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

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Basic information

Entry
Database: PDB / ID: 7ouv
TitleCrystal structure of human filamin C domains 14-15 cardiovascular disease causing mutation S1624L
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: 1.8 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 13, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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


Theoretical massNumber of molelcules
Total (without water)43,0142
Polymers43,0142
Non-polymers00
Water6,197344
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-8 kcal/mol
Surface area20220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.133, 70.498, 156.937
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: 21507.105 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / Source method: isolated from a natural source / Formula: H2O
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: 2.52 Å3/Da / Density % sol: 51.12 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M SPG pH 5.0, 25% w/v PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→39.23 Å / Num. obs: 41232 / % possible obs: 99.64 % / Redundancy: 12.6 % / Biso Wilson estimate: 33.52 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1469 / Rpim(I) all: 0.04388 / Rrim(I) all: 0.1535 / Net I/σ(I): 9.99
Reflection shellResolution: 1.8→1.864 Å / Rmerge(I) obs: 2.913 / Mean I/σ(I) obs: 0.76 / Num. unique obs: 4057 / CC1/2: 0.478 / Rpim(I) all: 0.8159 / Rrim(I) all: 3.027 / % possible all: 99.8

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Processing

Software
NameVersionClassification
XDS1.19.2_4158data scaling
PHENIX1.19.2_4158refinement
XDSdata reduction
GDAdata collection
PHASERphasing
Cootmodel building
PDB-REDOrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: unreleased

Resolution: 1.8→39.23 Å / SU ML: 0.2682 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.0411
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2402 1416 3.44 %
Rwork0.2126 39719 -
obs0.2136 41135 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.36 Å2
Refinement stepCycle: LAST / Resolution: 1.8→39.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3005 0 0 344 3349
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00353105
X-RAY DIFFRACTIONf_angle_d0.67544243
X-RAY DIFFRACTIONf_chiral_restr0.0538483
X-RAY DIFFRACTIONf_plane_restr0.0058566
X-RAY DIFFRACTIONf_dihedral_angle_d5.0671444
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.860.351400.33693914X-RAY DIFFRACTION99.88
1.86-1.940.32741370.29133890X-RAY DIFFRACTION99.93
1.94-2.030.30461410.27033931X-RAY DIFFRACTION99.95
2.03-2.130.25631400.22523924X-RAY DIFFRACTION99.93
2.13-2.270.26291400.20993938X-RAY DIFFRACTION99.98
2.27-2.440.26061430.19893983X-RAY DIFFRACTION100
2.44-2.690.29041410.21343948X-RAY DIFFRACTION99.93
2.69-3.080.22441410.20633990X-RAY DIFFRACTION99.95
3.08-3.880.21171450.19134037X-RAY DIFFRACTION99.74
3.88-39.230.22431480.21024164X-RAY DIFFRACTION98.13
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)
10.697389370847-0.952748022636-0.7877797550511.343632608821.211673439611.273466663640.47245487308-0.04469530691020.423062586733-0.463056096222-0.0900344492498-0.226623414854-0.8936416786720.309379065503-0.0156328639370.333093541307-0.02277661908030.002641861745080.413421916835-0.05467533398080.49788725272337.136055065860.930730105677.8221084397
20.6570759542170.1927989458060.03662943635510.3365154430060.6825421353611.605038074480.08707963696-0.03809285847680.03056124525930.0651859851561-0.03625491089050.01201454879570.0497940453408-0.03786624282984.59503317668E-60.3777470205910.01168733835990.006766556971520.3677070915440.01500648858780.41194022674533.744743150454.456574105168.1119641523
30.911387919897-0.75577079423-0.3693782029031.482796258560.1383142439761.41992042554-0.02128603890330.244042086707-0.300118954943-0.2719924041520.09513322904790.1298046624780.182823975121-0.0916485952321-0.0001091625826940.3275202205390.00932606546704-0.03525193555520.3541846870230.04258661233140.32885889760223.31062724536.737664509248.7602359723
42.31848221809-0.418714484390.4235243123542.915442256840.01046027190060.902268834246-0.0500937079087-0.1951844469540.1190915035850.1345672763460.07165896527190.06509348051390.0567052899106-0.16661358629-4.9647193593E-60.298096376950.0318222284619-0.05431723418010.390645529556-0.006639823685290.24823191465522.313932944139.543365131852.1180734855
52.557470820130.5977240784340.9931283555411.330063099340.999157845710.909160130782-0.08350890637540.3833920440860.0134600295578-0.2680413457360.0962395673068-0.01023465326930.1141728040480.238457774377-0.0001067488590450.384522645033-0.00958008381476-0.01511826006670.3547377009140.01886176324590.3563268401319.9203676879353.40435658848.7654120631
61.44244393159-0.392373717236-0.2781813297511.037233983091.001244983320.9631354928890.02048287680550.06242983707480.1678212141090.2787385119940.1173537476060.0786068084248-0.2701634507920.05878722257580.09704441274340.239334790956-0.0339015072667-0.08384874415220.299936327349-0.08003435057470.25186771147513.813648112347.95450716622.2483052249
72.717456859511.620683816551.221978624643.129240803930.3687324808441.67434188763-0.09423907412170.286512008472-0.259951669956-0.1239668844620.159925316264-0.157606148632-0.05363041812990.2476460566685.7274683506E-50.324961942668-0.0659876023438-0.006358754090920.357384348827-0.0112696132740.24618870312917.854924486235.594805409526.7752594245
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 18 )AA2 - 181 - 17
22chain 'A' and (resid 19 through 94 )AA19 - 9418 - 93
33chain 'A' and (resid 95 through 138 )AA95 - 13894 - 137
44chain 'A' and (resid 139 through 205 )AA139 - 205138 - 204
55chain 'B' and (resid 4 through 76 )BB4 - 761 - 73
66chain 'B' and (resid 77 through 125 )BB77 - 12574 - 122
77chain 'B' and (resid 126 through 205 )BB126 - 205123 - 202

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