[English] 日本語
Yorodumi
- PDB-2lhi: Solution structure of Ca2+/CNA1 peptide-bound yCaM -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2lhi
TitleSolution structure of Ca2+/CNA1 peptide-bound yCaM
ComponentsCalmodulin,Serine/threonine-protein phosphatase 2B catalytic subunit A1
KeywordsMETAL BINDING PROTEIN / yeast calmodulin / CNA1
Function / homology
Function and homology information


: / Ca2+ pathway / : / adaptation of signaling pathway by response to pheromone involved in conjugation with cellular fusion / regulation of membrane tubulation / spindle pole body organization / cell budding / myosin I complex / central plaque of spindle pole body / regulation of microtubule nucleation ...: / Ca2+ pathway / : / adaptation of signaling pathway by response to pheromone involved in conjugation with cellular fusion / regulation of membrane tubulation / spindle pole body organization / cell budding / myosin I complex / central plaque of spindle pole body / regulation of microtubule nucleation / cellular bud / positive regulation of Arp2/3 complex-mediated actin nucleation / myosin V complex / karyogamy involved in conjugation with cellular fusion / calmodulin-dependent protein phosphatase activity / calcineurin complex / vacuole fusion, non-autophagic / microautophagy / calcineurin-mediated signaling / fungal-type cell wall organization / actin cortical patch / incipient cellular bud site / cellular bud tip / intracellular monoatomic ion homeostasis / cellular bud neck / mating projection tip / vesicle transport along actin filament / phosphatidylinositol biosynthetic process / mitogen-activated protein kinase binding / protein-serine/threonine phosphatase / enzyme regulator activity / cytoskeleton organization / Neutrophil degranulation / receptor-mediated endocytosis / endocytosis / protein import into nucleus / calcium-dependent protein binding / calmodulin binding / calcium ion binding / metal ion binding / cytoplasm
Similarity search - Function
PP2B, metallophosphatase domain / PP2B / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / EF-hand / Recoverin; domain 1 ...PP2B, metallophosphatase domain / PP2B / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 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
Calmodulin / Serine/threonine-protein phosphatase 2B catalytic subunit A1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailslowest energy, model 1
AuthorsOgura, K. / Takahashi, K. / Kobashigawa, Y. / Yoshida, R. / Itoh, H. / Yazawa, M. / Inagaki, F.
CitationJournal: Genes Cells / Year: 2012
Title: Solution structures of yeast Saccharomyces cerevisiae calmodulin in calcium- and target peptide-bound states reveal similarities and differences to vertebrate calmodulin.
Authors: Ogura, K. / Kumeta, H. / Takahasi, K. / Kobashigawa, Y. / Yoshida, R. / Itoh, H. / Yazawa, M. / Inagaki, F.
History
DepositionAug 10, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_nmr_software / struct / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_name_com.name ..._entity.pdbx_description / _entity_name_com.name / _pdbx_nmr_software.name / _struct.pdbx_descriptor
Revision 1.2Jun 14, 2023Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / 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_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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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: Calmodulin,Serine/threonine-protein phosphatase 2B catalytic subunit A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4024
Polymers19,2821
Non-polymers1203
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 / 100target function
RepresentativeModel #1lowest energy

-
Components

#1: Protein Calmodulin,Serine/threonine-protein phosphatase 2B catalytic subunit A1 / CaM / Calcineurin A1 / Calmodulin-binding protein 1


Mass: 19281.553 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THE FUSION PROTEIN OF CALMODULIN (RESIDUE 1-146), LINKER (GSSTG) AND CALCINEURIN A1 (RESIDUES 453-476)
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: CMD1, YBR109C, YBR0904, CMP1, CNA1, L9753.6, YLR433C / Production host: Escherichia coli (E. coli) / References: UniProt: P06787, UniProt: P23287
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / 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 HN(CO)CA
1613D HNCA
1713D CBCA(CO)NH
1813D HN(CA)CB
1913D HBHA(CO)NH
11013D C(CO)NH
11113D (H)CCH-TOCSY aliphatic
11213D CCH-TOCSY
11312D (HB)CB(CGCD)HD
11412D (HB)CB(CGCDCE)HE
11513D 1H-15N NOESY
11613D 1H-13C NOESY aliphatic
11713D 1H-13C NOESY aromatic
11813D (H)CCH-TOCSY aromatic

-
Sample preparation

DetailsContents: 1 mM [U-99% 13C; U-99% 15N] yCaM_GS_CNA1-1, 20 mM MES-2, 150 mM sodium chloride-3, 5 mM CaCl2-4, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMyCaM_GS_CNA1-1[U-99% 13C; U-99% 15N]1
20 mMMES-21
150 mMsodium chloride-31
5 mMCaCl2-41
Sample conditionsIonic strength: 150 / pH: 6.3 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA8002
Varian INOVAVarianINOVA6003

-
Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe5.2Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.113Goddardchemical shift assignment
Sparky3.113Goddardpeak picking
Sparky3.113Goddardrefinement
CYANA2.1Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
TALOS2003.027.13.05Cornilescu, Delaglio and Baxstructure solution
RNMRTKv3Mobli M, Maciejewski MW, Gryk MR, Hoch JC.processing
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 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