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- PDB-7p0e: Crystal structure of human filamin C domains 14-15 cardiovascular... -

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Basic information

Entry
Database: PDB / ID: 7p0e
TitleCrystal structure of human filamin C domains 14-15 cardiovascular disease causing mutation G1676R
ComponentsIsoform 2 of Filamin-C
KeywordsSTRUCTURAL PROTEIN / Ig-like / mechanosensing / muscle protein / heart
Function / homology
Function and homology information


Cell-extracellular matrix interactions / costamere / ankyrin binding / sarcomere organization / sarcoplasm / intercellular bridge / cytoskeletal protein binding / sarcolemma / Z disc / actin filament binding ...Cell-extracellular matrix interactions / costamere / ankyrin binding / sarcomere organization / sarcoplasm / intercellular bridge / cytoskeletal protein binding / sarcolemma / Z disc / actin filament binding / cytoskeleton / focal adhesion / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Filamin family / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-like / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Calponin homology domain ...Filamin family / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-like / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Immunoglobulin E-set / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMlynek, G. / Djinovic-Carugo, K.
CitationJournal: To Be Published
Title: Analysis and prediction of pathogenic missense variants in human filamin C
Authors: Mlynek, G. / Djinovic-Carugo, K.
History
DepositionJun 29, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform 2 of Filamin-C
B: Isoform 2 of Filamin-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5937
Polymers43,1622
Non-polymers4305
Water5,765320
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, SEC-MALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-5 kcal/mol
Surface area19650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.150, 59.460, 180.070
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Isoform 2 of Filamin-C / FLN-C / FLNc / ABP-280-like protein / ABP-L / Actin-binding-like protein / Filamin-2 / Gamma-filamin


Mass: 21581.168 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FLNC, ABPL, FLN2 / Production host: Escherichia coli (E. coli) / Variant (production host): R2pLysS / References: UniProt: Q14315
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.43 Å3/Da / Density % sol: 49.34 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion / pH: 6
Details: 0.1 M BIS-TRIS pH 6.0, 26.3 % w/v PEG 3350, 5% w/v Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9655 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9655 Å / Relative weight: 1
ReflectionResolution: 1.6→38.26 Å / Num. obs: 53624 / % possible obs: 94.02 % / Redundancy: 4 % / Biso Wilson estimate: 29.81 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.06401 / Rpim(I) all: 0.03494 / Rrim(I) all: 0.0733 / Net I/σ(I): 9.97
Reflection shellResolution: 1.6→1.657 Å / Mean I/σ(I) obs: 0.5 / Num. unique obs: 4752 / Rpim(I) all: 1.166 / Rrim(I) all: 2.508 / % possible all: 79.64

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Processing

Software
NameVersionClassification
EDNA1.19.2_4158data collection
MxCuBEdata collection
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
PDB-REDOrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7OUU

7ouu


Resolution: 1.6→38.26 Å / SU ML: 0.2723 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.6104
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2209 1446 2.71 %
Rwork0.1872 51826 -
obs0.1881 53272 94.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.93 Å2
Refinement stepCycle: LAST / Resolution: 1.6→38.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3000 0 28 320 3348
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01533122
X-RAY DIFFRACTIONf_angle_d1.23434251
X-RAY DIFFRACTIONf_chiral_restr0.0789479
X-RAY DIFFRACTIONf_plane_restr0.0105564
X-RAY DIFFRACTIONf_dihedral_angle_d6.4065453
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.660.44431210.39884337X-RAY DIFFRACTION79.65
1.66-1.720.38671320.34094814X-RAY DIFFRACTION88.75
1.72-1.80.33411390.28384968X-RAY DIFFRACTION91.33
1.8-1.90.30681420.24545075X-RAY DIFFRACTION93.7
1.9-2.020.29521470.21525251X-RAY DIFFRACTION96.12
2.02-2.170.23941490.18565328X-RAY DIFFRACTION96.99
2.17-2.390.21931500.18395390X-RAY DIFFRACTION98.23
2.39-2.740.24911520.19135413X-RAY DIFFRACTION97.99
2.74-3.450.22281540.17665503X-RAY DIFFRACTION98.9
3.45-38.260.17331600.16375747X-RAY DIFFRACTION98.17
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)
12.502763473851.6370348281-1.603638272811.97393289577-1.568336974632.80439593322-0.2484227337050.2756646755760.0581556200932-0.2719701108590.2368258025220.08211255070350.268276250168-0.103750659682-0.04991590446910.2676867155090.01547275428740.008082030595140.1759143640950.001945713090590.251995834038-6.14447871129-5.66778979163-3.59426975405
21.339996203090.24992000737-0.5976807373061.65135297359-0.4733786482052.22046256722-0.266580787223-0.0361171571743-0.1767580290290.02915715167660.03906900766160.06316436266110.6150155529290.179601074130.2375575950170.172799581950.01838259818650.01854186639430.1611114312620.04601971182150.287384948279-11.7434957656-7.9533015773610.3535848213
34.47667900333-1.20592815472-0.1875506017643.953349246970.6085811644883.359226251830.01344971957620.008993803647040.185183598738-0.120366918048-0.0432879132082-0.04937230273690.01886561645830.03097148330090.01400561275740.2394363404760.004388990169450.06004307532830.229354539610.02195167962620.180576492414-15.8301902265-0.2841488066419.1086657215
42.45992691616-0.670385291999-1.029125501110.9830095130220.4630482974514.91318909052-0.072238445152-0.09970478051280.03989674495840.2359334810220.02922457931960.169949318634-0.0724872105388-0.3084534056570.01515095309670.260413055703-0.01969252327970.0646519781970.1821707769370.02772051691310.258102972489-35.2004826531-5.5020746235175.2133718073
53.44301415931-3.98878504457-2.949180499354.712455988163.715607378163.475746220890.4888909330450.5086985360110.301630929291-0.422901204961-0.313899992645-0.356756878356-0.436544757857-0.323630388776-0.316017189780.39847909881-0.06283128396310.1260512545930.28602252686-0.006779329038020.34946293706-30.0928264982-1.7502154615367.955610871
60.516580399279-0.230042556335-0.7838042271151.53352731275-0.9391300367643.40283473458-0.02501597746980.1602911355860.041437267589-0.0950847301761-0.004506129673470.06997199083950.20684960008-0.04838301735110.04836955780320.164663798954-0.03614047674130.01095966096880.254447313547-0.02556652328050.271784177953-31.0404693789-7.1765503789258.7522986853
72.25649311070.110375724184-0.3084790946356.64600917774-2.445918748273.853398215240.2440666862440.1868687149240.410974109710.145013924826-0.270142134088-0.119539669486-0.2392022412870.0924709311267-0.06681165046210.292732920931-0.06355795165310.02555086343680.48569789404-0.02140411584390.257002939142-27.4677398545-0.51182578045246.5466727961
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1535 through 1607 )AA1535 - 16071 - 73
22chain 'A' and (resid 1608 through 1656 )AA1608 - 165674 - 122
33chain 'A' and (resid 1657 through 1736 )AA1657 - 1736123 - 202
44chain 'B' and (resid 1535 through 1579 )BD1535 - 15791 - 45
55chain 'B' and (resid 1580 through 1596 )BD1580 - 159646 - 62
66chain 'B' and (resid 1597 through 1656 )BD1597 - 165663 - 122
77chain 'B' and (resid 1657 through 1736 )BD1657 - 1736123 - 202

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