[English] 日本語
Yorodumi
- PDB-2bp3: Crystal structure of Filamin A domain 17 and GPIb alpha cytoplasm... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2bp3
TitleCrystal structure of Filamin A domain 17 and GPIb alpha cytoplasmic domain complex
Components
  • FILAMIN A
  • PLATELET GLYCOPROTEIN IB ALPHA CHAIN
KeywordsSTRUCTURAL PROTEIN / CYTOSKELETON-COMPLEX / ACTIN BINDING PROTEIN / CYTOSKELETON / COMPLEX
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 / thrombin-activated receptor activity / 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 / Enhanced binding of GP1BA variant to VWF multimer:collagen ...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 / thrombin-activated receptor activity / 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 / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / actin crosslink formation / blood coagulation, intrinsic pathway / tubulin deacetylation / OAS antiviral response / positive regulation of actin filament bundle assembly / positive regulation of neuron migration / Defective F9 activation / protein localization to bicellular tight junction / Platelet Adhesion to exposed collagen / Fc-gamma receptor I complex binding / Cell-extracellular matrix interactions / apical dendrite / positive regulation of potassium ion transmembrane transport / 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 / SMAD binding / regulation of blood coagulation / receptor clustering / Platelet Aggregation (Plug Formation) / cortical cytoskeleton / 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 / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / release of sequestered calcium ion into cytosol / positive regulation of substrate adhesion-dependent cell spreading / extracellular matrix / protein sequestering activity / regulation of cell migration / dendritic shaft / protein localization to plasma membrane / actin filament / establishment of protein localization / mRNA transcription by RNA polymerase II / G protein-coupled receptor binding / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / cerebral cortex development / negative regulation of protein catabolic process / platelet activation / positive regulation of protein import into nucleus / small GTPase binding / platelet aggregation / kinase binding / Z disc / cell morphogenesis / blood coagulation / 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 / cell surface receptor signaling pathway / positive regulation of canonical NF-kappaB signal transduction / postsynapse / cell adhesion / protein stabilization / cadherin binding / external side of plasma membrane / focal adhesion / negative regulation of apoptotic process / nucleolus / perinuclear region of cytoplasm / glutamatergic synapse / cell surface / protein homodimerization activity / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Filamin family / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-like / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Actinin-type actin-binding domain signature 1. ...Filamin family / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-like / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Calponin homology (CH) domain / Leucine-rich repeats, bacterial type / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Immunoglobulin E-set / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Platelet glycoprotein Ib alpha chain / Filamin-A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsPudas, R. / Ylanne, J.
CitationJournal: Blood / Year: 2006
Title: The Structure of the Gpib-Filamin a Complex.
Authors: Nakamura, F. / Pudas, R. / Heikkinen, O. / Permi, P. / Kilpelainen, I. / Munday, A.D. / Hartwig, J.H. / Stossel, T.P. / Ylanne, J.
History
DepositionApr 18, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
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
S: PLATELET GLYCOPROTEIN IB ALPHA CHAIN
T: PLATELET GLYCOPROTEIN IB ALPHA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2626
Polymers25,0784
Non-polymers1842
Water50428
1
A: FILAMIN A
T: PLATELET GLYCOPROTEIN IB ALPHA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6313
Polymers12,5392
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: FILAMIN A
S: PLATELET GLYCOPROTEIN IB ALPHA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6313
Polymers12,5392
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)41.900, 62.800, 122.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
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: 9976.017 Da / Num. of mol.: 2 / Fragment: ROD DOMAIN, RESIDUES 1863-1956
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX4T-3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P21333
#2: Protein/peptide PLATELET GLYCOPROTEIN IB ALPHA CHAIN / GLYCOPROTEIN B ALPHA / GLYCOPROTEIN IBALPHA / GP-IB ALPHA / GPIBA / GPIB-ALPHA / CD42B-ALPHA / CD42B


Mass: 2563.014 Da / Num. of mol.: 2 / Fragment: CYTOPLASMIC DOMAIN, RESIDUES 572-593 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P07359
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE THREE N-TERMINAL RESIDUES OF CHAINS A AND B ARE FROM THE EXPRESSION VECTOR.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.62 Å3/Da / Density % sol: 65.78 %
Crystal growpH: 8.2
Details: 1.75M AMMONIUM PHOSPHATE, PH 8.2, AFTER MICROSEEDING: 1.25M AMMONIUM SULFATE PH 8.2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9795
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 5, 2004 / Details: TOROIDAL MIRROR
RadiationMonochromator: SILICON (1 1 1) CHANNEL-CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.32→19.88 Å / Num. obs: 12876 / % possible obs: 86.9 % / Redundancy: 6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14
Reflection shellResolution: 2.31→2.45 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3.13 / % possible all: 56.7

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1V05

1v05


Resolution: 2.32→19.88 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.92 / SU B: 5.978 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R: 0.263 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. FLEXIBLE SIDE CHAINS OF SOME RESIDUES LOCATED IN THE LOOP REGIONS COULD NOT BE BUILD USING AVAILABLE DENSITY AND THESE RESIDUES WERE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. FLEXIBLE SIDE CHAINS OF SOME RESIDUES LOCATED IN THE LOOP REGIONS COULD NOT BE BUILD USING AVAILABLE DENSITY AND THESE RESIDUES WERE MODELED: A 1881 ASN, A 1882 LYS, A 1892 ASP, A 1916 GLN, B 1891 LYS, B 1892 ASP, B 1909 GLU, B 1916 GLN, B 1917 ASP
RfactorNum. reflection% reflectionSelection details
Rfree0.256 645 5 %RANDOM
Rwork0.214 ---
obs0.216 12211 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 57.94 Å2
Baniso -1Baniso -2Baniso -3
1--2.78 Å20 Å20 Å2
2--4.3 Å20 Å2
3----1.52 Å2
Refinement stepCycle: LAST / Resolution: 2.32→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1553 0 12 28 1593
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221600
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4631.9742181
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7535204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.70123.55959
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.46215227
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.175157
X-RAY DIFFRACTIONr_chiral_restr0.0970.2248
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021223
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2190.2570
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21037
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.270
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2510.233
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1980.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.65541056
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.1761674
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.0954609
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.3466507
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: 2.31→2.38 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 27 -
Rwork0.256 503 -
obs--100 %

+
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