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- PDB-2bp3: Crystal structure of Filamin A domain 17 and GPIb alpha cytoplasm... -

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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 platelet activation / positive regulation of neural precursor cell proliferation / 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 / Platelet Aggregation (Plug Formation) / receptor clustering / cortical cytoskeleton / semaphorin-plexin signaling pathway / RHO GTPases activate PAKs / cilium assembly / mitotic spindle assembly / potassium channel regulator activity / : / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / 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 / establishment of protein localization / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / G protein-coupled receptor binding / negative regulation of protein catabolic process / cerebral cortex development / positive regulation of protein import into nucleus / platelet activation / mRNA transcription by RNA polymerase II / small GTPase binding / extracellular matrix / platelet aggregation / kinase binding / Z disc / cell morphogenesis / blood coagulation / cell-cell junction / actin filament binding / Platelet degranulation / actin cytoskeleton / growth cone / actin cytoskeleton organization / GTPase binding / DNA-binding transcription factor binding / perikaryon / transmembrane transporter binding / cell surface receptor signaling pathway / positive regulation of canonical NF-kappaB signal transduction / cell adhesion / postsynapse / 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 / membrane / nucleus / 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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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.

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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: 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

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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

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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 %

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