[English] 日本語
Yorodumi
- PDB-2btf: THE STRUCTURE OF CRYSTALLINE PROFILIN-BETA-ACTIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2btf
TitleTHE STRUCTURE OF CRYSTALLINE PROFILIN-BETA-ACTIN
Components
  • BETA-ACTIN
  • PROFILIN
KeywordsACETYLATION AND ACTIN-BINDING
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 / cellular response to cytochalasin B / VEGFA-VEGFR2 Pathway / positive regulation of actin filament bundle assembly / regulation of transepithelial transport / regulation of actin filament polymerization / morphogenesis of a polarized epithelium / structural constituent of postsynaptic actin cytoskeleton / protein localization to adherens junction / Clathrin-mediated endocytosis / dense body / postsynaptic actin cytoskeleton / Tat protein binding / apical protein localization / adherens junction assembly / tight junction / regulation of norepinephrine uptake / apical junction complex / transporter regulator activity / nitric-oxide synthase binding / NuA4 histone acetyltransferase complex / establishment or maintenance of cell polarity / cortical cytoskeleton / brush border / kinesin binding / regulation of synaptic vesicle endocytosis / positive regulation of double-strand break repair via homologous recombination / regulation of protein localization to plasma membrane / 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 / actin cytoskeleton / lamellipodium / 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 / cytosol / cytoplasm
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 / STRONTIUM ION / Profilin-1 / Actin, cytoplasmic 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.55 Å
AuthorsSchutt, C.E. / Myslik, J.C. / Rozycki, M.D. / Goonesekere, N.C.W.
Citation
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.
#1: Journal: To be Published
Title: Structural Aspects of Actin Binding Proteins Current Opinion in Cell Biology
Authors: Rozycki, M.D. / Myslik, J.C. / Schutt, C.E. / Lindberg, U.
#2: Journal: FEBS Lett. / Year: 1993
Title: Mutagenesis of Human Profilin Locates its Poly(L-Proline)-Binding Site to a Hydrophobic Patch of Aromatic Amino Acids
Authors: Bjorkegren, C. / Rozycki, M. / Schutt, C.E. / Lindberg, U. / Karlsson, R.
#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
DepositionJan 18, 1994Processing site: BNL
Revision 1.0Jun 22, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 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 1.4Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX RESIDUES ARE INCLUDED AT THE BEGINNING OF HELICES IF THEY PARTICIPATE IN HYDROGEN BONDING AND ...HELIX RESIDUES ARE INCLUDED AT THE BEGINNING OF HELICES IF THEY PARTICIPATE IN HYDROGEN BONDING AND ARE "PARTIALLY" HELICAL, EVEN IF THE ENTIRE RESIDUE DOES NOT FIT HELICAL CRITERIA.
Remark 700SHEET PROFILIN IS DESCRIBED IN JRNL REFERENCE AS HAVING A SIX-MEMBERED BETA-SHEET WHICH SHARES A ...SHEET PROFILIN IS DESCRIBED IN JRNL REFERENCE AS HAVING A SIX-MEMBERED BETA-SHEET WHICH SHARES A STRAND WITH A SECOND TWO-MEMBERED SHEET. TO CONFORM WITH PROTEIN DATA BANK GUIDELINES, THESE SHEETS ARE COMBINED INTO A SINGLE SEVEN-MEMBERED SHEET (SP1) IN THIS ENTRY. STRAND NUMBERING ALSO DIFFERS FROM THE JRNL REFERENCE. SECONDARY STRUCTURE ASSIGNMENTS FOR BETA-ACTIN ARE SIMILAR TO THOSE USED FOR ALPHA-ACTIN (PROTEIN DATA BANK ENTRY 1ATN) WITH MINOR CHANGES. HOWEVER, THE NOMENCLATURE USED HEREIN DIFFERS FROM THAT USED IN THE ABOVE ENTRY. ALSO, STRAND A4B DESCRIBED IN THAT ENTRY IS NOT INCLUDED HERE BECAUSE THE "ALTERNATIVE" STRAND TO ONE IN STRAND A4A (CORRESPONDING TO SA4 IN THIS ENTRY) IS ONLY TWO RESIDUES IN LENGTH. IN CONTRAST, SHEET SA3 IS INCLUDED BECAUSE IT CONTAINS TWO STRANDS AND A WELL-DEFINED TYPE II TURN, EVEN THOUGH THE TWO STRANDS CONTAIN ONLY TWO RESIDUES EACH. RESIDUE P 31 IS A BETA-BULGE. RESIDUE P 73 IS A BETA-BULGE, REDIRECTING STRAND 6.

-
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)57,2544
Polymers56,6592
Non-polymers5952
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-55 kcal/mol
Surface area21270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.950, 71.300, 171.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUE ACE A IS THE N-ACETYL MOIETY OF ACTIN. / 2: RESIDUE A 73 IS 3-METHYL HISTIDYL. / 3: RESIDUE ACE P IS THE N-ACETYL MOIETY OF PROFILIN. / 4: RESIDUE P 31 IS A BETA-BULGE. / 5: RESIDUE P 73 IS A BETA-BULGE, REDIRECTING STRAND 6.

-
Components

#1: Protein BETA-ACTIN


Mass: 41690.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / References: UniProt: P60712
#2: Protein PROFILIN


Mass: 14968.185 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / References: UniProt: P02584
#3: Chemical ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Sr
#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
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.6 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Details: referred to 'Segura, M. & Lindberg, U.', (1984) J.Biol.Chem., 259, 3949-3954
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1150 mM1reservoirNaCl
22 mM1reservoirMgCl2
30.5 mMATP1reservoir
40.5 mMDTT1reservoir

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.55 Å / Num. obs: 16158 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.065

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.199 / Rfactor obs: 0.199 / Highest resolution: 2.55 Å
Refinement stepCycle: LAST / Highest resolution: 2.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3962 0 38 0 4000
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
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_deg3.8
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
Refinement
*PLUS
Lowest resolution: 8 Å / σ(F): 3 / Rfactor obs: 0.199 / Rfactor Rwork: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 19.9 Å2
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.8
LS refinement shell
*PLUS
Highest resolution: 2.55 Å / Lowest resolution: 2.66 Å / Total num. of bins used: 8 / Num. reflection obs: 1539 / Rfactor obs: 0.2961

+
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