[English] 日本語
Yorodumi
- PDB-1izn: Crystal Structure of Actin Filament Capping Protein CapZ -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1izn
TitleCrystal Structure of Actin Filament Capping Protein CapZ
Components
  • CapZ alpha-1 subunit
  • CapZ beta-1 subunit
KeywordsPROTEIN BINDING / HETERODIMER / CAPPING PROTEIN / ACTIN FILAMENT BARBED END CAPPING
Function / homology
Function and homology information


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 / WASH complex / sperm connecting piece / F-actin capping protein complex ...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 / WASH complex / sperm connecting piece / F-actin capping protein complex / negative regulation of filopodium assembly / cell junction assembly / barbed-end actin filament capping / actin polymerization or depolymerization / regulation of cell morphogenesis / regulation of lamellipodium assembly / lamellipodium assembly / cortical cytoskeleton / brush border / cytoskeleton organization / hippocampal mossy fiber to CA3 synapse / Schaffer collateral - CA1 synapse / cell morphogenesis / Z disc / actin filament binding / lamellipodium / actin cytoskeleton organization / postsynaptic density / membrane / plasma membrane / cytosol
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 / Ribosomal protein S3 C-terminal 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 / Special / Alpha-Beta Complex / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / F-actin-capping protein subunit alpha-1 / F-actin-capping protein subunit beta isoforms 1 and 2
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsYamashita, A. / Maeda, K. / Maeda, Y.
CitationJournal: EMBO J. / Year: 2003
Title: Crystal structure of CapZ: structural basis for actin filament barbed end capping
Authors: Yamashita, A. / Maeda, K. / Maeda, Y.
History
DepositionOct 10, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: CapZ alpha-1 subunit
B: CapZ beta-1 subunit
C: CapZ alpha-1 subunit
D: CapZ beta-1 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,0588
Polymers128,8104
Non-polymers2484
Water9,242513
1
A: CapZ alpha-1 subunit
B: CapZ beta-1 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5294
Polymers64,4052
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7870 Å2
ΔGint-44 kcal/mol
Surface area26630 Å2
MethodPISA
2
C: CapZ alpha-1 subunit
D: CapZ beta-1 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5294
Polymers64,4052
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7970 Å2
ΔGint-43 kcal/mol
Surface area26500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.200, 57.200, 99.200
Angle α, β, γ (deg.)90.00, 113.00, 90.00
Int Tables number4
Space group name H-MP1211
DetailsChains A and B, C and D are biological heterodimer assemblies respectively.

-
Components

#1: Protein CapZ alpha-1 subunit / F-ACTIN CAPPING PROTEIN ALPHA-1 SUBUNIT


Mass: 33001.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: pET3d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)plysS / References: UniProt: P13127
#2: Protein CapZ beta-1 subunit / F-actin capping protein beta subunit isoform 1


Mass: 31403.449 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken)
Description: The cDNAs encoding alpha-1 and beta-1 subunits were cloned in a single vector
Plasmid: pET3d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)plysS / References: UniProt: P14315
#3: Chemical
ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 513 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG3350, magnesium nitrate, MES-NAOH, Jeffamine M-600, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
25 mMTris-HCl1droppH8.0
31 mMdithiothreitol1drop
45 %Jeffamine M-6001drop
518 %PEG33501reservoir
60.2 M1reservoirMg(NO3)2
70.1 MMES-NaOH1reservoirpH6.0

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45PX / Wavelength: 1.02 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Apr 24, 2002 / Details: CYLINDRICAL BEND MIRROR
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 61111 / Num. obs: 61088 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3.75 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 26
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.265 / % possible all: 100
Reflection
*PLUS
Num. measured all: 228951
Reflection shell
*PLUS
% possible obs: 100 %

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.1→50 Å / Data cutoff high rms absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.262 2970 4.93 %RANDOM
Rwork0.222 ---
all-60190 --
obs-60190 100 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.24 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 43.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.994 Å20 Å2-2.679 Å2
2--1.989 Å20 Å2
3----0.994 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8743 0 16 513 9272
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.378
X-RAY DIFFRACTIONc_dihedral_angle_d23.156
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_mcbond_it1.4441.5
X-RAY DIFFRACTIONc_mcangle_it2.4262
X-RAY DIFFRACTIONc_scbond_it1.9362
X-RAY DIFFRACTIONc_scangle_it2.9162.5
LS refinement shellResolution: 2.1→2.18 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.34 279 4.7 %
Rwork0.276 5661 -
obs-5940 100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3NO3.PARAMNO3.TOP
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.156
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77

+
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