 2013
Title: Structural studies of cerebral cavernous malformations 2 (CCM2) reveal a folded helical domain at its C-terminus.
Authors: Fisher, O.S. / Zhang, R. / Li, X. / Murphy, J.W. / Demeler, B. / Boggon, T.J.

History

Deposition	Jun 25, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 19, 2012	Provider: repository / Type: Initial release
Revision 1.1	Feb 27, 2013	Group: Database references
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4fqn.cif.gz	163.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4fqn.ent.gz	133 KB	Display	PDB format
PDBx/mmJSON format	4fqn.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/fq/4fqn ftp://data.pdbj.org/pub/pdb/validation_reports/fq/4fqn	HTTPS FTP

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Related structure data

Similar structure data	6ao3-4 6gz1-d 4db9-4 1n5z-3 4im6-d 4hu7-3 4tzh-1 4cy9-d 3rfi-2 4db9-3 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

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#88 - Apr 2007 Clathrin similarity (2)

Deposited unit

A: Malcavernin

B: Malcavernin

C: Malcavernin

D: Malcavernin

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

1

A: Malcavernin

B: Malcavernin

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

2

C: Malcavernin

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

3

D: Malcavernin

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

Unit cell

Length a, b, c (Å)	62.166, 64.196, 89.460
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Details

Chains A and B form a dimer

#1: Protein	Malcavernin / Cerebral cavernous malformations 2 protein Mass: 11162.600 Da / Num. of mol.: 4 / Fragment: C-terminal domain (unp residues 283-379) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: C7orf22, CCM2, PP10187 / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q9BSQ5
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Malcavernin / Cerebral cavernous malformations 2 protein

Mass: 11162.600 Da / Num. of mol.: 4 / Fragment: C-terminal domain (unp residues 283-379)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: C7orf22, CCM2, PP10187 / Plasmid: pET32 / Production host:

Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q9BSQ5

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 312 / 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 Å³/Da / Density % sol: 38.47 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 2.072M ammonium sulfate, 0.2M potassium formate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS

/ Beamline: X25 / Wavelength: 0.9778 Å

Detector

Type: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 30, 2012

Radiation

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

Radiation wavelength

Wavelength: 0.9778 Å / Relative weight: 1

Reflection

Resolution: 1.9→35 Å / Num. all: 341945 / Num. obs: 29059 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.8 % / B_iso Wilson estimate: 22.8 Å² / R_sym value: 0.181 / Net I/σ(I): 13.7

Reflection shell

Resolution (Å)	Redundancy (%)	Mean I/σ(I) obs	Num. unique all	R_sym value	Diffraction-ID	% possible all
1.9-1.97	8.5	1.6	2805	0	1	100
1.97-2.05	10.4	2.5	2870	0.933	1	100
2.05-2.14	11.3	3.5	2857	0.775	1	100
2.14-2.25	12.6	5	2872	0.62	1	100
2.25-2.39	12.2	6.7	2876	0.466	1	100
2.39-2.58	12.7	8.5	2872	0.372	1	100
2.39-2.58	12.7	8.5	2872	0.372	1	100
2.58-2.84	12.7	11.7	2918	0.256	1	100
2.84-3.25	12.5	17.3	2925	0.153	1	100
3.25-4.09	12.7	26.1	2965	0.094	1	100
4.09-35	11.8	30.3	3099	0.077	1	100

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Processing

Software

Name	Version	Classification
PHENIX	1.7.3_928	refinement
PDB_EXTRACT	3.11	data extraction
CBASS		data collection
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX	autosol	phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.9→35 Å / Occupancy max: 1 / Occupancy min: 0.11 / SU ML: 0.25 / σ(F): 1.34 / Phase error: 21.07 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.219	1467	5.06 %	RANDOM
R_work	0.183	-	-	-
obs	0.1848	28998	99.35 %	-
all	-	28998	-	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 49.289 Å² / k_sol: 0.411 e/Å³

Displacement parameters

B_iso max: 91.32 Å² / B_iso mean: 27.1697 Å² / B_iso min: 10.36 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.1262 Å²	0 Å²	-0 Å²
2-	-	3.3593 Å²	0 Å²
3-	-	-	-4.4855 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→35 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2854	0	0	312	3166

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	3028
X-RAY DIFFRACTION	f_angle_d	1.012	4097
X-RAY DIFFRACTION	f_chiral_restr	0.064	455
X-RAY DIFFRACTION	f_plane_restr	0.004	532
X-RAY DIFFRACTION	f_dihedral_angle_d	15.189	1177

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.9-1.961	0.3234	148	0.2918	2560	2708	100
1.961-2.0395	0.2395	150	0.2268	2710	2860	100
2.0395-2.1323	0.2243	153	0.1972	2724	2877	100
2.1323-2.2447	0.2445	127	0.1889	2753	2880	100
2.2447-2.3852	0.2311	152	0.1872	2738	2890	100
2.3852-2.5693	0.2414	146	0.1888	2743	2889	100
2.5693-2.8278	0.2184	153	0.1866	2752	2905	100
2.8278-3.2366	0.2272	160	0.1731	2778	2938	100
3.2366-4.0765	0.1801	147	0.1496	2813	2960	100
4.0765-32.1026	0.1999	131	0.1807	2960	3091	100

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	5.521	-7.4707	2.2853	2.0009	-2.4379	4.0925	-0.5598	-0.5922	-0.1952	1.262	0.7072	0.9878	-0.4137	-0.678	-0.0465	0.2481	0.038	0.0106	0.1341	-0.0195	0.2553	24.2433	35.1783	15.1492
2	9.5601	-5.9551	0.1757	3.7418	-0.4025	4.2541	0.1914	-0.6659	-0.1942	0.1318	0.041	0.2633	0.3748	0.0987	-0.2634	0.1636	-0.055	-0.0057	0.1475	0.0039	0.1611	27.8534	25.857	16.4214
3	7.7026	6.4244	0.6957	8.0393	1.3546	5.1057	0.0766	-0.0301	-0.4798	0.2878	-0.3312	0.0099	0.3224	-0.2363	0.2063	0.1865	-0.0136	0.0148	0.1353	-0.0416	0.1469	19.911	14.1747	14.3646
4	3.8237	2.9332	-0.9397	7.81	0.0741	0.9424	-0.0972	0.4031	-0.0491	-0.4316	0.0465	0.3326	0.0286	-0.9612	-0.0326	0.1652	-0.0575	-0.0056	0.4297	0.0117	0.1476	10.0128	22.147	13.822
5	3.1477	3.0699	-2.0197	6.0927	-0.2973	2.1883	0.3063	-0.1346	0.2565	0.4532	-0.2059	0.387	-0.168	-0.2664	-0.089	0.1455	0.0338	0.0408	0.323	0.0189	0.1551	9.4795	26.8281	22.2891
6	5.9513	1.148	0.2566	3.1253	0.057	5.7407	0.4447	-0.1657	-0.2436	0.6219	-0.4034	0.0134	0.1583	0.0477	0.0077	0.2506	-0.0193	0.029	0.1666	0.0142	0.129	13.4593	16.6107	24.4187
7	4.5063	1.9393	-0.8643	9.074	0.2708	4.1188	-0.2012	-0.1758	0.0204	0.1587	-0.0108	-0.1014	-0.0299	0.425	0.151	0.1907	-0.0209	0.0021	0.2662	-0.008	0.1112	18.3329	25.9891	29.7994
8	1.9994	9.0128	-4.0519	7.3219	-3.8337	4.2499	-0.3865	-0.1778	-1.8842	0.2136	-0.2848	-2.0678	1.5777	1.4271	0.4903	0.4957	0.1364	0.0802	0.4429	-0.0837	0.5077	14.0295	16.1833	32.6864
9	7.2135	4.7411	-0.1824	3.8419	-0.5281	2.3451	-0.0364	-0.068	0.0219	-0.1551	-0.0066	-0.0148	0.0124	0.0344	0.0517	0.1476	0.0255	-0.0046	0.1076	-0.0133	0.1143	27.9752	26.3576	7.0804
10	4.5211	2.3855	0.4869	3.0735	0.2615	1.3659	-0.2164	0.0312	0.1953	-0.2495	0.1913	0.0274	-0.2704	-0.1348	0.0243	0.2221	0.0554	0.0048	0.1086	-0.008	0.1401	23.6368	38.4833	4.0468
11	5.4156	-0.6215	-0.0042	5.2304	1.7742	5.0985	-0.1976	0.4826	0.2881	-0.4387	0.28	0.0449	-0.09	0.0304	-0.1555	0.1534	-0.0186	-0.0014	0.1379	0.0149	0.1175	31.8977	35.0393	-2.3304
12	4.3495	1.226	-1.4318	8.2388	-5.2382	3.5955	-0.0586	0.4626	-0.0627	-0.1442	-0.1171	-0.083	0.2567	-0.0123	0.169	0.1956	-0.0297	-0.0301	0.2487	-0.0104	0.1101	23.7967	30.6506	-8.6302
13	5.3113	-5.2071	-4.0098	9.045	2.9625	7.8585	0.0653	1.1347	0.7683	-0.5094	0.1505	-0.7229	-0.5046	0.5283	-0.2468	0.3052	-0.1421	-0.0292	0.345	0.0141	0.2121	20.72	9.1622	-7.9396
14	5.9009	-0.9143	-0.6577	4.889	1.6245	2.0886	-0.1917	0.2035	0.4131	-0.1796	0.2528	-0.3217	-0.0008	0.1612	-0.0713	0.1696	-0.045	0.0094	0.1515	-0.0046	0.0971	17.8057	12.68	1.0264
15	6.9611	0.472	0.5696	5.2411	1.3316	4.3391	-0.0863	-0.2482	0.0105	0.1784	0.1762	-0.2292	0.3089	0.0535	-0.0416	0.1815	0.0124	-0.0192	0.1008	-0.0153	0.1596	16.9002	2.879	5.1234
16	5.7851	-0.5292	-2.2495	5.5301	-2.5521	8.9514	-0.1354	0.0391	-0.8156	-0.3056	0.3249	-0.2435	0.8417	0.3993	-0.1116	0.2392	0.0117	-0.0213	0.1874	-0.0846	0.2818	19.9373	-5.3199	-0.6467
17	7.7812	-4.7928	2.9231	9.2948	-5.0302	5.4952	0.37	-0.8626	-0.4928	0.7876	0.4716	0.0182	0.5855	-0.7695	-0.6501	0.394	-0.0437	-0.1241	0.2586	-0.0144	0.2497	36.1248	34.8559	27.3823
18	6.4232	-1.033	-1.4957	2.1218	-0.0283	2.8557	0.057	-0.3724	-0.3702	-0.0633	-0.0149	-0.0651	0.2502	0.2301	-0.037	0.1917	-0.0013	-0.0361	0.1697	-0.0059	0.1254	38.9836	26.4891	17.9806
19	5.0552	-1.5901	0.1052	4.4857	0.1839	4.2954	-0.1032	-1.0839	0.2554	0.677	0.4874	-0.6436	-0.0432	0.9512	-0.2751	0.2848	0.032	-0.037	0.5572	-0.1156	0.3038	50.3829	28.9797	22.5665

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 282:287)	A	282 - 287
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 288:292)	A	288 - 292
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 293:308)	A	293 - 308
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 309:326)	A	309 - 326
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 327:343)	A	327 - 343
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 344:356)	A	344 - 356
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 357:371)	A	357 - 371
8	X-RAY DIFFRACTION	8	chain 'A' and (resseq 372:376)	A	372 - 376
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 283:308)	B	283 - 308
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 309:343)	B	309 - 343
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 344:356)	B	344 - 356
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 357:375)	B	357 - 375
13	X-RAY DIFFRACTION	13	chain 'C' and (resseq 292:306)	C	292 - 306
14	X-RAY DIFFRACTION	14	chain 'C' and (resseq 307:326)	C	307 - 326
15	X-RAY DIFFRACTION	15	chain 'C' and (resseq 327:352)	C	327 - 352
16	X-RAY DIFFRACTION	16	chain 'C' and (resseq 353:376)	C	353 - 376
17	X-RAY DIFFRACTION	17	chain 'D' and (resseq 299:311)	D	299 - 311
18	X-RAY DIFFRACTION	18	chain 'D' and (resseq 312:343)	D	312 - 343
19	X-RAY DIFFRACTION	19	chain 'D' and (resseq 344:375)	D	344 - 375

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