[English] 日本語
Yorodumi
- PDB-6sl3: ALPHA-ACTININ FROM ENTAMOEBA HISTOLYTICA in orthorhombic space group -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6sl3
TitleALPHA-ACTININ FROM ENTAMOEBA HISTOLYTICA in orthorhombic space group
ComponentsCalponin homology domain protein putative
KeywordsSTRUCTURAL PROTEIN / Actinin / Actin Binding Domain / Spectrin Repear / Calmodulin-like domain / Calcium Regulation
Function / homology
Function and homology information


actin binding / cytoskeleton / calcium ion binding / cytoplasm
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / Calponin-like domain / Ca2+ insensitive EF hand / Actin-binding Protein, T-fimbrin; domain 1 / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / Calponin-like domain / Ca2+ insensitive EF hand / Actin-binding Protein, T-fimbrin; domain 1 / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / EF-hand / Recoverin; domain 1 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Calponin homology domain protein, putative
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsPinotsis, N. / Khan, M.B. / Djinovic-Carugo, K.
Funding support Austria, 2items
OrganizationGrant numberCountry
Austrian Science Fund Austria
Marie Sklodowska-Curie Actions, FragNET ITN238423
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Calcium modulates the domain flexibility and function of an alpha-actinin similar to the ancestral alpha-actinin.
Authors: Pinotsis, N. / Zielinska, K. / Babuta, M. / Arolas, J.L. / Kostan, J. / Khan, M.B. / Schreiner, C. / Salmazo, A. / Ciccarelli, L. / Puchinger, M. / Gkougkoulia, E.A. / Ribeiro Jr., E.A. / ...Authors: Pinotsis, N. / Zielinska, K. / Babuta, M. / Arolas, J.L. / Kostan, J. / Khan, M.B. / Schreiner, C. / Salmazo, A. / Ciccarelli, L. / Puchinger, M. / Gkougkoulia, E.A. / Ribeiro Jr., E.A. / Marlovits, T.C. / Bhattacharya, A. / Djinovic-Carugo, K.
History
DepositionAug 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Calponin homology domain protein putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,8122
Polymers69,7721
Non-polymers401
Water00
1
A: Calponin homology domain protein putative
hetero molecules

A: Calponin homology domain protein putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,6234
Polymers139,5432
Non-polymers802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area8880 Å2
ΔGint-24 kcal/mol
Surface area62680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.210, 71.830, 241.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221
Space group name HallP2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2

-
Components

#1: Protein Calponin homology domain protein putative / Calponin homology domain protein / putative


Mass: 69771.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: CL6EHI_199000, EHI_199000 / Production host: Escherichia coli (E. coli) / References: UniProt: C4LWU6
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 92 mM bicine/trizma base (pH 8.5), 27.6 mM CaCl2, 27.6 mM MgCl2, 11.5% (w/v) PEG 3,350, 11.5% (w/v) PEG 1,000, 11.5% (v/v) MPD

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.005755 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.005755 Å / Relative weight: 1
ReflectionResolution: 3.1→46.24 Å / Num. obs: 14460 / % possible obs: 99.1 % / Redundancy: 7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.133 / Net I/σ(I): 8.57
Reflection shellResolution: 3.1→3.17 Å / Mean I/σ(I) obs: 0.48 / Num. unique obs: 967 / CC1/2: 0.433

-
Processing

Software
NameClassification
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SL2

6sl2


Resolution: 3.1→46.23 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.32451 --
Rwork0.25907 --
obs0.26829 12224 99.08 %
Refinement stepCycle: LAST / Resolution: 3.1→46.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4730 0 1 0 4731

+
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