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- PDB-6eel: Crystal Structure of Myoferlin C2A with divalent cation -

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Basic information

Entry
Database: PDB / ID: 6eel
TitleCrystal Structure of Myoferlin C2A with divalent cation
ComponentsMyoferlin
KeywordsMETAL BINDING PROTEIN / ferlin / C2 domain / calcium-binding
Function / homology
Function and homology information


regulation of neurotransmitter secretion / plasma membrane repair / blood circulation / centriolar satellite / caveola / muscle contraction / phospholipid binding / synaptic vesicle membrane / nuclear envelope / cytoplasmic vesicle ...regulation of neurotransmitter secretion / plasma membrane repair / blood circulation / centriolar satellite / caveola / muscle contraction / phospholipid binding / synaptic vesicle membrane / nuclear envelope / cytoplasmic vesicle / nuclear membrane / intracellular membrane-bounded organelle / calcium ion binding / extracellular exosome / plasma membrane
Similarity search - Function
Ferlin A-domain / FerA (NUC095) domain / FerA / Ferlin B-domain / FerIin domain / Ferlin, C-terminal domain / Ferlin, second C2 domain / Ferlin family / Ferlin, third C2 domain / Ferlin, fourth C2 domain ...Ferlin A-domain / FerA (NUC095) domain / FerA / Ferlin B-domain / FerIin domain / Ferlin, C-terminal domain / Ferlin, second C2 domain / Ferlin family / Ferlin, third C2 domain / Ferlin, fourth C2 domain / Ferlin, fifth C2 domain / Ferlin, sixth C2 domain / Ferlin, first C2 domain / FerB (NUC096) domain / FerI (NUC094) domain / Ferlin C-terminus / FerB / FerI / Peroxin/Ferlin domain / Dysferlin domain, N-terminal region. / Dysferlin domain, C-terminal region. / C2 domain / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / C2 domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
STRONTIUM ION / Myoferlin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsSutton, R.B. / Harsini, F.M. / Rice, A.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)AR063634 United States
CitationJournal: J.Mol.Biol. / Year: 2019
Title: Structural Basis for the Distinct Membrane Binding Activity of the Homologous C2A Domains of Myoferlin and Dysferlin.
Authors: Harsini, F.M. / Bui, A.A. / Rice, A.M. / Chebrolu, S. / Fuson, K.L. / Turtoi, A. / Bradberry, M. / Chapman, E.R. / Sutton, R.B.
History
DepositionAug 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: 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_ncs_dom_lim
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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myoferlin
B: Myoferlin
C: Myoferlin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3079
Polymers42,7813
Non-polymers5266
Water8,521473
1
A: Myoferlin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4363
Polymers14,2601
Non-polymers1752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Myoferlin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4363
Polymers14,2601
Non-polymers1752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Myoferlin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4363
Polymers14,2601
Non-polymers1752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.350, 83.110, 94.280
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 0 / Auth seq-ID: 4 - 132 / Label seq-ID: 1 - 129

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Myoferlin / / Fer-1-like protein 3


Mass: 14260.422 Da / Num. of mol.: 3 / Fragment: residues 1-125
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYOF, FER1L3, KIAA1207 / Plasmid: p202 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NZM1
#2: Chemical
ChemComp-SR / STRONTIUM ION / Strontium


Mass: 87.620 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Sr
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 473 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.27 %
Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop / Details: orthorhombic shaped crystals

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.1271 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 1.929→62.345 Å / Num. obs: 28742 / % possible obs: 99.8 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.06 / Rrim(I) all: 0.135 / Rsym value: 0.112 / Net I/av σ(I): 5.6 / Net I/σ(I): 9.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.93-2.034.90.6451.141650.3480.7770.64599.9
2.03-2.164.90.4021.738970.2140.480.40299.9
2.16-2.314.90.3761.636700.1980.4440.37699.9
2.31-2.494.90.2223.234520.1170.2650.22299.9
2.49-2.734.90.164.431610.0850.1910.1699.9
2.73-3.054.90.0997.228970.0520.1180.09999.9
3.05-3.524.80.05911.425670.0320.0720.05999.6
3.52-4.314.70.05411.221940.030.0660.05499.6
4.31-6.14.50.04712.617200.0250.0550.04799.6
6.1-62.3454.50.03413.710190.0190.0410.03499.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALA3.3.22data scaling
REFMAC5.8.0155refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DMH

2dmh


Resolution: 1.93→62.34 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.924 / SU B: 7.953 / SU ML: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.196 / ESU R Free: 0.171
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.232 2793 9.8 %RANDOM
Rwork0.1807 ---
obs0.1857 25836 99.52 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 120.94 Å2 / Biso mean: 29.21 Å2 / Biso min: 9.11 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å2-0 Å2-0 Å2
2---0.53 Å20 Å2
3---1.11 Å2
Refinement stepCycle: final / Resolution: 1.93→62.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3009 0 6 473 3488
Biso mean--29.93 32.02 -
Num. residues----387
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.023068
X-RAY DIFFRACTIONr_bond_other_d0.0020.023106
X-RAY DIFFRACTIONr_angle_refined_deg1.8531.9964152
X-RAY DIFFRACTIONr_angle_other_deg0.95637206
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2045390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.37826.154117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.72715595
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.921159
X-RAY DIFFRACTIONr_chiral_restr0.1070.2502
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213351
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02588
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A74160.1
12B74160.1
21A74420.09
22C74420.09
31B74400.11
32C74400.11
LS refinement shellResolution: 1.929→1.979 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 190 -
Rwork0.266 1922 -
all-2112 -
obs--99.76 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
16.44713.4595-1.59435.6638-2.63216.0695-0.71310.0763-0.3012-0.53940.0989-0.84860.45040.68290.61420.18540.03370.05790.12640.02140.16630.1265.913-31.45
23.44230.71660.76371.41140.48662.2817-0.1051-0.10230.2032-0.09960.00720.0533-0.0726-0.14690.0980.11810.0081-0.0190.0607-0.01340.0235-11.5618.662-26.693
314.87290.4251.2734.9474-0.273215.8003-0.01330.50721.3728-0.7625-0.00771.3674-1.3936-1.23830.02110.39210.1442-0.21480.4391-0.0320.5015-25.72514.518-29.159
44.62850.7966-0.32873.68980.21643.13930.0635-0.18380.07660.135-0.0486-0.19710.07930.172-0.01490.1495-0.0097-0.03430.10390.01870.0274-4.7966.951-20.016
58.1946-4.6304-1.27893.67410.98961.0863-0.1714-0.17230.00590.1870.1857-0.18030.07540.2104-0.01430.195-0.0031-0.00750.1790.00310.14910.5960.179-43.4
61.2190.6820.64543.7124-1.34241.7482-0.05910.08210.16680.08320.25030.4896-0.018-0.3101-0.19120.0815-0.0023-0.01410.15250.06140.0868-16.4964.812-47.487
75.9957-2.1902-1.02982.1365-0.41970.99520.0210.35810.296-0.2034-0.0126-0.22750.14230.1146-0.00840.1727-0.0120.01880.2168-0.01180.057-0.8920.119-50.844
87.19814.3889-2.268619.9632-1.258618.0167-0.27131.2163-0.3749-0.20530.01250.93121.245-1.61810.25880.3062-0.1951-0.00380.5546-0.09940.3376-24.285-1.265-53.52
919.0211-1.04860.08650.86160.06120.325-0.12240.10080.3288-0.15180.0992-0.012-0.0409-0.07690.02320.18960.02810.00020.2080.04250.1763-9.9048.31-55.049
106.2603-1.6512-4.63791.59251.67368.2590.01330.04050.22940.08750.0897-0.78040.29450.8954-0.1030.1448-0.0114-0.01920.2292-0.0030.48477.677.697-46.18
116.8655-2.54823.77532.9012-1.28747.93380.07430.18090.3079-0.1598-0.0795-0.2065-0.2617-0.02010.00520.1609-0.0090.0360.05620.07730.1462-8.23511.643-51.083
129.08942.03944.69544.65031.80717.3691-0.41840.27380.27960.07460.2473-0.6655-0.57190.74510.17110.1557-0.017-0.03150.10940.00050.15520.157-7.414-32.497
135.16940.7552.80712.99921.29784.9881-0.0514-0.1576-0.1237-0.00930.00270.3450.0134-0.44940.04870.0835-0.0060.00190.06730.01610.0794-16.493-14.998-34.146
141.233-0.82330.34582.444-0.32231.2826-0.0448-0.05730.00750.0270.01530.0172-0.0189-0.05020.02950.10660.01550.00280.05930.00340.0097-7.816-11.664-32.542
1510.68820.9159-8.33991.62780.631910.76360.1457-0.1938-0.16340.5-0.13670.7331-0.3285-0.8062-0.0090.46270.10040.27570.42930.09550.6888-25.663-13.252-27.976
1612.35210.4627-1.91563.1952-0.0651.85950.31370.115-0.3874-0.1389-0.15510.19580.1708-0.1546-0.15860.1717-0.0156-0.04430.12920.00810.1033-13.111-20.891-34.073
178.2173-4.99557.32888.0978-5.314612.0322-0.3060.80440.5533-0.10070.0172-1.5967-0.25741.6010.28880.1892-0.05320.05790.4624-0.12220.46047.464-14.117-36.413
186.03913.6404-0.66258.07230.281.25490.2566-0.1413-0.1852-0.0023-0.2114-0.10860.22850.1112-0.04510.16710.0187-0.04440.1073-0.00970.0161-8.541-19.697-38.878
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 17
2X-RAY DIFFRACTION2A18 - 78
3X-RAY DIFFRACTION3A79 - 85
4X-RAY DIFFRACTION4A86 - 132
5X-RAY DIFFRACTION5B4 - 17
6X-RAY DIFFRACTION6B18 - 54
7X-RAY DIFFRACTION7B55 - 78
8X-RAY DIFFRACTION8B79 - 86
9X-RAY DIFFRACTION9B87 - 94
10X-RAY DIFFRACTION10B95 - 108
11X-RAY DIFFRACTION11B109 - 132
12X-RAY DIFFRACTION12C4 - 17
13X-RAY DIFFRACTION13C18 - 41
14X-RAY DIFFRACTION14C42 - 78
15X-RAY DIFFRACTION15C79 - 85
16X-RAY DIFFRACTION16C86 - 94
17X-RAY DIFFRACTION17C95 - 108
18X-RAY DIFFRACTION18C109 - 132

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