PDB-4iqh: Crystal Structure Analysis of Dysferlin C2A variant 1 (C2Av1)

ID or keywords:

Entry

Database: PDB / ID: 4iqh

Title

Crystal Structure Analysis of Dysferlin C2A variant 1 (C2Av1)

Components

Dysferlin

Keywords

MEMBRANE PROTEIN / C2 domain / membrane repair / acidic phospholipid binding / peripheral membrane protein

Function / homology

Function and homology information

monocyte activation involved in immune response / T-tubule organization / vesicle fusion / regulation of neurotransmitter secretion / plasma membrane repair / macrophage activation involved in immune response / calcium-dependent phospholipid binding / negative regulation of phagocytosis / centriolar satellite / endocytic vesicle ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.764 Å

Authors

Sutton, R.B. / Fuson, K.L.

Citation

Journal: Structure / Year: 2014
Title: Alternate Splicing of Dysferlin C2A Confers Ca(2+)-Dependent and Ca(2+)-Independent Binding for Membrane Repair.
Authors: Fuson, K. / Rice, A. / Mahling, R. / Snow, A. / Nayak, K. / Shanbhogue, P. / Meyer, A.G. / Redpath, G.M. / Hinderliter, A. / Cooper, S.T. / Sutton, R.B.

History

Deposition	Jan 11, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 18, 2013	Provider: repository / Type: Initial release
Revision 1.1	Jan 29, 2014	Group: Database references
Revision 1.2	Apr 25, 2018	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.3	Sep 20, 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	4iqh.cif.gz	230.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4iqh.ent.gz	190.3 KB	Display	PDB format
PDBx/mmJSON format	4iqh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4iqh_validation.pdf.gz	451.1 KB	Display	wwPDB validaton report
Full document	4iqh_full_validation.pdf.gz	462.5 KB	Display
Data in XML	4iqh_validation.xml.gz	25.1 KB	Display
Data in CIF	4iqh_validation.cif.gz	37.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/iq/4iqh ftp://data.pdbj.org/pub/pdb/validation_reports/iq/4iqh	HTTPS FTP

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Related structure data

Related structure data	4ihbSC 2dmh 3l9b S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1jzw-d 5j0d-d 6sw3-2 1sk0-d 1sjz-d 1sk2-d 1s3d-d 2rnw-d 1sd8-d 1i9d-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

4ihbSC

2dmh

3l9b

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#196 - Apr 2016 Lead Poisoning similarity (6) #148 - Apr 2012 Ras Protein similarity (5) #239 - Nov 2019 Phospholipase A2 similarity (5) #44 - Aug 2003 Calmodulin similarity (1) #28 - Apr 2002 Anthrax Toxin similarity (1)

Deposited unit

A: Dysferlin

B: Dysferlin

C: Dysferlin

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

1

A: Dysferlin

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

2

B: Dysferlin

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

3

C: Dysferlin

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

Unit cell

Length a, b, c (Å)	71.160, 71.160, 137.450
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

Components on special symmetry positions

ID	Model	Components
1	1	A-409- HOH

#1: Protein	Dysferlin / Dystrophy-associated fer-1-like protein / Fer-1-like protein 1 Mass: 14328.525 Da / Num. of mol.: 3 / Fragment: C2A DOMAIN of Dysferlin_v1, UNP residues 1-124 / Mutation: C3A Source method: isolated from a genetically manipulated source Details: His-tagged-MBP-fusion protein / Source: (gene. exp.) Homo sapiens (human) / Gene: DYSF, Dysferlin, FER1L1 / Plasmid: p202 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O75923
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 610 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	THE SEQUENCE OF THIS ISOFORM DIFFERS FROM THE CANONICAL SEQUENCE AS FOLLOWS:RESIDUES 1-29: ...THE SEQUENCE OF THIS ISOFORM DIFFERS FROM THE CANONICAL SEQUENCE AS FOLLOWS:RESIDUES 1-29: MLRVFILYAENVHTPDTDISDAYCSAVFA CHANGED TO: MLCCLLVRASNLPSAKKDRRSDPVASLTFR

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.34 Å³/Da / Density % sol: 47.37 %
Crystal grow	Temperature: 280 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 16% PEG 20000, 0.1M sodium citrate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 280K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	90	1
2		1

Diffraction source

Source	Site	Beamline	Type	ID	Wavelength (Å)
ROTATING ANODE			RIGAKU	1	1.5418
SYNCHROTRON	SSRL	BL7-1		2	0.97

Detector

Type	ID	Detector	Date
Mercury 3	1	CCD	Jan 1, 2012
ADSC QUANTUM 315	2	CCD	Mar 1, 2012

Radiation

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

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1.5418	1
2	0.97	1

Reflection

Resolution: 1.76→30 Å / Num. all: 40108 / Num. obs: 36605 / % possible obs: 95.7 % / Redundancy: 6.6 % / R_sym value: 0.075

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Processing

Software

Name	Version	Classification
HKL-3000		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.8.1_1168)	refinement
HKL-3000		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4IHB

4ihb

Resolution: 1.764→30 Å / SU ML: 0.21 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.19 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2153	3489	9.9 %	RANDOM
R_work	0.1923	-	-	-
obs	0.1945	35247	87.17 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.764→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2976	0	0	610	3586

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.024	3089
X-RAY DIFFRACTION	f_angle_d	1.816	4198
X-RAY DIFFRACTION	f_dihedral_angle_d	16.297	1183
X-RAY DIFFRACTION	f_chiral_restr	0.126	492
X-RAY DIFFRACTION	f_plane_restr	0.012	537

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 (%)
1.7641-1.7882	0.3031	156	0.2585	1421	X-RAY DIFFRACTION	100
1.7882-1.8138	0.2391	149	0.2437	1428	X-RAY DIFFRACTION	99
1.8138-1.8409	0.2763	149	0.2312	1446	X-RAY DIFFRACTION	100
1.8409-1.8696	0.2833	172	0.2577	1430	X-RAY DIFFRACTION	100
1.8696-1.9003	0.472	97	0.4166	968	X-RAY DIFFRACTION	68
1.9003-1.933	0.5799	83	0.4926	795	X-RAY DIFFRACTION	55
1.933-1.9682	0.3324	75	0.269	594	X-RAY DIFFRACTION	42
1.9682-2.006	0.2394	164	0.2219	1410	X-RAY DIFFRACTION	98
2.006-2.047	0.2479	166	0.2088	1434	X-RAY DIFFRACTION	100
2.047-2.0915	0.3978	70	0.327	612	X-RAY DIFFRACTION	42
2.0915-2.1401	0.2515	151	0.2097	1414	X-RAY DIFFRACTION	99
2.1401-2.1936	0.2136	143	0.1751	1447	X-RAY DIFFRACTION	100
2.1936-2.2529	0.2652	125	0.2118	1020	X-RAY DIFFRACTION	100
2.2529-2.3192	0.2152	125	0.1988	1179	X-RAY DIFFRACTION	100
2.3192-2.3941	0.198	173	0.1809	1438	X-RAY DIFFRACTION	100
2.3941-2.4796	0.2206	163	0.1778	1454	X-RAY DIFFRACTION	100
2.4796-2.5788	0.2023	151	0.177	1474	X-RAY DIFFRACTION	100
2.5788-2.6962	0.2159	99	0.1967	1010	X-RAY DIFFRACTION	69
2.6962-2.8383	0.1899	159	0.1816	1461	X-RAY DIFFRACTION	100
2.8383-3.016	0.2194	177	0.1838	1438	X-RAY DIFFRACTION	100
3.016-3.2487	0.1854	171	0.1699	1480	X-RAY DIFFRACTION	100
3.2487-3.5753	0.1834	129	0.1595	1269	X-RAY DIFFRACTION	85
3.5753-4.092	0.1946	120	0.1601	1029	X-RAY DIFFRACTION	69
4.092-5.1527	0.1462	171	0.1387	1494	X-RAY DIFFRACTION	100
5.1527-34.4511	0.2049	151	0.1941	1613	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	8.2171	-4.9899	3.522	4.7485	-1.8313	3.3957	-0.0979	0.2277	0.9302	0.0993	-0.163	-0.7154	-0.075	0.189	0.1007	0.1663	-0.0224	0.0013	0.1145	-0.0238	0.186	-5.6815	-6.3052	6.9689
2	2.0324	-3.4968	-1.0954	8.6969	0.9021	1.0717	0.0979	0.3164	0.4067	-0.265	-0.1578	0.6285	-0.3894	-0.3895	0.0944	0.2275	0.0666	0.0262	0.2204	0.0433	0.2328	-25.553	6.6329	5.9245
3	5.4085	1.4199	2.3215	5.796	-5.7005	8.4373	-0.0895	-0.5075	0.7163	0.5316	0.0695	-0.0771	-0.2885	0.0168	0.0017	0.1682	0.0218	-0.0196	0.1777	-0.0759	0.1578	-8.4916	-2.7611	17.5419
4	3.7893	-1.8659	1.831	3.4163	-1.4298	2.6797	0.0018	0.107	0.4601	0.0937	-0.0709	-0.3634	0.0011	0.2112	0.0705	0.1572	0.0069	0.0106	0.1158	-0.035	0.1326	-8.5965	-3.0069	10.1675
5	3.5559	-5.0674	1.5308	6.6899	-2.1192	0.8616	-0.3389	-0.3764	0.0818	0.9348	0.3563	0.0859	-0.3241	0.029	0.044	0.2089	-0.0063	0.0111	0.1898	-0.0066	0.1618	-16.8634	-2.6248	13.7621
6	4.2888	-0.8072	-0.4898	4.5765	0.2037	3.1494	-0.109	-0.0615	0.5849	0.6314	0.0257	0.568	-0.5469	-0.2824	0.1133	0.2314	0.0268	-0.0253	0.1519	-0.0303	0.1995	-20.8622	3.4871	14.3798
7	3.9359	-3.7882	-3.1802	3.6455	3.0293	2.556	-0.1402	-0.1715	0.2313	-0.2318	0.4079	0.5741	0.2636	-0.5283	-0.2848	0.249	-0.0179	-0.0146	0.2011	0.0318	0.1965	-7.9629	-19.1069	11.2959
8	8.6763	-4.2559	-1.7625	2.8701	0.7944	0.3151	0.0913	0.0366	0.0274	0.0549	-0.0941	0.0923	0.0171	-0.017	0.0143	0.1663	-0.0221	-0.0111	0.1248	-0.0173	0.1155	-17.6206	-11.8199	8.6313
9	4.3465	-1.0356	3.6781	6.8355	-3.098	5.0168	-0.1322	0.1773	0.7063	0.0465	-0.0508	-0.5126	-0.2212	0.2668	0.1391	0.1506	-0.0095	0.0095	0.0561	-0.0359	0.0707	-7.648	-10.2547	6.5526
10	3.3189	-1.0414	1.1155	1.9843	-0.8248	2.1261	-0.1049	0.1665	0.3173	0.0533	-0.0705	-0.3466	-0.1434	0.2415	0.172	0.1466	-0.0502	0.0015	0.1561	0.0206	0.1367	-23.902	14.9069	38.2402
11	1.9666	-0.7238	-0.4485	1.6598	0.0306	1.1411	-0.0318	0.1589	0.0645	-0.1383	0.0034	-0.1621	-0.0256	0.113	0.0147	0.1504	-0.0318	-0.0029	0.1711	0.0042	0.0954	-26.9252	9.0393	35.7396
12	7.4738	2.182	-1.8261	1.7639	0.0235	1.5167	-0.2856	-0.1619	-0.6296	0.0084	0.0153	-0.2119	0.2752	0.0277	0.2294	0.1863	0.0342	-0.0287	0.1898	0.0351	0.1114	-39.9409	20.1338	8.5702
13	3.4269	-0.4612	0.5509	0.2739	0.5561	1.6416	0.0416	0.1056	0.141	0.2365	-0.5786	-1.6007	-0.5138	1.3284	0.2691	0.3208	-0.1637	-0.1981	0.5973	0.2442	0.8186	-15.6824	32.3692	7.1787
14	1.58	0.7538	-1.1411	2.6423	-1.5131	3.0454	-0.0677	-0.3491	-0.3066	0.0884	-0.0948	-0.4144	0.0454	0.2615	0.224	0.1632	0.0326	-0.0198	0.2093	0.0566	0.1976	-30.1674	21.0598	11.1223
15	2.1047	1.3492	1.3579	7.6357	-3.1328	3.9533	-0.0281	-1.1083	-0.1994	0.262	-0.0627	0.159	0.0737	-0.1489	-0.0174	0.1872	-0.0121	0.029	0.2934	0.0925	0.115	-48.9378	22.775	19.0859
16	2.3405	0.8146	0.7577	4.462	0.257	3.8678	0.0652	-0.7482	-0.0594	0.657	-0.1652	-0.8925	0.1221	0.4499	0.187	0.2743	-0.0209	-0.1334	0.2898	0.0823	0.2747	-25.5206	28.1729	15.9434
17	4.8541	2.0018	-0.7807	2.7815	-0.1458	0.2495	0.0537	-0.2915	0.1654	0.2267	-0.0445	-0.0666	-0.0006	0.0467	0.0045	0.1661	0.0154	-0.021	0.1644	0.0007	0.0685	-40.0765	30.6174	9.3208

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -1 through 11 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 12 through 26 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 27 through 36 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 37 through 65 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 66 through 73 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 74 through 89 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 90 through 94 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 95 through 117 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 118 through 126 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 0 through 65 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 66 through 126 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid -1 through 11 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 12 through 23 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 24 through 55 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 56 through 65 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 66 through 89 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 90 through 126 )

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