PDB-4ihb: X-RAY STRUCTURE OF THE canonical C2A DOMAIN FROM HUMAN DYSFERLIN

ID or keywords:

Entry

Database: PDB / ID: 4ihb

Title

X-RAY STRUCTURE OF THE canonical C2A DOMAIN FROM HUMAN DYSFERLIN

Components

Dysferlin

Keywords

MEMBRANE PROTEIN / BETA SANDWICH / TYPE II C2 DOMAIN / MUSCULAR DYSTROPHY / MEMBRANE REPAIR / PLASMA MEMBRANE

Function / homology

Function and homology information

monocyte activation involved in immune response / regulation of neurotransmitter secretion / calcium-dependent phospholipid binding / macrophage activation involved in immune response / negative regulation of phagocytosis / endocytic vesicle / Smooth Muscle Contraction / T-tubule / cytoplasmic vesicle membrane / sarcolemma ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.044 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	Dec 18, 2012	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 / _diffrn_source.type
Revision 1.3	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4ihb.cif.gz	326.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4ihb.ent.gz	269.1 KB	Display	PDB format
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Validation report

Summary document	4ihb_validation.pdf.gz	513.1 KB	Display	wwPDB validaton report
Full document	4ihb_full_validation.pdf.gz	548.5 KB	Display
Data in XML	4ihb_validation.xml.gz	37.5 KB	Display
Data in CIF	4ihb_validation.cif.gz	50.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ih/4ihb ftp://data.pdbj.org/pub/pdb/validation_reports/ih/4ihb	HTTPS FTP

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Related structure data

Related structure data	4iqhC 2dmhS 3l9b S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5qu4-2 3u99-d 5bt3-d 6ay3-1 4nyv-2 2co2-d 5lpm-2 3di5-d 3qzs-2 1xcv-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) 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

4iqhC

2dmhS

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

D: Dysferlin

E: Dysferlin

F: Dysferlin

hetero molecules

89.2 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Dysferlin

hetero molecules

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

2

B: Dysferlin

hetero molecules

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

3

C: Dysferlin

hetero molecules

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

4

D: Dysferlin

hetero molecules

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

5

E: Dysferlin

hetero molecules

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

6

F: Dysferlin

hetero molecules

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

7

A: Dysferlin

B: Dysferlin

C: Dysferlin

hetero molecules

A: Dysferlin

B: Dysferlin

C: Dysferlin

hetero molecules

defined by software
89.1 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

8

D: Dysferlin

E: Dysferlin

F: Dysferlin

hetero molecules

D: Dysferlin

E: Dysferlin

F: Dysferlin

hetero molecules

defined by software
89.3 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	102.413, 70.670, 118.310
Angle α, β, γ (deg.)	90.00, 113.39, 90.00
Int Tables number	5
Space group name H-M	I121

Components on special symmetry positions

ID	Model	Components
1	1	F-349- HOH

#1: Protein	Dysferlin / Dystrophy-associated fer-1-like protein / Fer-1-like protein 1 Mass: 14563.558 Da / Num. of mol.: 6 / Fragment: C2A DOMAIN, UNP residues 1-124 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DYSF, FER1L1 / Plasmid: PGEX4T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O75923
#2: Chemical	... ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 39 / Source method: obtained synthetically / Formula: CH₂O₂
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.25 Å³/Da / Density % sol: 45.3 %
Crystal grow	Temperature: 284 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: 2M Sodium Formate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 284K

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Data collection

Diffraction

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

Diffraction source

Source	Site	Beamline	Type	ID	Wavelength (Å)
ROTATING ANODE			RIGAKU	1	1.5418
SYNCHROTRON	SSRL	BL7-1		2	0.97946

Detector

Type	ID	Detector	Details	Date
Mercury 3	1	CCD	Integrated MaxFlux confocal optic
ADSC QUANTUM 315	2	CCD		Jun 4, 2010

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	SINGLE WAVELENGTH	M	x-ray	1
2	SINGLE WAVELENGTH	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1.5418	1
2	0.97946	1

Reflection

Resolution: 2.04→56 Å / Num. all: 49251 / Num. obs: 49251 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / R_merge(I) obs: 0.073

Reflection shell

Resolution: 2.04→2.15 Å / Redundancy: 3.6 % / R_merge(I) obs: 0.415 / Mean I/σ(I) obs: 0.415 / % possible all: 99.5

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.8.1_1168)	refinement
HKL-2000		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2DMH

2dmh

Resolution: 2.044→33.902 Å / SU ML: 0.27 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.8 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2401	4918	10.07 %	random
R_work	0.2	-	-	-
obs	0.2041	48842	99.19 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.044→33.902 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5917	0	118	287	6322

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	6175
X-RAY DIFFRACTION	f_angle_d	1.347	8337
X-RAY DIFFRACTION	f_dihedral_angle_d	16.307	2223
X-RAY DIFFRACTION	f_chiral_restr	0.089	959
X-RAY DIFFRACTION	f_plane_restr	0.006	1062

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 (%)
2.044-2.0673	0.3178	193	0.2591	1438	X-RAY DIFFRACTION	99
2.0673-2.0916	0.3207	180	0.2494	1430	X-RAY DIFFRACTION	100
2.0916-2.1171	0.265	150	0.238	1465	X-RAY DIFFRACTION	100
2.1171-2.1439	0.252	150	0.2379	1519	X-RAY DIFFRACTION	100
2.1439-2.1721	0.2914	163	0.2253	1420	X-RAY DIFFRACTION	99
2.1721-2.2018	0.265	174	0.2295	1478	X-RAY DIFFRACTION	100
2.2018-2.2333	0.2653	171	0.2276	1440	X-RAY DIFFRACTION	100
2.2333-2.2666	0.297	162	0.2253	1495	X-RAY DIFFRACTION	100
2.2666-2.302	0.287	152	0.2256	1438	X-RAY DIFFRACTION	99
2.302-2.3398	0.3099	163	0.2216	1469	X-RAY DIFFRACTION	99
2.3398-2.3801	0.2912	155	0.2355	1455	X-RAY DIFFRACTION	100
2.3801-2.4234	0.2702	146	0.2198	1512	X-RAY DIFFRACTION	100
2.4234-2.47	0.2849	142	0.2348	1447	X-RAY DIFFRACTION	99
2.47-2.5204	0.2972	163	0.2218	1488	X-RAY DIFFRACTION	100
2.5204-2.5752	0.2728	169	0.2252	1423	X-RAY DIFFRACTION	100
2.5752-2.635	0.2684	170	0.2241	1472	X-RAY DIFFRACTION	99
2.635-2.7009	0.2723	176	0.2085	1463	X-RAY DIFFRACTION	99
2.7009-2.7739	0.2566	160	0.2088	1449	X-RAY DIFFRACTION	99
2.7739-2.8555	0.2395	183	0.2057	1431	X-RAY DIFFRACTION	99
2.8555-2.9476	0.2854	160	0.2085	1481	X-RAY DIFFRACTION	99
2.9476-3.0529	0.2501	167	0.1984	1479	X-RAY DIFFRACTION	100
3.0529-3.175	0.2585	164	0.2011	1434	X-RAY DIFFRACTION	99
3.175-3.3194	0.2161	168	0.1833	1471	X-RAY DIFFRACTION	100
3.3194-3.4943	0.2181	157	0.1644	1487	X-RAY DIFFRACTION	99
3.4943-3.7129	0.1849	164	0.1768	1472	X-RAY DIFFRACTION	99
3.7129-3.9992	0.2197	178	0.1787	1447	X-RAY DIFFRACTION	100
3.9992-4.4009	0.1907	168	0.1591	1501	X-RAY DIFFRACTION	99
4.4009-5.0359	0.1886	128	0.1538	1487	X-RAY DIFFRACTION	98
5.0359-6.3379	0.2301	167	0.206	1412	X-RAY DIFFRACTION	95
6.3379-33.9063	0.2267	175	0.2483	1521	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	5.1079	4.8625	2.3846	9.5237	4.3423	3.7823	-0.2799	0.4797	-0.2564	-0.2027	0.5917	0.0841	0.3208	0.0586	-0.2604	0.3062	-0.0359	-0.0398	0.314	0.0535	0.216	7.4971	2.0438	-72.6345
2	4.7637	0.0405	-1.0248	5.2496	0.6968	6.9738	0.0107	-0.0959	0.3161	0.0536	0.0952	0.3319	0.055	-0.5273	-0.0616	0.1363	0.0362	-0.0424	0.2883	0.0302	0.2966	3.9361	8.0676	-67.9181
3	0.6141	0.8767	-2.359	6.3538	-3.1585	9.5904	-1.157	1.242	-0.2866	-0.5138	0.3776	3.5609	1.7009	-2.1584	-0.3747	0.3905	0.1693	-0.3458	1.9081	-0.3515	1.3571	-6.596	-1.2021	-77.3974
4	4.2737	2.9016	2.5039	6.7868	3.7731	3.3879	0.406	-0.5877	-0.3171	0.6541	-0.3397	0.1529	0.4767	-0.4139	-0.011	0.2731	-0.0516	0.0218	0.3214	0.0872	0.2572	9.0786	2.6624	-61.0833
5	6.0272	1.2581	0.2216	6.8003	-0.8587	4.2835	-0.175	-0.3977	0.5027	0.1316	0.0125	0.5045	-0.2283	-0.2933	0.1033	0.1862	0.0148	0.0017	0.2677	-0.0864	0.2141	20.4301	16.0692	-34.5654
6	4.9098	-1.2204	1.5545	5.7312	-2.2252	2.8645	-0.0772	-0.1541	-0.0865	-0.0821	0.1903	0.4956	-0.0047	-0.3626	-0.1058	0.1672	0.0127	-0.0064	0.2182	-0.0198	0.1836	17.771	10.4592	-42.0016
7	4.7743	-0.8155	0.7342	3.3852	-1.0407	4.4291	-0.0764	-0.3149	-0.3021	0.3917	0.2346	0.2259	0.3232	-0.261	-0.1486	0.2757	0.0034	-0.0021	0.1442	0.0523	0.2956	17.9458	-23.945	-44.594
8	5.5496	0.8174	3.4671	3.7958	3.4635	7.9467	-0.3084	-0.2984	2.0008	-0.025	0.4333	1.1054	-1.6637	-2.218	0.1621	0.4387	0.1938	0.0266	0.7134	0.4685	0.8322	6.9701	-15.6031	-48.4369
9	4.6348	4.7941	4.9464	6.8443	4.6742	5.3764	1.2459	-0.6736	0.415	4.2821	0.3623	1.6411	2.0612	-1.2002	-0.4839	1.4072	0.2373	0.4028	1.0375	0.4215	1.0762	15.1388	-28.9971	-30.2224
10	2.9456	0.6855	-0.0013	0.5206	-1.5712	3.2188	0.022	-0.0544	0.2554	0.1119	0.218	0.225	-0.6247	-0.5786	-0.2379	0.3138	0.0359	0.024	0.2077	0.0204	0.3888	15.4297	-12.5486	-47.2134
11	3.7813	-2.5271	-1.3436	9.016	4.3192	3.0665	0.2663	0.45	-0.5017	-0.9595	-0.626	0.0917	-0.3513	-0.5158	0.3429	0.2577	0.0297	0.0249	0.1699	-0.0071	0.2129	-31.5072	35.6569	-74.6919
12	9.6334	-1.5734	-5.4584	0.332	0.7673	4.6848	2.3706	-1.8695	2.9818	0.1141	-1.232	-0.6456	-2.5757	0.5801	-0.6461	1.6623	-0.2018	-0.1074	0.5823	-0.2398	1.1523	-25.1107	59.2714	-65.5121
13	6.3927	-3.0091	-2.1975	2.5021	0.6046	4.3223	-0.1947	0.2873	0.2393	0.0626	0.0507	0.0086	-0.7037	0.029	0.1134	0.384	-0.0416	0.0139	0.2042	0.0506	0.2474	-28.8036	46.3364	-75.8905
14	6.1827	0.3444	2.1125	2.7653	0.3437	5.022	1.1237	0.8594	-0.126	-0.4283	-2.2177	-1.6905	-0.4463	1.0195	0.1165	0.3106	0.0196	0.1962	0.7572	0.2131	0.4465	-19.5211	43.7525	-75.7588
15	5.0071	3.7127	-0.0492	8.7853	-0.143	3.9804	-0.0366	-0.1248	-0.3498	0.2422	0.0628	-0.5347	-0.1298	0.8309	-0.0645	0.1568	-0.064	-0.0387	0.4115	0.0065	0.2237	-23.3317	38.092	-67.172
16	3.9702	-0.1149	0.8838	3.6861	-0.8642	4.7353	0.0137	0.1847	-0.006	0.3116	-0.1078	-0.3309	-0.0911	0.6816	0.1306	0.151	-0.0375	-0.0248	0.2621	-0.0081	0.1995	-7.9986	35.6974	-38.234
17	4.1764	-1.4327	1.1229	6.0565	-0.8599	3.8148	0.2125	0.6445	-0.1445	-0.54	-0.2834	-0.3324	0.0745	0.5109	0.1653	0.1795	-0.0367	0.0823	0.3754	-0.0611	0.1866	-8.7335	33.4454	-47.5853
18	4.7275	1.286	1.5373	3.516	2.4032	6.8826	0.0593	0.0873	-0.1759	-0.3138	0.2155	-0.2807	0.4135	0.3783	-0.2046	0.2829	0.0293	-0.0049	0.1325	-0.0196	0.2633	-21.2876	7.9418	-63.9386
19	2.0579	3.2723	-2.8489	5.1643	-4.3362	5.0683	-0.2068	2.5298	-2.989	-4.2537	0.5792	-3.3424	2.2823	5.0302	-0.3045	1.7478	0.6317	0.2552	2.3317	-0.6239	1.6609	-21.6514	0.9371	-78.2799
20	3.3017	1.4231	2.3932	2.4499	1.8565	7.7346	-0.0758	0.1713	0.4104	-0.2828	0.0442	-0.1089	-0.4168	0.4103	0.0113	0.2448	0.0167	0.0279	0.1596	0.015	0.2816	-21.1944	17.266	-62.7351

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 21 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 22 through 71 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 72 through 79 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 80 through 125 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 0 through 77 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 78 through 125 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 0 through 53 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 54 through 71 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 72 through 79 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 80 through 126 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid -1 through 9 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 10 through 21 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 22 through 53 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 54 through 79 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 80 through 126 )
16	X-RAY DIFFRACTION	16	chain 'E' and (resid 0 through 53 )
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 54 through 125 )
18	X-RAY DIFFRACTION	18	chain 'F' and (resid 0 through 71 )
19	X-RAY DIFFRACTION	19	chain 'F' and (resid 72 through 79 )
20	X-RAY DIFFRACTION	20	chain 'F' and (resid 80 through 125 )

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