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- PDB-5dcp: Crystal structure of the human filamin B Ig-like domains 16-17 -

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Basic information

Entry
Database: PDB / ID: 5dcp
TitleCrystal structure of the human filamin B Ig-like domains 16-17
ComponentsFilamin-B
KeywordsSTRUCTURAL PROTEIN / CYTOSKELETON / ADHESION / IMMUNOGLOBULIN-LIKE / ACTIN BINDING PROTEIN
Function / homology
Function and homology information


epithelial cell morphogenesis / keratinocyte development / brush border / skeletal muscle tissue development / stress fiber / phagocytic vesicle / cellular response to type II interferon / ISG15 antiviral mechanism / Z disc / actin filament binding ...epithelial cell morphogenesis / keratinocyte development / brush border / skeletal muscle tissue development / stress fiber / phagocytic vesicle / cellular response to type II interferon / ISG15 antiviral mechanism / Z disc / actin filament binding / actin cytoskeleton / actin binding / actin cytoskeleton organization / cell cortex / cadherin binding / focal adhesion / signal transduction / RNA binding / extracellular exosome / identical protein binding / membrane / 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 / molecular replacement / Resolution: 2.49 Å
AuthorsSeppala, J. / Pentikainen, U. / Ylanne, J.
CitationJournal: Sci Rep / Year: 2017
Title: Skeletal Dysplasia Mutations Effect on Human Filamins' Structure and Mechanosensing.
Authors: Seppala, J. / Bernardi, R.C. / Haataja, T.J.K. / Hellman, M. / Pentikainen, O.T. / Schulten, K. / Permi, P. / Ylanne, J. / Pentikainen, U.
History
DepositionAug 24, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 11, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_wavelength_list
Revision 1.3Jan 10, 2024Group: 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: Filamin-B
B: Filamin-B


Theoretical massNumber of molelcules
Total (without water)37,4982
Polymers37,4982
Non-polymers00
Water19811
1
A: Filamin-B


Theoretical massNumber of molelcules
Total (without water)18,7491
Polymers18,7491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Filamin-B


Theoretical massNumber of molelcules
Total (without water)18,7491
Polymers18,7491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.620, 80.620, 118.016
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Filamin-B / FLN-B / ABP-278 / ABP-280 homolog / Actin-binding-like protein / Beta-filamin / Filamin homolog 1 / ...FLN-B / ABP-278 / ABP-280 homolog / Actin-binding-like protein / Beta-filamin / Filamin homolog 1 / Fh1 / Filamin-3 / Thyroid autoantigen / Truncated actin-binding protein / Truncated ABP


Mass: 18749.146 Da / Num. of mol.: 2 / Fragment: UNP residues 1737-1911
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FLNB, FLN1L, FLN3, TABP, TAP / Plasmid: pGTvL1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: O75369
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.95 Å3/Da / Density % sol: 58.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 3.5 M Sodium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.98 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2013 / Details: bent cylindrical mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.49→50 Å / Num. obs: 16042 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 12.4 % / Biso Wilson estimate: 63.353 Å2 / Rmerge F obs: 0.997 / Rmerge(I) obs: 0.099 / Rrim(I) all: 0.106 / Χ2: 1.034 / Net I/σ(I): 12.79 / Num. measured all: 129873
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.49-2.556.90.8030.5793.148198115511110.62296.2
2.55-2.620.8950.5214.0410069115011500.553100
2.62-2.70.8930.4424.879726111311130.47100
2.7-2.780.9190.3526.149376107110710.374100
2.78-2.880.9690.287.438976103610360.297100
2.88-2.980.9690.238.78862103110310.244100
2.98-3.090.9820.17610.5883009829820.187100
3.09-3.210.9840.14813.1876959289280.158100
3.21-3.360.9920.1215.0673469079070.129100
3.36-3.520.9910.10616.366058818810.114100
3.52-3.710.9930.09517.255998158140.10399.9
3.71-3.940.9930.09519.4964187877870.102100
3.94-4.210.9950.08720.6562067567560.092100
4.21-4.550.9960.08621.1355536866860.092100
4.55-4.980.9950.08521.551916526520.09100
4.98-5.570.9940.08221.1744145785780.088100
5.57-6.430.9950.08220.137915175170.088100
6.43-7.870.9940.07419.6730694604600.08100
7.87-11.140.9960.06822.2529193613610.072100
11.140.9970.07120.715602262210.07797.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMACrefmac_5.7.0029refinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2K7P

2k7p


Resolution: 2.49→40.34 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.925 / SU B: 9.096 / SU ML: 0.203 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.34 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2502 802 5 %RANDOM
Rwork0.2057 ---
obs0.208 15238 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 157.07 Å2 / Biso mean: 64.445 Å2 / Biso min: 32.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.28 Å2-1.28 Å20 Å2
2---1.28 Å20 Å2
3---4.14 Å2
Refinement stepCycle: final / Resolution: 2.49→40.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2386 0 0 11 2397
Biso mean---49.31 -
Num. residues----322
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192448
X-RAY DIFFRACTIONr_bond_other_d0.0010.022269
X-RAY DIFFRACTIONr_angle_refined_deg1.6811.9713353
X-RAY DIFFRACTIONr_angle_other_deg0.79735261
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6015316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.6362588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.32515343
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.605152
X-RAY DIFFRACTIONr_chiral_restr0.0950.2393
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212746
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02492
LS refinement shellResolution: 2.49→2.555 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 56 -
Rwork0.31 1055 -
all-1111 -
obs--95.53 %

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