[English] 日本語
Yorodumi
- PDB-2n8y: Holo form of Calmodulin-Like Domain of Human Non-Muscle alpha-act... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2n8y
TitleHolo form of Calmodulin-Like Domain of Human Non-Muscle alpha-actinin 1
ComponentsAlpha-actinin-1
KeywordsCalcium binding protein
Function / homology
Function and homology information


platelet morphogenesis / structural constituent of postsynapse / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / actin filament network formation / vinculin binding / muscle cell development / fascia adherens / focal adhesion assembly / RHOF GTPase cycle / RHOD GTPase cycle ...platelet morphogenesis / structural constituent of postsynapse / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / actin filament network formation / vinculin binding / muscle cell development / fascia adherens / focal adhesion assembly / RHOF GTPase cycle / RHOD GTPase cycle / Nephrin family interactions / platelet formation / Syndecan interactions / cortical actin cytoskeleton / pseudopodium / actin filament bundle assembly / brush border / RHOBTB2 GTPase cycle / stress fiber / ruffle / nuclear receptor coactivator activity / platelet alpha granule lumen / cell projection / actin filament organization / Z disc / actin filament binding / cell-cell junction / double-stranded RNA binding / integrin binding / Platelet degranulation / cell junction / actin cytoskeleton organization / regulation of apoptotic process / transmembrane transporter binding / focal adhesion / glutamatergic synapse / calcium ion binding / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / plasma membrane / cytosol / cytoplasm
Similarity search - Function
EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / EF-hand domain / Spectrin repeat / Spectrin repeat / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Spectrin/alpha-actinin ...EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / EF-hand domain / Spectrin repeat / Spectrin repeat / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Spectrin/alpha-actinin / Spectrin repeats / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / EF-hand / Recoverin; 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, water refinement
Model detailslowest energy, model1
AuthorsDrmota Prebil, S. / Slapsak, U. / de Almeida Ribeiro, E. / Pavsic, M. / Ilc, G. / Zielinska, K. / Hartl, M. / Backman, L. / Plavec, J. / Lenarcic, B. / Djinovic-Carugo, K.
CitationJournal: Sci Rep / Year: 2016
Title: Structure and calcium-binding studies of calmodulin-like domain of human non-muscle alpha-actinin-1.
Authors: Drmota Prebil, S. / Slapsak, U. / Pavsic, M. / Ilc, G. / Puz, V. / de Almeida Ribeiro, E. / Anrather, D. / Hartl, M. / Backman, L. / Plavec, J. / Lenarcic, B. / Djinovic-Carugo, K.
History
DepositionOct 28, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_nmr_data / _pdbx_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _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: Alpha-actinin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0272
Polymers16,9871
Non-polymers401
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Alpha-actinin-1 / / Alpha-actinin cytoskeletal isoform / F-actin cross-linking protein / Non-muscle alpha-actinin-1


Mass: 16986.770 Da / Num. of mol.: 1 / Fragment: EF-hand domains 1 and 2, residues 743-892
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACTN1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: P12814
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1413D HNCO
1513D HNCA
1613D HN(CO)CA
1713D HN(CA)CB
1813D CBCA(CO)NH
1913D C(CO)NH
11013D HBHA(CO)NH
11113D (H)CCH-TOCSY
11213D 1H-15N NOESY
11313D 1H-13C NOESY aliphatic
11413D 1H-13C NOESY aromatic

-
Sample preparation

DetailsContents: 1 mM [U-100% 13C; U-100% 15N] Calmodulin-Like Domain of alpha-actinin 1, 20 mM HEPES, 100 mM Sodium chloride, 1.5 mM DTT, 0.05 mM EGTA, 20 mM Calcium chloride, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMCalmodulin-Like Domain of alpha-actinin 1-1[U-100% 13C; U-100% 15N]1
20 mMHEPES-21
100 mMSodium chloride-31
1.5 mMDTT-41
0.05 mMEGTA-51
20 mMCalcium chloride-61
Sample conditionsIonic strength: 0.1 / pH: 7.6 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Varian VNMRS / Manufacturer: Varian / Model: VNMRS / Field strength: 800 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
SparkyCornilescu, Delaglio and Baxpeak picking
TALOSCornilescu, Delaglio and Baxprediction of protein backbone torsion angles
YASARAKrieger, Koraimann, Vriendrefinement
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing, water refinement / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20

+
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