[English] 日本語
Yorodumi
- PDB-2j3s: Crystal structure of the human filamin A Ig domains 19 to 21 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2j3s
TitleCrystal structure of the human filamin A Ig domains 19 to 21
ComponentsFILAMIN-A
KeywordsSTRUCTURAL PROTEIN / CYTOSKELETON / PHOSPHORYLATION
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 / formation of radial glial scaffolds / Myb complex / adenylate cyclase-inhibiting dopamine receptor signaling pathway / positive regulation of integrin-mediated signaling pathway / blood coagulation, intrinsic pathway / OAS antiviral response / protein localization to bicellular tight junction ...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 / formation of radial glial scaffolds / Myb complex / adenylate cyclase-inhibiting dopamine receptor signaling pathway / positive regulation of integrin-mediated signaling pathway / blood coagulation, intrinsic pathway / OAS antiviral response / protein localization to bicellular tight junction / actin crosslink formation / positive regulation of actin filament bundle assembly / positive regulation of neuron migration / tubulin deacetylation / megakaryocyte development / Cell-extracellular matrix interactions / positive regulation of platelet activation / positive regulation of potassium ion transmembrane transport / apical dendrite / Fc-gamma receptor I complex binding / positive regulation of neural precursor cell proliferation / protein localization to cell surface / negative regulation of transcription by RNA polymerase I / podosome / wound healing, spreading of cells / GP1b-IX-V activation signalling / SMAD binding / receptor clustering / cortical cytoskeleton / RHO GTPases activate PAKs / semaphorin-plexin signaling pathway / mitotic spindle assembly / cilium assembly / potassium channel regulator activity / release of sequestered calcium ion into cytosol / positive regulation of substrate adhesion-dependent cell spreading / regulation of cell migration / protein localization to plasma membrane / dendritic shaft / actin filament / establishment of protein localization / negative regulation of protein catabolic process / protein sequestering activity / cerebral cortex development / positive regulation of protein import into nucleus / platelet aggregation / mRNA transcription by RNA polymerase II / G protein-coupled receptor binding / small GTPase binding / kinase binding / Z disc / cell-cell junction / actin filament binding / actin cytoskeleton / Platelet degranulation / growth cone / actin cytoskeleton organization / GTPase binding / DNA-binding transcription factor binding / perikaryon / transmembrane transporter binding / positive regulation of canonical NF-kappaB signal transduction / postsynapse / protein stabilization / cadherin binding / focal adhesion / nucleolus / negative regulation of apoptotic process / perinuclear region of cytoplasm / glutamatergic synapse / protein homodimerization activity / RNA binding / extracellular exosome / extracellular region / membrane / nucleus / 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
BROMIDE ION / 1,4-DIETHYLENE DIOXIDE / Filamin-A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKiema, T.-R. / Ylanne, J.
CitationJournal: Embo J. / Year: 2007
Title: Structure of Three Tandem Filamin Domains Reveals Auto-Inhibition of Ligand-Binding.
Authors: Lad, Y. / Kiema, T.-R. / Jiang, P. / Pentikanen, O.T. / Coles, C.H. / Campbell, I.D. / Calderwood, D.A. / Ylanne, J.
History
DepositionAug 23, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
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)61,7969
Polymers61,1922
Non-polymers6047
Water41423
1
A: FILAMIN-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8524
Polymers30,5961
Non-polymers2563
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FILAMIN-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9445
Polymers30,5961
Non-polymers3484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.280, 78.390, 229.040
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 (eV)
11A
21B
12A
22B

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111THRTHRARGARGAA2135 - 214894 - 107
211THRTHRARGARGBB2135 - 214894 - 107
121GLYGLYALAALAAA2236 - 2326195 - 285
221GLYGLYALAALABB2236 - 2326195 - 285
112METMETVALVALAA-1 - 21343 - 93
212METMETVALVALBB-1 - 21343 - 93

NCS ensembles :
ID
1
2

-
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 / NONMUSCLE FILAMIN


Mass: 30595.975 Da / Num. of mol.: 2
Fragment: IMMUNOGLOBULIN-LIKE DOMAINS 19 TO 21, RESIDUES 2045-2329
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P21333
#2: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#3: Chemical
ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H8O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE THREE N-TERMINAL RESIDUES GLY ALA MET ORIGINATE FROM THE EXPRESSION PLASMID.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growpH: 6.1
Details: PROTEIN WAS CRYSTALLIZED FROM 1.6M AMMONIUM SULPHATE, 0.1M CITRIC ACID PH 6.1, 10% DIOXANE.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.91975
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 4, 2004 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91975 Å / Relative weight: 1
ReflectionResolution: 2.5→43.44 Å / Num. obs: 22693 / % possible obs: 99 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 17
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 5 / % possible all: 91

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1V05

1v05


Resolution: 2.5→43.44 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.85 / SU B: 22.911 / SU ML: 0.248 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.552 / ESU R Free: 0.331 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SOME OF THE SIDECHAIN ATOMS OF RESIDUES A 2051 ARG, A 2059 GLU, A 2074 ASP, A 2077 TYR, A 2089 LYS, A 2098 GLU, A 2123 GLN, A 2177 GLN, A ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SOME OF THE SIDECHAIN ATOMS OF RESIDUES A 2051 ARG, A 2059 GLU, A 2074 ASP, A 2077 TYR, A 2089 LYS, A 2098 GLU, A 2123 GLN, A 2177 GLN, A 2187 GLU, A 2289 LYS B 2051 ARG, B 2058 HIS, B 2077 TYR, B 2098 GLU, B 2133 LYS, B2137 GLU, B 2149 ARG, B 2201 ARG, B 2202 PHE, B 2203 VAL, B 2206 GLU, B 2212 VAL, B 2228 PHE, B 2239 HIS, B 2240 LYS, B2280 LYS, B 2282 GLU, B 2289 LYS, B2290 ASP, B 2311 PHE AND B 2314 GLU HAVE A POORLY DEFINED ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.297 2270 10 %RANDOM
Rwork0.252 ---
obs0.257 20422 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å20 Å2
2--3.07 Å20 Å2
3----3.51 Å2
Refinement stepCycle: LAST / Resolution: 2.5→43.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3724 0 32 23 3779
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223835
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.9645187
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6045490
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.72623.669169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.60815579
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9631528
X-RAY DIFFRACTIONr_chiral_restr0.1190.2556
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022975
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2280.21452
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3160.22512
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2150
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2610.2123
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5121.52512
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.82223955
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.33331452
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1134.51232
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

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A779tight positional0.050.05
12B779tight positional0.050.05
21A689tight positional0.040.05
22B689tight positional0.040.05
11A779tight thermal0.130.5
12B779tight thermal0.130.5
21A689tight thermal0.10.5
22B689tight thermal0.10.5
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.456 150 -
Rwork0.351 1347 -
obs--100 %
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)
12.25180.02260.79863.03031.34954.4957-0.108-0.0802-0.0180.21520.1078-0.03790.11230.20530.0002-0.27740.11080.0076-0.32380.0561-0.1254-10.924-6.1518.656
21.9599-0.23460.07051.7250.18219.11710.1526-0.19860.11480.06840.14710.0309-0.601-1.6826-0.2997-0.14720.0782-0.02110.13190.0789-0.107-6.107-11.35548.594
38.708-4.510.33439.5371-1.8113.38790.1260.5207-0.2146-0.5077-0.155-0.4380.76260.54120.0290.0349-0.0195-0.0153-0.0255-0.12350.0226-13.624-20.891-14.597
411.83590.9155-4.87060.6758-3.962323.25430.01831.55851.46771.14011.14790.4426-0.2075-6.9024-1.16620.208-0.23890.24332.27750.39060.4277-20.467-15.29271.875
54.1132-2.445-0.30043.4483-0.193311.8233-0.1985-0.542-0.220.44370.24050.24480.2712-0.2947-0.0420.00640.15940.0535-0.00130.0720.0518-23.9141.82241.77
63.2547-1.29670.98783.14850.32998.46750.0244-0.0495-0.2246-0.0124-0.05390.17310.2497-0.01780.0295-0.29210.08930.0146-0.3005-0.006-0.03570.67-24.66515.856
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2135 - 2148
2X-RAY DIFFRACTION1A2236 - 2328
3X-RAY DIFFRACTION2B2135 - 2148
4X-RAY DIFFRACTION2B2236 - 2328
5X-RAY DIFFRACTION3A2149 - 2235
6X-RAY DIFFRACTION4B2149 - 2232
7X-RAY DIFFRACTION5A-1 - 2134
8X-RAY DIFFRACTION6B-1 - 2134

+
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