[English] 日本語
Yorodumi
- PDB-2v8f: Mouse Profilin IIa in complex with a double repeat from the FH1 d... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2v8f
TitleMouse Profilin IIa in complex with a double repeat from the FH1 domain of mDia1
Components
  • PROFILIN-2
  • PROTEIN DIAPHANOUS HOMOLOG 1
KeywordsPROTEIN BINDING / ALTERNATIVE SPLICING / PROTEIN-BINDING / CYTOPLASM / ACETYLATION / CYTOSKELETON / ACTIN-BINDING
Function / homology
Function and homology information


Signaling by ROBO receptors / negative regulation of neuron projection regeneration / presynaptic actin cytoskeleton organization / negative regulation of ruffle assembly / multicellular organismal locomotion / ERBB2 Regulates Cell Motility / RHOF GTPase cycle / RHOC GTPase cycle / RHOD GTPase cycle / actin nucleation ...Signaling by ROBO receptors / negative regulation of neuron projection regeneration / presynaptic actin cytoskeleton organization / negative regulation of ruffle assembly / multicellular organismal locomotion / ERBB2 Regulates Cell Motility / RHOF GTPase cycle / RHOC GTPase cycle / RHOD GTPase cycle / actin nucleation / neuron projection retraction / modification of postsynaptic actin cytoskeleton / RHOB GTPase cycle / negative regulation of epithelial cell migration / RHO GTPases Activate Formins / RHOA GTPase cycle / profilin binding / negative regulation of actin filament polymerization / regulation of microtubule-based process / axon midline choice point recognition / positive regulation of actin filament polymerization / regulation of synaptic vesicle exocytosis / brush border / synaptic vesicle endocytosis / actin monomer binding / ephrin receptor signaling pathway / positive regulation of peptidyl-serine phosphorylation / positive regulation of stress fiber assembly / phosphatidylinositol-4,5-bisphosphate binding / cytoskeleton organization / actin filament polymerization / presynaptic modulation of chemical synaptic transmission / Neutrophil degranulation / sensory perception of sound / modulation of chemical synaptic transmission / terminal bouton / brain development / Schaffer collateral - CA1 synapse / small GTPase binding / spindle / ruffle membrane / neuron projection development / protein localization / presynapse / regulation of cell shape / actin binding / actin cytoskeleton organization / gene expression / transmembrane transporter binding / cytoskeleton / postsynapse / neuron projection / protein stabilization / centrosome / glutamatergic synapse / ATP hydrolysis activity / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Formin Homology Region 1 / Diaphanous, GTPase-binding domain superfamily / : / Diaphanous autoregulatory (DAD) domain / Diaphanous autoregulatory domain (DAD) profile. / Profilin1/2/3, vertebrate / Formin, FH3 domain / Formin, GTPase-binding domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain ...Formin Homology Region 1 / Diaphanous, GTPase-binding domain superfamily / : / Diaphanous autoregulatory (DAD) domain / Diaphanous autoregulatory domain (DAD) profile. / Profilin1/2/3, vertebrate / Formin, FH3 domain / Formin, GTPase-binding domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain profile. / Formin, FH2 domain / Formin, FH2 domain superfamily / Formin Homology 2 Domain / Formin homology-2 (FH2) domain profile. / Formin Homology 2 Domain / Profilin conserved site / Profilin signature. / Profilin / Profilin / : / Profilin / Profilin superfamily / Dynein light chain 2a, cytoplasmic / Beta-Lactamase / Armadillo-like helical / Armadillo-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Protein diaphanous homolog 1 / Profilin-2 / Profilin-2
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsKursula, P. / Kursula, I. / Downer, J. / Witke, W. / Wilmanns, M.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: High-Resolution Structural Analysis of Mammalian Profilin 2A Complex Formation with Two Physiological Ligands: The Formin Homology 1 Domain of Mdia1 and the Proline-Rich Domain of Vasp.
Authors: Kursula, P. / Kursula, I. / Massimi, M. / Song, Y.H. / Downer, J. / Stanley, W.A. / Witke, W. / Wilmanns, M.
History
DepositionAug 7, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _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: PROFILIN-2
B: PROFILIN-2
C: PROTEIN DIAPHANOUS HOMOLOG 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,79111
Polymers32,1363
Non-polymers6558
Water6,431357
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-91.3 kcal/mol
Surface area13690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.380, 37.270, 88.750
Angle α, β, γ (deg.)90.00, 98.58, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein / Protein/peptide , 2 types, 3 molecules ABC

#1: Protein PROFILIN-2 / PROFILIN IIA


Mass: 15064.216 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PMW172 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q3V171, UniProt: Q9JJV2*PLUS
#2: Protein/peptide PROTEIN DIAPHANOUS HOMOLOG 1 / DIAPHANOUS-RELATED FORMIN-1 / DRF1 / P140MDIA / MDIA1


Mass: 2007.414 Da / Num. of mol.: 1 / Fragment: FH1 DOMAIN, RESIDUES 635-655 / Source method: obtained synthetically
Details: TWO PROLINE-RICH REPEATS DERIVED FROM THE MOUSE HOMOLOGUE OF DIAPHANOUS 1 (MDIA1).
Source: (synth.) MUS MUSCULUS (house mouse) / References: UniProt: O08808

-
Non-polymers , 5 types, 365 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 1.65 Å3/Da / Density % sol: 25.01 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.0408
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0408 Å / Relative weight: 1
ReflectionResolution: 1.1→20 Å / Num. obs: 93713 / % possible obs: 92.8 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.3
Reflection shellResolution: 1.1→1.2 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.9 / % possible all: 75.4

-
Processing

Software
NameClassification
SHELXrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1D1J

1d1j


Resolution: 1.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: FINAL ROUND OF B FACTOR REFINEMENT DONE IN PHENIX.REFINE
RfactorNum. reflection% reflectionSelection details
Rfree0.173 -2 %RANDOM
obs0.146 -92.8 %-
all-93713 --
Refinement stepCycle: LAST / Resolution: 1.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2198 0 36 357 2591

+
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