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- PDB-1hlu: STRUCTURE OF BOVINE BETA-ACTIN-PROFILIN COMPLEX WITH ACTIN BOUND ... -

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Basic information

Entry
Database: PDB / ID: 1hlu
TitleSTRUCTURE OF BOVINE BETA-ACTIN-PROFILIN COMPLEX WITH ACTIN BOUND ATP PHOSPHATES SOLVENT ACCESSIBLE
Components
  • BETA-ACTIN
  • PROFILIN
KeywordsCOMPLEX (ACETYLATION/ACTIN-BINDING) / COMPLEX (ACETYLATION-ACTIN-BINDING) / ACTIN / PROFILIN / CONFORMATIONAL CHANGES / CYTOSKELETON / COMPLEX (ACETYLATION-ACTIN-BINDING) complex
Function / homology
Function and homology information


PCP/CE pathway / Adherens junctions interactions / Cell-extracellular matrix interactions / B-WICH complex positively regulates rRNA expression / Gap junction degradation / Formation of annular gap junctions / MAP2K and MAPK activation / RHOF GTPase cycle / EPHB-mediated forward signaling / Regulation of actin dynamics for phagocytic cup formation ...PCP/CE pathway / Adherens junctions interactions / Cell-extracellular matrix interactions / B-WICH complex positively regulates rRNA expression / Gap junction degradation / Formation of annular gap junctions / MAP2K and MAPK activation / RHOF GTPase cycle / EPHB-mediated forward signaling / Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / DNA Damage Recognition in GG-NER / UCH proteinases / VEGFA-VEGFR2 Pathway / structural constituent of postsynaptic actin cytoskeleton / positive regulation of actin filament bundle assembly / dense body / regulation of actin filament polymerization / Clathrin-mediated endocytosis / NuA4 histone acetyltransferase complex / axonogenesis / cell motility / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / actin cytoskeleton / actin binding / actin cytoskeleton organization / cytoskeleton / hydrolase activity / axon / focal adhesion / synapse / protein kinase binding / protein-containing complex / ATP binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Profilin1/2/3, vertebrate / : / Profilin conserved site / Profilin signature. / Profilin / Profilin / Profilin / Profilin superfamily / Dynein light chain 2a, cytoplasmic / ATPase, substrate binding domain, subdomain 4 ...Profilin1/2/3, vertebrate / : / Profilin conserved site / Profilin signature. / Profilin / Profilin / Profilin / Profilin superfamily / Dynein light chain 2a, cytoplasmic / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Beta-Lactamase / Actin / Actin family / Actin / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Profilin-1 / Actin, cytoplasmic 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsChik, J.K. / Lindberg, U. / Schutt, C.E.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: The structure of an open state of beta-actin at 2.65 A resolution.
Authors: Chik, J.K. / Lindberg, U. / Schutt, C.E.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization and Structure Determination of Bovine Profilin at 2.0 A Resolution
Authors: Cedergren-Zeppezauer, E.S. / Goonesekere, N.C. / Rozycki, M.D. / Myslik, J.C. / Dauter, Z. / Lindberg, U. / Schutt, C.E.
#2: Journal: Nature / Year: 1993
Title: The Structure of Crystalline Profilin-Beta-Actin
Authors: Schutt, C.E. / Myslik, J.C. / Rozycki, M.D. / Goonesekere, N.C. / Lindberg, U.
#3: Journal: J.Mol.Biol. / Year: 1989
Title: Molecular Packing in Profilin: Actin Crystals and its Implications
Authors: Schutt, C.E. / Lindberg, U. / Myslik, J. / Strauss, N.
History
DepositionMay 30, 1997Processing site: BNL
Revision 1.0Oct 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA-ACTIN
P: PROFILIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2064
Polymers56,6592
Non-polymers5472
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.140, 72.240, 185.700
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 BETA-ACTIN


Mass: 41690.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: THYMUS / References: UniProt: P60712
#2: Protein PROFILIN


Mass: 14968.185 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: THYMUS / References: UniProt: P02584
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
Compound detailsTHIS COMPLEX CONTAINS PROFILIN BOUND TO BETA-ACTIN (NONMUSCLE ISOFORM OF ACTIN). THE COMPLEX ...THIS COMPLEX CONTAINS PROFILIN BOUND TO BETA-ACTIN (NONMUSCLE ISOFORM OF ACTIN). THE COMPLEX REPRESENTED HERE CORRESPONDS TO THE MAJOR PROFILIN-ACTIN CONTACT OBSERVED IN CRYSTALS, AND PROBABLY CORRESPONDS TO THE SOLUTION STRUCTURE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 6

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.5 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: other / Details: Rozycki, M.D., (1991) Methods Enzymol., 196, 100.

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Jun 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 13869 / % possible obs: 87.3 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 13.5
Reflection shellResolution: 2.65→2.7 Å / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 2.4 / % possible all: 69
Reflection shell
*PLUS
% possible obs: 69 % / Num. unique obs: 533

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BTF

2btf


Resolution: 2.65→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.33 -10 %
Rwork0.201 --
obs0.201 11504 87 %
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.65→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3967 0 34 0 4001
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.33
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 17.4 Å2
LS refinement shell
*PLUS
Highest resolution: 2.65 Å / Lowest resolution: 2.77 Å / Num. reflection obs: 1165

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