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- PDB-2wa7: Structure of the M202V mutant of human filamin b actin binding do... -

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Basic information

Entry
Database: PDB / ID: 2wa7
TitleStructure of the M202V mutant of human filamin b actin binding domain at 1.85 Angstrom resolution
ComponentsFILAMIN-B
KeywordsSTRUCTURAL PROTEIN / DISEASE MUTATION / SKELETAL DYSPLASIA / ACTIN-CROSSLINKING / MYOGENESIS / CYTOSKELETON / ACTIN-BINDING / CALPONIN HOMOLOGY DOMAIN / PHOSPHOPROTEIN / DIFFERENTIATION / ATELOSTEOGENESIS / MUTANT / FILAMIN / DWARFISM / CH DOMAIN / DEVELOPMENTAL 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 / neuronal cell body / signal transduction / RNA binding / extracellular exosome / identical protein binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Filamin family / Calponin-like domain / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Actin-binding Protein, T-fimbrin; domain 1 / 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. ...Filamin family / Calponin-like domain / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Actin-binding Protein, T-fimbrin; domain 1 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CACODYLATE ION / CARBONATE ION / Filamin-B
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSawyer, G.M. / Clark, A.R. / Robertson, S.P. / Sutherland-Smith, A.J.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Disease-Associated Substitutions in the Filamin B Actin Binding Domain Confer Enhanced Actin Binding Affinity in the Absence of Major Structural Disturbance: Insights from the Crystal ...Title: Disease-Associated Substitutions in the Filamin B Actin Binding Domain Confer Enhanced Actin Binding Affinity in the Absence of Major Structural Disturbance: Insights from the Crystal Structures of Filamin B Actin Binding Domains.
Authors: Sawyer, G.M. / Clark, A.R. / Robertson, S.P. / Sutherland-Smith, A.J.
History
DepositionFeb 3, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 1, 2015Group: Data collection
Revision 1.3Mar 29, 2017Group: Structure summary
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FILAMIN-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4205
Polymers28,1031
Non-polymers3174
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)46.079, 69.828, 87.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein FILAMIN-B / M202V MUTANT FILAMIN B ACTIN-BINDING DOMAIN / FLN-B / TRUNCATED ABP / FH1 / BETA-FILAMIN / ACTIN- ...M202V MUTANT FILAMIN B ACTIN-BINDING DOMAIN / FLN-B / TRUNCATED ABP / FH1 / BETA-FILAMIN / ACTIN-BINDING-LIKE PROTEIN / THYROID AUTOANTIGEN / TRUNCATED ACTIN-BINDING PROTEIN / ABP-280 HOMOLOG / ABP-278 / FILAMIN 3 / FILAMIN HOMOLOG 1


Mass: 28103.121 Da / Num. of mol.: 1 / Fragment: ACTIN-BINDING DOMAIN, RESIDUES 2-242 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: ARSENIC SULFUR LINK AT CYS 178 / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PPROEXHTB-FLNB-ABDM202V / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O75369
#2: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#3: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, MET 202 TO VAL
Nonpolymer detailsCACODYLATE ION (CAC): COVALENT BOND OF ARSENIC WITH SULFUR AT CYS 178
Sequence detailsTHE SEQUENCE IS DESCRIBED IN KRAKOW ET AL. (2004) NAT GENET, 36 (4) PGS 405-410. CLEAVAGE WITH RTEV ...THE SEQUENCE IS DESCRIBED IN KRAKOW ET AL. (2004) NAT GENET, 36 (4) PGS 405-410. CLEAVAGE WITH RTEV PROTEASE LEAVES THE LEADER GLY ALA MET ALA STARTING AT -2. CLONING INTO NCOI CREATED MET ALA INSTEAD OF MET AT POSITION 1.

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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: 2.5 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growpH: 6.5
Details: PROTEIN WAS CRYSTALLIZED FROM 20% PEG 8000, 0.2 M MAGNESIUM ACETATE AND 0.1 M SODIUM CACODYLATE PH 6.5.

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 22, 2007 / Details: OSMIC BLUE CONFOCAL MIRRORS
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→27.83 Å / Num. obs: 23537 / % possible obs: 95.5 % / Observed criterion σ(I): 2.2 / Redundancy: 4.7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 25.8
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.2 / % possible all: 79.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WA5

2wa5


Resolution: 1.85→27.83 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.102 / SU ML: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES -2-11, 133-136, 241-242 ARE DISORDERED. RESIDUES GLY ALA MET ALA PRO VAL THR GLU LYS ASP LEU ALA GLU ASP (-2- 11), ASP ASP ASP ALA ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES -2-11, 133-136, 241-242 ARE DISORDERED. RESIDUES GLY ALA MET ALA PRO VAL THR GLU LYS ASP LEU ALA GLU ASP (-2- 11), ASP ASP ASP ALA (133-136), AND LYS LEU ( 241-242) WERE EXCLUDED DUE TO INSUFFICIENT ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.23314 1187 5.1 %RANDOM
Rwork0.19146 ---
obs0.19358 22311 95.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.187 Å2
Baniso -1Baniso -2Baniso -3
1--2.15 Å20 Å20 Å2
2---0.24 Å20 Å2
3---2.39 Å2
Refinement stepCycle: LAST / Resolution: 1.85→27.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1831 0 16 204 2051
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221918
X-RAY DIFFRACTIONr_bond_other_d0.0010.021316
X-RAY DIFFRACTIONr_angle_refined_deg1.1481.9572609
X-RAY DIFFRACTIONr_angle_other_deg0.9013.0013226
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2585233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.48124.94591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.36715346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.051511
X-RAY DIFFRACTIONr_chiral_restr0.0710.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022096
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02358
X-RAY DIFFRACTIONr_nbd_refined0.2110.2444
X-RAY DIFFRACTIONr_nbd_other0.1770.21363
X-RAY DIFFRACTIONr_nbtor_refined0.1690.2936
X-RAY DIFFRACTIONr_nbtor_other0.0840.2872
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2155
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1120.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1970.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.57931506
X-RAY DIFFRACTIONr_mcbond_other0.3673450
X-RAY DIFFRACTIONr_mcangle_it1.88641864
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.2413908
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.7314740
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 60 -
Rwork0.32 1195 -
obs--69.76 %
Refinement TLS params.Method: refined / Origin x: 18.443 Å / Origin y: -10.481 Å / Origin z: -15.952 Å
111213212223313233
T-0.0828 Å2-0.0172 Å20.0089 Å2--0.3045 Å2-0.0078 Å2---0.3685 Å2
L1.4418 °2-1.4152 °2-1.0962 °2-2.5276 °20.984 °2--2.2224 °2
S-0.0939 Å °-0.0056 Å °-0.1896 Å °0.1721 Å °-0.0694 Å °0.2492 Å °0.1462 Å °0.0095 Å °0.1633 Å °

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