[English] 日本語
Yorodumi
- PDB-1rk9: Solution Structure of Human alpha-Parvalbumin (Minimized Average ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1rk9
TitleSolution Structure of Human alpha-Parvalbumin (Minimized Average Structure)
ComponentsParvalbumin alpha
KeywordsMETAL BINDING PROTEIN / calcium / parvalbumin / EF-hand / lanthanide / Structural Proteomics in Europe / SPINE / Structural Genomics
Function / homology
Function and homology information


inhibitory chemical synaptic transmission / excitatory chemical synaptic transmission / Transcriptional Regulation by MECP2 / gene expression / axon / calcium ion binding / synapse / cytoplasm
Similarity search - Function
Parvalbumin / EF-hand domain pair / EF-hand / Recoverin; domain 1 / EF-hand domain pair / 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 ...Parvalbumin / EF-hand domain pair / EF-hand / Recoverin; domain 1 / EF-hand domain pair / 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 / distance geometry; simulated annealing; molecular dynamics; torsion angle dynamics pseudocontact shifts; residue diploar couplings
Model type detailsminimized average
AuthorsBaig, I. / Bertini, I. / Del Bianco, C. / Gupta, Y.K. / Lee, Y.-M. / Luchinat, C. / Quattrone, A. / Structural Proteomics in Europe (SPINE)
CitationJournal: Biochemistry / Year: 2004
Title: Paramagnetism-based refinement strategy for the solution structure of human alpha-parvalbumin
Authors: Baig, I. / Bertini, I. / Del Bianco, C. / Gupta, Y.K. / Lee, Y.-M. / Luchinat, C. / Quattrone, A.
History
DepositionNov 21, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / 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_nmr_software.name / _pdbx_nmr_spectrometer.model / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Parvalbumin alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1583
Polymers12,0781
Non-polymers802
Water00
1


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

-
Components

#1: Protein Parvalbumin alpha / alpha-Parvalbumin / parvalbumin


Mass: 12077.771 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P20472
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
1312D NOESY
1412D TOCSY
151HNHA
NMR detailsText: All spectrometers are equipped with a triple resonance (TXI) 5 mm probe with a z-axis pulse field gradient, and the 500 MHz spectrometer is equipped with a triple resonance cryo-probe. This ...Text: All spectrometers are equipped with a triple resonance (TXI) 5 mm probe with a z-axis pulse field gradient, and the 500 MHz spectrometer is equipped with a triple resonance cryo-probe. This structure was determined using pseudocontact shifts and residue dipolar couplings with all diamagnetic restraints

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.5 mM Parvalbumin U-15N,13C; 100mM NaCl; 90% H2O, 10% D2O; pH 7.0; for CaCaPV90% H2O/10% D2O
20.6 mM Parvalbumin U-15N; 100mM NaCl; 90% H2O, 10% D2O; pH 7.0; for CaCaPV90% H2O/10% D2O
31.5 mM Parvalbumin U-15N,13C; 100mM NaCl; 90% H2O, 10% D2O; pH 7.0; for CaDyPV90% H2O/10% D2O
40.6 mM Parvalbumin U-15N; 100mM NaCl; 90% H2O, 10% D2O; pH 7.0; for CaDyPV90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100 mM NaCl 7ambient 298 K
2100 mM NaCl 7ambient 298 K
3100 mM NaCl 7ambient 298 K
4100 mM NaCl 7ambient 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE7001
Bruker AVANCEBrukerAVANCE6002
Bruker AVANCEBrukerAVANCE5003

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.1Brungercollection
XwinNMR3.1Brungerprocessing
XEASY1.3Guntertdata analysis
DYANA1.5Guntertstructure solution
Amber5Rearlmanrefinement
RefinementMethod: distance geometry; simulated annealing; molecular dynamics; torsion angle dynamics pseudocontact shifts; residue diploar couplings
Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 1

+
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