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- PDB-7jof: Calcium-bound C2A Domain from Human Dysferlin -

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Basic information

Entry
Database: PDB / ID: 7jof
TitleCalcium-bound C2A Domain from Human Dysferlin
ComponentsIsoform 6 of Dysferlin
KeywordsMEMBRANE PROTEIN / Membrane repair / calcium-binding / C2 domain / phospholipid binding
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 ...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 / phospholipid binding / centriolar satellite / synaptic vesicle membrane / late endosome / early endosome / endosome / calcium ion binding / extracellular exosome / plasma membrane
Similarity search - Function
Ferlin A-domain / FerA (NUC095) domain / FerA / Peroxin/Ferlin domain / Dysferlin domain, N-terminal region. / Dysferlin domain, C-terminal region. / Ferlin B-domain / FerIin domain / Ferlin, C-terminal domain / Ferlin, second C2 domain ...Ferlin A-domain / FerA (NUC095) domain / FerA / Peroxin/Ferlin domain / Dysferlin domain, N-terminal region. / Dysferlin domain, C-terminal region. / 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 / Ferlin dsRNA-binding domain-like domain / FerB / FerI / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTadayon, R. / Wang, Y. / Santamaria, L. / Mercier, P. / Forristal, C. / Shaw, G.S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)FRN-93520 Canada
CitationJournal: Biochem.J. / Year: 2021
Title: Calcium binds and rigidifies the dysferlin C2A domain in a tightly coupled manner.
Authors: Wang, Y. / Tadayon, R. / Santamaria, L. / Mercier, P. / Forristal, C.J. / Shaw, G.S.
History
DepositionAug 6, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 6 of Dysferlin
B: Isoform 6 of Dysferlin
C: Isoform 6 of Dysferlin
D: Isoform 6 of Dysferlin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,38412
Polymers59,0634
Non-polymers3218
Water6,810378
1
A: Isoform 6 of Dysferlin
hetero molecules

B: Isoform 6 of Dysferlin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6926
Polymers29,5322
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area1460 Å2
ΔGint-52 kcal/mol
Surface area13180 Å2
MethodPISA
2
C: Isoform 6 of Dysferlin
hetero molecules

D: Isoform 6 of Dysferlin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6926
Polymers29,5322
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area1400 Å2
ΔGint-52 kcal/mol
Surface area13310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.520, 54.780, 57.340
Angle α, β, γ (deg.)116.800, 103.470, 92.920
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Isoform 6 of Dysferlin / Dystrophy-associated fer-1-like protein / Fer-1-like protein 1


Mass: 14765.858 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DYSF, FER1L1 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O75923
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.06 Å3/Da / Density % sol: 40.27 %
Crystal growTemperature: 283.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 mM magnesium chloride hexahydrate, 0.1 M Tris hydrochloride, and 30% Polyethylene glycol 4,000 (commercial reagent kit from Hampton Research, HR2-130) at pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Feb 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 1.99→23.72 Å / Num. obs: 28309 / % possible obs: 87.6 % / Redundancy: 1.7 % / Biso Wilson estimate: 12.26 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.061 / Rrim(I) all: 0.086 / Net I/σ(I): 9 / Num. measured all: 47404
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.99-2.041.60.155236914410.9170.1550.2194.560.6
8.91-23.721.90.0425402880.980.0420.05918.979.3

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ihb

4ihb


Resolution: 2→9.986 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 24.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2487 1365 4.89 %
Rwork0.2412 26562 -
obs0.2415 27927 88.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.31 Å2 / Biso mean: 17.5728 Å2 / Biso min: 1.68 Å2
Refinement stepCycle: final / Resolution: 2→9.986 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3842 0 8 378 4228
Biso mean--8.63 19.39 -
Num. residues----496
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.07090.2839900.2684206568
2.0709-2.1530.25521210.2506266788
2.153-2.24990.27821480.2519267589
2.2499-2.3670.29471330.2535272989
3.3841-4.20980.25481100.2118279392
4.2098-9.9860.21261490.2141268189

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