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- PDB-1fil: HUMAN PLATELET PROFILIN I CRYSTALLIZED IN HIGH SALT ACTIN-BINDING... -

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Basic information

Entry
Database: PDB / ID: 1fil
TitleHUMAN PLATELET PROFILIN I CRYSTALLIZED IN HIGH SALT ACTIN-BINDING PROTEIN
ComponentsPROFILIN
KeywordsCONTRACTILE PROTEIN / ACETYLATION / ACTIN-BINDING PROTEIN / MULTIGENE FAMILY
Function / homology
Function and homology information


synapse maturation / adenyl-nucleotide exchange factor activity / modification of postsynaptic actin cytoskeleton / negative regulation of actin filament bundle assembly / positive regulation of actin filament bundle assembly / negative regulation of actin filament polymerization / regulation of actin filament polymerization / Signaling by ROBO receptors / positive regulation of ATP-dependent activity / proline-rich region binding ...synapse maturation / adenyl-nucleotide exchange factor activity / modification of postsynaptic actin cytoskeleton / negative regulation of actin filament bundle assembly / positive regulation of actin filament bundle assembly / negative regulation of actin filament polymerization / regulation of actin filament polymerization / Signaling by ROBO receptors / positive regulation of ATP-dependent activity / proline-rich region binding / PCP/CE pathway / positive regulation of ruffle assembly / negative regulation of stress fiber assembly / positive regulation of actin filament polymerization / positive regulation of epithelial cell migration / actin monomer binding / phosphatidylinositol-4,5-bisphosphate binding / phosphotyrosine residue binding / neural tube closure / RHO GTPases Activate Formins / modulation of chemical synaptic transmission / small GTPase binding / Platelet degranulation / actin binding / actin cytoskeleton organization / cell cortex / blood microparticle / cytoskeleton / protein stabilization / cadherin binding / focal adhesion / regulation of transcription by RNA polymerase II / glutamatergic synapse / RNA binding / extracellular exosome / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Profilin1/2/3, vertebrate / Profilin conserved site / Profilin signature. / Profilin / Profilin / : / Profilin / Profilin superfamily / Dynein light chain 2a, cytoplasmic / Beta-Lactamase ...Profilin1/2/3, vertebrate / Profilin conserved site / Profilin signature. / Profilin / Profilin / : / Profilin / Profilin superfamily / Dynein light chain 2a, cytoplasmic / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / molecular replacement / Resolution: 2 Å
AuthorsFedorov, A.A. / Pollard, T.D. / Almo, S.C.
Citation
Journal: To be Published
Title: Crystal Structure of Human Profilin at 2.0 Angstroms Resolution
Authors: Fedorov, A.A. / Pollard, T.D. / Almo, S.C.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Purification, Characterization and Crystallization of Human Platelet Profilin Expressed in Escherichia Coli
Authors: Fedorov, A.A. / Pollard, T.D. / Almo, S.C.
#2: Journal: Annu.Rev.Cell Biol. / Year: 1994
Title: Structure of Actin Binding Proteins:Insights About Function at Atomic Resolution
Authors: Pollard, T.D. / Almo, S.C. / Quirk, S. / Vinson, V. / Lattman, E.E.
History
DepositionApr 29, 1996Processing site: BNL
Revision 1.0Nov 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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: PROFILIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0362
Polymers14,9401
Non-polymers961
Water84747
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.050, 31.770, 62.820
Angle α, β, γ (deg.)90.00, 123.41, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PROFILIN


Mass: 14940.021 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CRYSTALLIZED FROM AMMONIUM SULFATE SOLUTION / Source: (gene. exp.) Homo sapiens (human) / Tissue: PLATELET / Production host: Escherichia coli (E. coli) / References: UniProt: P07737
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.09 Å3/Da / Density % sol: 59 %
Crystal growpH: 6.7
Details: CRYSTALLIZED FROM AMMONIUM SULFATE SOLUTION, pH 6.7

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: 1993
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→28.3 Å / Num. obs: 8076 / % possible obs: 94.1 % / Observed criterion σ(I): 2 / Redundancy: 1.28 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 18.2

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Processing

Software
NameClassification
X-PLORmodel building
PROFFTrefinement
X-PLORrefinement
XDSdata reduction
XSCALEdata scaling
X-PLORphasing
RefinementMethod to determine structure: molecular replacement
Starting model: 1FIL

Resolution: 2→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.191 --
obs-7591 90.1 %
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1046 0 5 47 1098
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.018
X-RAY DIFFRACTIONp_angle_d0.0310.03
X-RAY DIFFRACTIONp_angle_deg2.64
X-RAY DIFFRACTIONp_planar_d0.0420.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.4951.5
X-RAY DIFFRACTIONp_mcangle_it2.5392
X-RAY DIFFRACTIONp_scbond_it2.3352
X-RAY DIFFRACTIONp_scangle_it3.6943
X-RAY DIFFRACTIONp_plane_restr0.010.02
X-RAY DIFFRACTIONp_chiral_restr0.1470.15
X-RAY DIFFRACTIONp_singtor_nbd0.1940.3
X-RAY DIFFRACTIONp_multtor_nbd0.1930.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1910.3
X-RAY DIFFRACTIONp_planar_tor1.42
X-RAY DIFFRACTIONp_staggered_tor17.310
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor37.710
X-RAY DIFFRACTIONp_special_tor

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