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- PDB-9dyq: Crystal structure of human dysferlin C2G domain -

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Basic information

Entry
Database: PDB / ID: 9dyq
TitleCrystal structure of human dysferlin C2G domain
ComponentsDysferlin
KeywordsMETAL BINDING PROTEIN / Dysferlin / ferlin / C2 domain / calcium ion-dependent phospholipid binding / LGMDR2
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 / 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 / Ferlin dsRNA-binding domain-like domain / FerB / FerI / Peroxin/Ferlin domain / Dysferlin domain, N-terminal region. / Dysferlin domain, C-terminal region. / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily
Similarity search - Domain/homology
ACETIC ACID / Dysferlin
Similarity search - Component
Biological speciesPuma concolor (puma)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsDominguez, M.J. / Sutton, R.B.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: To Be Published
Title: Crystal structure of human dysferlin C2G domain
Authors: Dominguez, M.J. / Sutton, R.B.
History
DepositionOct 14, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dysferlin
B: Dysferlin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,53414
Polymers54,9752
Non-polymers55912
Water75742
1
A: Dysferlin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7957
Polymers27,4871
Non-polymers3086
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dysferlin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7397
Polymers27,4871
Non-polymers2516
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.942, 109.760, 59.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1807 through 1832 or resid 1834...
d_2ens_1(chain "B" and (resid 1807 through 1832 or resid 1834...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11METMETGLYGLYAA1807 - 18326 - 31
d_12LYSLYSPHEPHEAA1834 - 184733 - 46
d_13GLUGLUASPASPAA1849 - 187648 - 75
d_14LEULEULEULEUAA1878 - 192777 - 126
d_15LEULEUASNASNAA1929 - 1930128 - 129
d_16METMETTRPTRPAA1932 - 1955131 - 154
d_17VALVALGLNGLNAA1957 - 1962156 - 161
d_18THRTHRARGARGAA1964 - 2000163 - 199
d_21METMETGLYGLYBB1807 - 18326 - 31
d_22LYSLYSPHEPHEBB1834 - 184733 - 46
d_23GLUGLUASPASPBB1849 - 187648 - 75
d_24LEULEULEULEUBB1878 - 192777 - 126
d_25LEULEUASNASNBB1929 - 1930128 - 129
d_26METMETTRPTRPBB1932 - 1955131 - 154
d_27VALVALGLNGLNBB1957 - 1962156 - 161
d_28THRTHRARGARGBB1964 - 2000163 - 199

NCS oper: (Code: givenMatrix: (0.994330689398, -0.0919208766796, -0.0534512165605), (-0.0921642714343, -0.995741598584, -0.00210140895017), (-0.0530304364713, 0.0070157878417, -0.998568250811)Vector: ...NCS oper: (Code: given
Matrix: (0.994330689398, -0.0919208766796, -0.0534512165605), (-0.0921642714343, -0.995741598584, -0.00210140895017), (-0.0530304364713, 0.0070157878417, -0.998568250811)
Vector: -0.0478958436758, -19.5272216745, -31.1954516991)

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 27487.404 Da / Num. of mol.: 2 / Fragment: C2G domain (UNP residues 1808-2001)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Puma concolor (puma) / Gene: DYSF, FER1L1 / Plasmid: p202 / Production host: Escherichia coli (E. coli) / References: UniProt: O75923

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Non-polymers , 5 types, 54 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.97 Å3/Da / Density % sol: 58.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 0.14 M calcium chloride, 10% 2-propanol, 15% glycerol, 0.07 M sodium acetate trihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 7, 2022
Details: Rh coated flat bent M0, toroidal focusing post-monochromator M
RadiationMonochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.05→52.04 Å / Num. obs: 35165 / % possible obs: 97.51 % / Redundancy: 12.1 % / Biso Wilson estimate: 45.46 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.1606 / Rpim(I) all: 0.04852 / Rrim(I) all: 0.1682 / Net I/σ(I): 6.62
Reflection shellResolution: 2.05→2.123 Å / Redundancy: 12.3 % / Rmerge(I) obs: 3.364 / Mean I/σ(I) obs: 0.69 / Num. unique obs: 3423 / CC1/2: 0.763 / CC star: 0.931 / Rpim(I) all: 1.021 / Rrim(I) all: 3.523 / % possible all: 97.29

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→52.04 Å / SU ML: 0.3953 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 38.2072
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2726 1667 4.88 %
Rwork0.2453 32471 -
obs0.2466 34138 97.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 80.46 Å2
Refinement stepCycle: LAST / Resolution: 2.05→52.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3224 0 23 42 3289
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00733425
X-RAY DIFFRACTIONf_angle_d1.16984628
X-RAY DIFFRACTIONf_chiral_restr0.0617469
X-RAY DIFFRACTIONf_plane_restr0.0093596
X-RAY DIFFRACTIONf_dihedral_angle_d18.92131272
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 3.22118886999 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.110.47531400.42492602X-RAY DIFFRACTION95.54
2.11-2.180.36991390.40412653X-RAY DIFFRACTION97.49
2.18-2.250.40681380.38142620X-RAY DIFFRACTION96.4
2.25-2.350.38731300.34312641X-RAY DIFFRACTION95.26
2.35-2.450.36561320.31872715X-RAY DIFFRACTION98.51
2.45-2.580.29691480.3112690X-RAY DIFFRACTION98.3
2.58-2.740.4231150.34842712X-RAY DIFFRACTION97.52
2.74-2.950.3061420.27552676X-RAY DIFFRACTION96.44
2.95-3.250.31851520.25312719X-RAY DIFFRACTION98.76
3.25-3.720.24541330.21322751X-RAY DIFFRACTION97.7
3.72-4.690.19221620.17862800X-RAY DIFFRACTION99.4
4.69-52.040.2481360.22152892X-RAY DIFFRACTION97.02
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)
11.000440999250.1193476522180.2141693920361.643181785020.3704570877090.5565328573730.06326692703470.1398099188490.000760602488167-0.1512694609430.07816868981670.3561151079250.2099334381350.0332126723881.06775759888E-90.3519966856520.0126183085718-0.01959214428450.392505502419-0.02634020589890.367419707887-24.8797.944-15.892
20.0186402386061-0.06959234821580.0276408661510.0480898975433-0.05173349500760.02847507598030.670941764426-0.6130747832870.3843436274830.08104521898810.2980207492120.137065070268-0.0960634537607-0.622003399857-7.36888511969E-61.79132359075-0.14982607215-0.1705588472361.37372882944-0.1701601206661.53420800183-8.259-6.41-6.256
31.21927478731-0.6090283231350.3409319907212.890972131140.2084677778721.68989633014-0.0655480893489-0.3714410424490.2308152467080.7680014346170.146255766520.06533170688630.09184921830820.4380120420840.09481224177260.4934601174560.06951336899320.02111746377580.436038685187-0.06278695605620.250288473869-24.4398.69-4.634
41.36976435132-0.607974554508-1.12218036270.8936690903180.2663272453281.09661395334-0.01399171064-0.174734477027-0.01801579867320.40519427011-0.06206733434040.3181263492520.3582852345020.192737299876-0.001935943018260.5507187776110.0661369224020.008153949335150.4891480670230.004049140226520.449581945867-28.8545.421-6.35
51.5877402052-1.341629420920.4650639981462.139059288150.9340371115321.4707070767-0.134785338537-0.02481117404110.1527508504290.5111232395440.4354157286270.3482897367460.256036130174-0.1540853867160.000101375075510.5794549277940.02169467899940.03160415566750.4446217763880.05479151044040.39324656039-25.547-27.181-12.667
60.91282149314-0.6212282610420.4687533868621.609789616260.3730069097740.4984085565480.311850530946-0.06698420744650.5703922265510.367129979473-0.06268410313490.0377196575233-0.546244431938-0.126774334461-1.412313383990.4306301987520.0477788739867-0.002880256908780.4150535207160.08868621612010.416488671418-21.799-17.632-19.933
7-0.006500151020740.02912080603110.04856863012360.08849017727550.1278606552270.1210114906390.09847035254430.881803478917-0.01516687113190.4302913283310.2008782401040.8116165241020.6754322680190.8035136937750.01195616997660.5066436437210.1145424190030.1190063631641.082145914850.08762620017940.843923611769-0.751-15.5-25.258
81.339356723430.760259555372-0.5424992604652.652057760651.223794802442.341589859290.0389846403210.248819359035-0.129357953738-0.2772251630240.01821263363410.182665792504-0.01287771497370.0424134433438-0.00021497550330.3859450552150.00482963835677-0.02101270365870.3939327749750.02610957375140.381134525241-27.706-27.799-24.94
90.41594503417-0.2423342966230.7794356413140.223968948348-0.121984147220.1261437842070.00174417202274-0.3656333331470.023469866703-0.252443199753-0.265293924132-0.197611400942-0.236571046944-0.00478371907917-0.0006235011250.348143378713-0.01016543023140.02875422842330.3894408557790.01967529321590.387197131075-29.499-17.12-22.424
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1807:1878 )A1807 - 1878
2X-RAY DIFFRACTION2( CHAIN A AND RESID 1879:1895 )A1879 - 1895
3X-RAY DIFFRACTION3( CHAIN A AND RESID 1896:1963 )A1896 - 1963
4X-RAY DIFFRACTION4( CHAIN A AND RESID 1964:2000 )A1964 - 2000
5X-RAY DIFFRACTION5( CHAIN B AND RESID 1807:1860 )B1807 - 1860
6X-RAY DIFFRACTION6( CHAIN B AND RESID 1861:1887 )B1861 - 1887
7X-RAY DIFFRACTION7( CHAIN B AND RESID 1888:1904 )B1888 - 1904
8X-RAY DIFFRACTION8( CHAIN B AND RESID 1905:1977 )B1905 - 1977
9X-RAY DIFFRACTION9( CHAIN B AND RESID 1978:2000 )B1978 - 2000

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