[English] 日本語
Yorodumi
- PDB-3hor: Structure of the actin-binding domain of human filamin A (reduced) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hor
TitleStructure of the actin-binding domain of human filamin A (reduced)
ComponentsFilamin-A
KeywordsSTRUCTURAL PROTEIN / Calponin homology domain / actin binding domain / Acetylation / Actin-binding / Alternative splicing / Cytoplasm / Cytoskeleton / Disease mutation / Phosphoprotein / Polymorphism
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 / adenylate cyclase-inhibiting dopamine receptor signaling pathway / formation of radial glial scaffolds / positive regulation of integrin-mediated signaling pathway / actin crosslink formation / 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 / adenylate cyclase-inhibiting dopamine receptor signaling pathway / formation of radial glial scaffolds / positive regulation of integrin-mediated signaling pathway / actin crosslink formation / tubulin deacetylation / blood coagulation, intrinsic pathway / OAS antiviral response / positive regulation of actin filament bundle assembly / positive regulation of neuron migration / protein localization to bicellular tight junction / Cell-extracellular matrix interactions / Fc-gamma receptor I complex binding / positive regulation of potassium ion transmembrane transport / apical dendrite / positive regulation of neural precursor cell proliferation / positive regulation of platelet activation / protein localization to cell surface / wound healing, spreading of cells / podosome / negative regulation of transcription by RNA polymerase I / megakaryocyte development / GP1b-IX-V activation signalling / receptor clustering / cortical cytoskeleton / SMAD binding / RHO GTPases activate PAKs / semaphorin-plexin signaling pathway / cilium assembly / mitotic spindle assembly / potassium channel regulator activity / negative regulation of DNA-binding transcription factor activity / release of sequestered calcium ion into cytosol / positive regulation of substrate adhesion-dependent cell spreading / protein sequestering activity / regulation of cell migration / dendritic shaft / protein localization to plasma membrane / actin filament / mRNA transcription by RNA polymerase II / establishment of protein localization / G protein-coupled receptor binding / negative regulation of protein catabolic process / cerebral cortex development / small GTPase binding / positive regulation of protein import into nucleus / platelet aggregation / kinase binding / Z disc / actin filament binding / cell-cell junction / Platelet degranulation / actin cytoskeleton / growth cone / GTPase binding / actin cytoskeleton organization / perikaryon / DNA-binding transcription factor binding / transmembrane transporter binding / positive regulation of canonical NF-kappaB signal transduction / postsynapse / protein stabilization / cadherin binding / focal adhesion / negative regulation of apoptotic process / nucleolus / perinuclear region of cytoplasm / glutamatergic synapse / protein homodimerization activity / RNA binding / extracellular exosome / extracellular region / nucleus / membrane / plasma membrane / cytosol / cytoplasm
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
PHOSPHATE ION / Filamin-A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsClark, A.R. / Sawyer, G.M. / Robertson, S.P. / Sutherland-Smith, A.J.
CitationJournal: Hum.Mol.Genet. / Year: 2009
Title: Skeletal dysplasias due to filamin A mutations result from a gain-of-function mechanism distinct from allelic neurological disorders
Authors: Clark, A.R. / Sawyer, G.M. / Robertson, S.P. / Sutherland-Smith, A.J.
History
DepositionJun 3, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Filamin-A
B: Filamin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3856
Polymers61,0052
Non-polymers3804
Water54030
1
A: Filamin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6933
Polymers30,5031
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Filamin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6933
Polymers30,5031
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.672, 72.290, 155.324
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILELYSLYSchain A and (resseq 44:58 or resseq 63:98 or resseq 100:153 or resseq 172:264 )AA44 - 5847 - 61
12ARGARGTHRTHRchain A and (resseq 44:58 or resseq 63:98 or resseq 100:153 or resseq 172:264 )AA63 - 9866 - 101
13ARGARGPROPROchain A and (resseq 44:58 or resseq 63:98 or resseq 100:153 or resseq 172:264 )AA100 - 153103 - 156
14LEULEUPHEPHEchain A and (resseq 44:58 or resseq 63:98 or resseq 100:153 or resseq 172:264 )AA172 - 264175 - 267
21ILEILELYSLYSchain B and (resseq 44:58 or resseq 63:98 or resseq 100:153 or resseq 172:264 )BB44 - 5847 - 61
22ARGARGTHRTHRchain B and (resseq 44:58 or resseq 63:98 or resseq 100:153 or resseq 172:264 )BB63 - 9866 - 101
23ARGARGPROPROchain B and (resseq 44:58 or resseq 63:98 or resseq 100:153 or resseq 172:264 )BB100 - 153103 - 156
24LEULEUPHEPHEchain B and (resseq 44:58 or resseq 63:98 or resseq 100:153 or resseq 172:264 )BB172 - 264175 - 267

-
Components

#1: Protein Filamin-A / Alpha-filamin / Filamin-1 / Endothelial actin-binding protein / Actin-binding protein 280 / ABP-280 ...Alpha-filamin / Filamin-1 / Endothelial actin-binding protein / Actin-binding protein 280 / ABP-280 / Non-muscle filamin


Mass: 30502.670 Da / Num. of mol.: 2 / Fragment: Actin-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FLNA / Plasmid: pProEX HTb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P21333
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG 4000, 0.2M lithium sulfate, 0.1M Tris HCl, 5mM DTT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 14, 2007 / Details: osmic 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: 2.7→42.1 Å / Num. obs: 17832 / % possible obs: 96.1 % / Redundancy: 4.1 % / Biso Wilson estimate: 42.98 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.4 / Num. measured all: 72824
Reflection shellResolution: 2.7→2.79 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2 / Num. unique all: 2487 / % possible all: 84

-
Processing

SoftwareName: PHENIX / Version: (phenix.refine) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3HOP

3hop


Resolution: 2.7→42.092 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.98 / σ(F): 1.24 / Phase error: 29.3 / Stereochemistry target values: MLHL
Details: THE REFINEMENT PROGRAM REFMAC 5.5.0072 WAS ALSO USED IN REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.2939 1561 5 %RANDOM; same as starting model
Rwork0.2251 29688 --
obs0.2284 16914 90.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.539 Å2 / ksol: 0.345 e/Å3
Displacement parametersBiso max: 199.49 Å2 / Biso mean: 46.999 Å2 / Biso min: 7 Å2
Baniso -1Baniso -2Baniso -3
1--4.075 Å20 Å2-0 Å2
2--16.98 Å20 Å2
3----12.905 Å2
Refinement stepCycle: LAST / Resolution: 2.7→42.092 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3325 0 20 30 3375
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083461
X-RAY DIFFRACTIONf_angle_d1.0974702
X-RAY DIFFRACTIONf_chiral_restr0.072532
X-RAY DIFFRACTIONf_plane_restr0.005595
X-RAY DIFFRACTIONf_dihedral_angle_d16.8131288
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1587X-RAY DIFFRACTIONPOSITIONAL0.496
12B1587X-RAY DIFFRACTIONPOSITIONAL0.496
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.78720.39761550.31822487X-RAY DIFFRACTION84
2.7872-2.88680.44481430.30172537X-RAY DIFFRACTION85
2.8868-3.00230.38961110.2842653X-RAY DIFFRACTION89
3.0023-3.13890.29211120.26162670X-RAY DIFFRACTION89
3.1389-3.30430.29321480.24392719X-RAY DIFFRACTION91
3.3043-3.51130.2761320.22212755X-RAY DIFFRACTION93
3.5113-3.78220.29271560.2052795X-RAY DIFFRACTION93
3.7822-4.16250.25271680.17452758X-RAY DIFFRACTION94
4.1625-4.76420.23551550.17242789X-RAY DIFFRACTION93
4.7642-5.99960.27461360.19292754X-RAY DIFFRACTION93
5.9996-42.09750.25261450.20972771X-RAY DIFFRACTION93
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)
10.9499-0.1576-0.38510.34050.1110.5267-0.0501-0.43510.13440.02050.0131-0.1020.09750.12720.03580.05710.0979-0.0355-0.0308-0.05420.0688-19.9719-5.043527.1185
20.8528-0.0078-0.52670.5066-1.11093.2424-0.10610.1236-0.0309-0.3194-0.0186-0.02750.6595-0.42850.08370.1426-0.00250.0170.080.03520.0633-12.9509-26.746313.6132
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA43 - 264
2X-RAY DIFFRACTION2chain BB44 - 269

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more