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- PDB-2wfn: Filamin A actin binding domain -

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Basic information

Entry
Database: PDB / ID: 2wfn
TitleFilamin A actin binding domain
ComponentsFILAMIN-A
KeywordsCONTRACTILE PROTEIN / PHOSPHOPROTEIN / DISEASE MUTATION / CYTOPLASM / ALTERNATIVE SPLICING / CYTOSKELETON / ACTIN-BINDING / POLYMORPHISM / ACETYLATION
Function / homology
Function and homology information


regulation of membrane repolarization during atrial cardiac muscle cell action potential / regulation of membrane repolarization during cardiac muscle cell action potential / establishment of Sertoli cell barrier / Myb complex / glycoprotein Ib-IX-V complex / formation of radial glial scaffolds / adenylate cyclase-inhibiting dopamine receptor signaling pathway / positive regulation of integrin-mediated signaling pathway / cytoplasmic sequestering of protein / tubulin deacetylation ...regulation of membrane repolarization during atrial cardiac muscle cell action potential / regulation of membrane repolarization during cardiac muscle cell action potential / establishment of Sertoli cell barrier / Myb complex / glycoprotein Ib-IX-V complex / formation of radial glial scaffolds / adenylate cyclase-inhibiting dopamine receptor signaling pathway / positive regulation of integrin-mediated signaling pathway / cytoplasmic sequestering of protein / tubulin deacetylation / actin crosslink formation / blood coagulation, intrinsic pathway / protein localization to bicellular tight junction / OAS antiviral response / positive regulation of actin filament bundle assembly / positive regulation of neuron migration / positive regulation of potassium ion transmembrane transport / Cell-extracellular matrix interactions / early endosome to late endosome transport / apical dendrite / Fc-gamma receptor I complex binding / cell-cell junction organization / positive regulation of neural precursor cell proliferation / positive regulation of platelet activation / protein localization to cell surface / wound healing, spreading of cells / negative regulation of transcription by RNA polymerase I / megakaryocyte development / GP1b-IX-V activation signalling / cortical cytoskeleton / positive regulation of axon regeneration / receptor clustering / SMAD binding / RHO GTPases activate PAKs / actin filament bundle / brush border / semaphorin-plexin signaling pathway / mitotic spindle assembly / cilium assembly / potassium channel regulator activity / epithelial to mesenchymal transition / blood vessel remodeling / axonal growth cone / heart morphogenesis / positive regulation of substrate adhesion-dependent cell spreading / release of sequestered calcium ion into cytosol / regulation of cell migration / dendritic shaft / protein localization to plasma membrane / G protein-coupled receptor binding / actin filament / protein kinase C binding / synapse organization / mRNA transcription by RNA polymerase II / establishment of protein localization / trans-Golgi network / negative regulation of protein catabolic process / negative regulation of DNA-binding transcription factor activity / cerebral cortex development / kinase binding / small GTPase binding / platelet aggregation / Z disc / positive regulation of protein import into nucleus / cell-cell junction / actin filament binding / actin cytoskeleton / Platelet degranulation / GTPase binding / negative regulation of neuron projection development / actin cytoskeleton organization / postsynapse / perikaryon / angiogenesis / DNA-binding transcription factor binding / positive regulation of canonical NF-kappaB signal transduction / transmembrane transporter binding / protein stabilization / cadherin binding / focal adhesion / glutamatergic synapse / nucleolus / negative regulation of apoptotic process / perinuclear region of cytoplasm / protein homodimerization activity / RNA binding / extracellular exosome / extracellular region / membrane / nucleus / 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
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsRuskamo, S. / Ylanne, J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Structure of the Human Filamin a Actin-Binding Domain
Authors: Ruskamo, S. / Ylanne, J.
History
DepositionApr 9, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Dec 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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-A
B: FILAMIN-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1769
Polymers62,5032
Non-polymers6727
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-94.5 kcal/mol
Surface area20970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.500, 125.900, 128.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: TRP / Beg label comp-ID: TRP / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 1 / Auth seq-ID: 41 - 278 / Label seq-ID: 41 - 278

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper: (Code: given
Matrix: (0.01338, 0.9976, 0.06789), (0.9977, -0.01789, 0.06579), (0.06685, 0.06685, -0.9955)
Vector: 55.31, -54.31, -33.66)

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Components

#1: Protein FILAMIN-A / FILAMIN A / ABP-280 / ALPHA-FILAMIN / FILAMIN-1 / ENDOTHELIAL ACTIN-BINDING PROTEIN / ACTIN-BINDING ...FILAMIN A / ABP-280 / ALPHA-FILAMIN / FILAMIN-1 / ENDOTHELIAL ACTIN-BINDING PROTEIN / ACTIN-BINDING PROTEIN 280 / NON-MUSCLE FILAMIN


Mass: 31251.645 Da / Num. of mol.: 2 / Fragment: ACTIN BINDING DOMAIN, RESIDUES 1-278
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 GOLD / References: UniProt: P21333
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 4.4 Å3/Da / Density % sol: 71 % / Description: NONE
Crystal growDetails: 1.7 M LITHIUM SULFATE, 0.1 M HEPES PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Details: MIRRORS
RadiationMonochromator: DIAMOND (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 3.2→42.2 Å / Num. obs: 14512 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.27 / Net I/σ(I): 10
Reflection shellResolution: 3.2→3.28 Å / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EYI

2eyi


Resolution: 3.2→42.16 Å / Cor.coef. Fo:Fc: 0.876 / Cor.coef. Fo:Fc free: 0.86 / SU B: 17.213 / SU ML: 0.289 / Cross valid method: THROUGHOUT / ESU R Free: 0.399 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.243 764 5 %RANDOM
Rwork0.225 ---
obs0.226 14512 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.2→42.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3655 0 35 6 3696
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223765
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0141.9735109
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9355451
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.85724.568162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.96115696
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8531524
X-RAY DIFFRACTIONr_chiral_restr0.0880.2569
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212758
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5522283
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.99833712
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.39821482
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.66631397
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 1823 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.030.05
2Btight positional0.030.05
1Atight thermal0.010.5
2Btight thermal0.010.5
LS refinement shellResolution: 3.2→3.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 55 -
Rwork0.333 1055 -
obs--100 %

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