[English] 日本語
Yorodumi
- PDB-2g9b: NMR solution structure of CA2+-loaded calbindin D28K -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2g9b
TitleNMR solution structure of CA2+-loaded calbindin D28K
ComponentsCalbindin
KeywordsMETAL BINDING PROTEIN / EF-HAND / CA2+-BINDING
Function / homology
Function and homology information


metanephric connecting tubule development / calcium ion binding involved in regulation of presynaptic cytosolic calcium ion concentration / calcium ion binding involved in regulation of postsynaptic cytosolic calcium ion concentration / metanephric distal convoluted tubule development / cuticular plate / metanephric part of ureteric bud development / retina layer formation / regulation of presynaptic cytosolic calcium ion concentration / response to auditory stimulus / vitamin D metabolic process ...metanephric connecting tubule development / calcium ion binding involved in regulation of presynaptic cytosolic calcium ion concentration / calcium ion binding involved in regulation of postsynaptic cytosolic calcium ion concentration / metanephric distal convoluted tubule development / cuticular plate / metanephric part of ureteric bud development / retina layer formation / regulation of presynaptic cytosolic calcium ion concentration / response to auditory stimulus / vitamin D metabolic process / vitamin D binding / short-term memory / stereocilium / metanephric collecting duct development / presynaptic cytosol / regulation of long-term synaptic potentiation / postsynaptic cytosol / : / cochlea development / calyx of Held / GABA-ergic synapse / long-term memory / hippocampal mossy fiber to CA3 synapse / locomotory behavior / regulation of synaptic plasticity / terminal bouton / retina development in camera-type eye / postsynapse / dendritic spine / learning or memory / neuron projection / axon / neuronal cell body / glutamatergic synapse / synapse / calcium ion binding / dendrite / zinc ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Calbindin / EF hand / 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 ...Calbindin / EF hand / 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 speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / Torsion angle dynamics, molecular dynamics simulated annealing refinement in explicit solvent (water)
AuthorsKojetin, D.J. / Venters, R.A. / Kordys, D.R. / Thompson, R.J. / Kumar, R. / Cavanagh, J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2006
Title: Structure, binding interface and hydrophobic transitions of Ca(2+)-loaded calbindin-D(28K).
Authors: Kojetin, D.J. / Venters, R.A. / Kordys, D.R. / Thompson, R.J. / Kumar, R. / Cavanagh, J.
History
DepositionMar 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Calbindin


Theoretical massNumber of molelcules
Total (without water)30,1731
Polymers30,1731
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 900structures with the least restraint violations, structures with the lowest restraint energy
RepresentativeModel #1fewest violations, lowest restraint energy

-
Components

#1: Protein Calbindin / Vitamin D-dependent calcium-binding protein / avian-type / Calbindin D28 / D-28K / Spot 35 protein


Mass: 30173.166 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Calb1 / Plasmid: PGEX-4T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P07171

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2114D 13C/15N-separated NOESY
2224D 13C/13C-separated NOESY
1333D CT 13C methyl-separated NOESY
243(4,2)D CT 13C/13C methyl-separated NOESY
1534D 13C/15N-separated NOESY
263(4,2)D 13C/15N-separated NOESY
1744D 15N/15N-separated NOESY
281(4,2)D 13C ali/13C aro-separated NOESY
NMR detailsText: This structure was determined using a combination of 3D, 4D and (4,2)D projection reconstruction techniques on perdeuterated and fully protonated samples.

-
Sample preparation

Details
Solution-IDContentsSolvent system
11mM calbindin D28k; U-15N,13C; 10 mM Tris, 1 mM DTT, 0.02% NaN3, 6 mM CaCl2, 90% H2O, 10% D2O90% H2O/10% D2O
21mM calbindin D28k; U-15N,13C; 10 mM Tris, 1 mM DTT, 0.02% NaN3, 6 mM CaCl2, 100% D2O100% D2O
31mM calbindin D28k; U-2H,15N,13C; Ile (d1 only), Leu, Val methyl protonated; 10 mM Tris, 1 mM DTT, 0.02% NaN3, 6 mM CaCl2, 90% H2O, 10% D2O90% H2O/10% D2O
41mM calbindin D28k; U-2H,15N; 10 mM Tris, 1 mM DTT, 0.02% NaN3, 6 mM CaCl2, 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
16 mM CACL2 7.0 AMBIENT 298 K
26 mM CACL2 6.2 AMBIENT 323 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002

-
Processing

NMR software
NameVersionDeveloperClassification
CNS1Brunger, A.T., Adams, P.D., Clore, G.M., Delano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.-S., Kuszewski, J., Nilges, M., Pannu, N.S., Read, R.J., Rice, L.M., Simonson, T., Warren, G.L.refinement
NMRPipe2.3Delaglio, F., Grzesiek, S., Vuister, G.W., Zhu, G., Pfeifer, J., Bax, A.structure solution
NMRView5Johnson, B.A., Blevins, R.A.structure solution
XPLOR-NIH2.9.4aSCHWIETERS, C.D. et al.refinement
RefinementMethod: Torsion angle dynamics, molecular dynamics simulated annealing refinement in explicit solvent (water)
Software ordinal: 1
Details: the structures are based on 6882 NOE distance constraints, 432 dihedral angle restraints, 36 hydrogen bond restraints and 304 residual dipolar coupling restraints
NMR representativeSelection criteria: fewest violations, lowest restraint energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest restraint energy
Conformers calculated total number: 900 / 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://pdbjlvh1.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