[English] 日本語
Yorodumi
- PDB-1hlu: STRUCTURE OF BOVINE BETA-ACTIN-PROFILIN COMPLEX WITH ACTIN BOUND ... -

+
Open data


ID or keywords:

Loading...

-
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 / Cell-extracellular matrix interactions / Adherens junctions interactions / Formation of the dystrophin-glycoprotein complex (DGC) / 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 ...PCP/CE pathway / Cell-extracellular matrix interactions / Adherens junctions interactions / Formation of the dystrophin-glycoprotein complex (DGC) / 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 / positive regulation of actin filament bundle assembly / cellular response to cytochalasin B / regulation of actin filament polymerization / regulation of transepithelial transport / Clathrin-mediated endocytosis / morphogenesis of a polarized epithelium / structural constituent of postsynaptic actin cytoskeleton / protein localization to adherens junction / dense body / postsynaptic actin cytoskeleton / Tat protein binding / adherens junction assembly / apical protein localization / tight junction / apical junction complex / regulation of norepinephrine uptake / transporter regulator activity / nitric-oxide synthase binding / cortical cytoskeleton / NuA4 histone acetyltransferase complex / establishment or maintenance of cell polarity / brush border / kinesin binding / regulation of synaptic vesicle endocytosis / regulation of protein localization to plasma membrane / positive regulation of double-strand break repair via homologous recombination / axonogenesis / calyx of Held / nitric-oxide synthase regulator activity / actin filament / adherens junction / cell motility / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Schaffer collateral - CA1 synapse / cytoplasmic ribonucleoprotein granule / nucleosome / lamellipodium / actin cytoskeleton / actin binding / actin cytoskeleton organization / cytoskeleton / regulation of cell cycle / ribonucleoprotein complex / axon / focal adhesion / synapse / protein kinase binding / glutamatergic synapse / protein-containing complex / ATP hydrolysis activity / ATP binding / identical protein binding / nucleus / membrane / 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 / Beta-Lactamase / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / 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 (domestic 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

#1: Protein BETA-ACTIN


Mass: 41690.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic 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 (domestic 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.

-
Experimental details

-
Experiment

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

-
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.

-
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

-
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

+
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