[English] 日本語
Yorodumi
- PDB-2kxp: Solution NMR structure of V-1 bound to capping protein (CP) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kxp
TitleSolution NMR structure of V-1 bound to capping protein (CP)
Components
  • F-actin-capping protein subunit alpha-1
  • F-actin-capping protein subunit beta isoforms 1 and 2
  • MyotrophinMTPN
KeywordsPROTEIN BINDING / protein-protein interaction / capping protein / V-1
Function / homology
Function and homology information


positive regulation of macromolecule biosynthetic process / regulation of barbed-end actin filament capping / Advanced glycosylation endproduct receptor signaling / RHOD GTPase cycle / RHOF GTPase cycle / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-independent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / Factors involved in megakaryocyte development and platelet production / cerebellar granule cell differentiation ...positive regulation of macromolecule biosynthetic process / regulation of barbed-end actin filament capping / Advanced glycosylation endproduct receptor signaling / RHOD GTPase cycle / RHOF GTPase cycle / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-independent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / Factors involved in megakaryocyte development and platelet production / cerebellar granule cell differentiation / WASH complex / sperm connecting piece / F-actin capping protein complex / negative regulation of filopodium assembly / skeletal muscle tissue regeneration / catecholamine metabolic process / cell junction assembly / barbed-end actin filament capping / actin polymerization or depolymerization / regulation of cell morphogenesis / regulation of lamellipodium assembly / lamellipodium assembly / regulation of cell size / cortical cytoskeleton / positive regulation of cardiac muscle hypertrophy / brush border / cytoskeleton organization / striated muscle cell differentiation / hippocampal mossy fiber to CA3 synapse / positive regulation of protein metabolic process / Schaffer collateral - CA1 synapse / cell morphogenesis / Z disc / cellular response to mechanical stimulus / actin filament binding / lamellipodium / positive regulation of NF-kappaB transcription factor activity / actin cytoskeleton organization / positive regulation of cell growth / sequence-specific DNA binding / postsynaptic density / axon / perinuclear region of cytoplasm / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Capz alpha-1 subunit / F-actin capping protein, alpha/beta subunit, N-terminal domain / F-actin capping protein, alpha subunit / F-actin capping protein, beta subunit / F-actin-capping protein subunit beta / F-actin capping protein, beta subunit, conserved site / F-actin-capping protein subunit beta, N-terminal domain / F-actin capping protein, beta subunit / F-actin capping protein beta subunit signature. / F-actin capping protein, alpha subunit, conserved site ...Capz alpha-1 subunit / F-actin capping protein, alpha/beta subunit, N-terminal domain / F-actin capping protein, alpha subunit / F-actin capping protein, beta subunit / F-actin-capping protein subunit beta / F-actin capping protein, beta subunit, conserved site / F-actin-capping protein subunit beta, N-terminal domain / F-actin capping protein, beta subunit / F-actin capping protein beta subunit signature. / F-actin capping protein, alpha subunit, conserved site / F-actin capping protein alpha subunit signature 1. / F-actin capping protein alpha subunit signature 2. / F-actin-capping protein subunit alpha / F-actin-capping protein subunit alpha/beta / F-actin-capping protein subunit alpha/beta, domain 2 / F-actin capping protein, alpha subunit, domain 1 / F-actin capping protein alpha subunit / Domain of unknown function DUF3447 / Ribosomal protein S3 C-terminal domain / Ankyrin repeat-containing domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Aspartate Aminotransferase, domain 1 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix non-globular / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Special / Alpha Horseshoe / Alpha-Beta Complex / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
F-actin-capping protein subunit alpha-1 / F-actin-capping protein subunit beta isoforms 1 and 2 / Myotrophin
Similarity search - Component
Biological speciesGallus gallus (chicken)
Mus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsZwolak, A. / Fujiwara, I. / Hammer III, J.A. / Tjandra, N.
CitationJournal: To be Published
Title: Solution NMR structure of V-1 bound to capping protein (CP)
Authors: Zwolak, A. / Fujiwara, I. / Hammer III, J.A. / Tjandra, N.
History
DepositionMay 11, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: F-actin-capping protein subunit alpha-1
B: F-actin-capping protein subunit beta isoforms 1 and 2
C: Myotrophin


Theoretical massNumber of molelcules
Total (without water)75,1403
Polymers75,1403
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein F-actin-capping protein subunit alpha-1 / CapZ 36/32 / Beta-actinin subunit I


Mass: 31719.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: CAPZA1 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P13127
#2: Protein F-actin-capping protein subunit beta isoforms 1 and 2 / CapZ B1 and B2 / CapZ 36/32 / Beta-actinin subunit II


Mass: 30541.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: CAPZB / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P14315
#3: Protein Myotrophin / MTPN / Protein V-1 / Granule cell differentiation protein


Mass: 12878.768 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mtpn, Gcdp / Plasmid: pET3a-51 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P62774

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-15N HSQC
1332D 1H-15N HSQC

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.35 mM [U-100% 15N; U-99% 2H] capping protein alpha1 subunit, 0.35 mM [U-100% 15N; U-99% 2H] capping protein beta1 subunit, 0.35 mM [U-99% 2H] V-1, 90% H2O/10% D2O90% H2O/10% D2O
20.35 mM [U-99% 2H] capping protein alpha1 subunit, 0.35 mM [U-99% 2H] capping protein beta1 subunit, 0.35 mM [U-100% 15N; U-99% 2H] V-1, 90% H2O/10% D2O90% H2O/10% D2O
30.35 mM [U-100% 15N; U-99% 2H] capping protein alpha1 subunit, 0.35 mM [U-100% 15N; U-99% 2H] capping protein beta1 subunit, 0.35 mM [U-99% 2H] M7C V-1, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.35 mMcapping protein alpha1 subunit[U-100% 15N; U-99% 2H]1
0.35 mMcapping protein beta1 subunit[U-100% 15N; U-99% 2H]1
0.35 mMV-1[U-99% 2H]1
0.35 mMcapping protein alpha1 subunit[U-99% 2H]2
0.35 mMcapping protein beta1 subunit[U-99% 2H]2
0.35 mMV-1[U-100% 15N; U-99% 2H]2
0.35 mMcapping protein alpha1 subunit[U-100% 15N; U-99% 2H]3
0.35 mMcapping protein beta1 subunit[U-100% 15N; U-99% 2H]3
0.35 mMM7C V-1[U-99% 2H]3
Sample conditionsIonic strength: 0.1 / pH: 6.5 / Pressure: ambient / Temperature: 305 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DRXBrukerDRX6002

-
Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PIPPGarrettchemical shift assignment
X-PLOR_NIH2.23Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1 / Details: RIGID BODY REFINEMENT
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

+
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