[English] 日本語
Yorodumi
- PDB-9dmr: Solution NMR structure of the calcium insensitive human LETM1 F-E... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9dmr
TitleSolution NMR structure of the calcium insensitive human LETM1 F-EF-hand domain mutant in the absence of calcium
ComponentsMitochondrial proton/calcium exchanger protein
KeywordsMETAL BINDING PROTEIN / EF-hand / F-EF-hand / LETM1 / mitochondrial
Function / homology
Function and homology information


calcium export from the mitochondrion / calcium:proton antiporter activity / mitochondrial potassium ion transmembrane transport / negative regulation of mitochondrial calcium ion concentration / regulation of cellular hyperosmotic salinity response / mitochondrial calcium ion transmembrane transport / inner mitochondrial membrane organization / Mitochondrial calcium ion transport / Complex III assembly / mitochondrial calcium ion homeostasis ...calcium export from the mitochondrion / calcium:proton antiporter activity / mitochondrial potassium ion transmembrane transport / negative regulation of mitochondrial calcium ion concentration / regulation of cellular hyperosmotic salinity response / mitochondrial calcium ion transmembrane transport / inner mitochondrial membrane organization / Mitochondrial calcium ion transport / Complex III assembly / mitochondrial calcium ion homeostasis / cristae formation / protein hexamerization / RHOG GTPase cycle / mitochondrion organization / protein homooligomerization / calcium ion transport / ribosome binding / mitochondrial inner membrane / calcium ion binding / mitochondrion
Similarity search - Function
LETM1-like, ribosome-binding domain / LETM1/MDM38-like / LETM1-like, RBD / Letm1 ribosome-binding (RBD) domain profile. / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Mitochondrial proton/calcium exchanger protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsLin, Q.T. / Stathopulos, P.B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)07171 Canada
CitationJournal: Febs Lett. / Year: 2025
Title: The apo LETM1 F-EF-hand adopts a closed conformation that underlies a multi-modal sensory role in mitochondria.
Authors: Lin, Q.T. / Colussi, D.M. / Stathopulos, P.B.
History
DepositionSep 14, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mitochondrial proton/calcium exchanger protein


Theoretical massNumber of molelcules
Total (without water)6,6951
Polymers6,6951
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Mitochondrial proton/calcium exchanger protein / Electroneutral mitochondrial K(+)/H(+)exchanger / KHE / Leucine zipper-EF-hand-containing ...Electroneutral mitochondrial K(+)/H(+)exchanger / KHE / Leucine zipper-EF-hand-containing transmembrane protein 1


Mass: 6694.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LETM1 / Production host: Escherichia coli (E. coli) / References: UniProt: O95202
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D 1H-15N NOESY
132isotropic13D CBCA(CO)NH
142isotropic13D HN(CA)CB
152isotropic13D H(CCO)NH
162isotropic13D HNCO
273isotropic12D 1H-13C HSQC
283isotropic13D (H)CCH-TOCSY
293isotropic13D 1H-13C NOESY

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM [U-99% 15N] Human leucine zipper EF-hand containing transmembrane protein-1 F-EF-hand domain, 20 mM TRIS, 50 mM sodium chloride, 10 mM CHAPS, 90% H2O/10% D2Osample_190% H2O/10% D2O
solution21 mM [U-99% 15N; U-99% 15N] Human leucine zipper EF-hand containing transmembrane protein-1 F-EF-hand domain, 20 mM TRIS, 50 mM sodium chloride, 10 mM CHAPS, 90% H2O/10% D2Osample_290% H2O/10% D2O
solution31 mM [U-99% 15N; U-99% 15N] Human leucine zipper EF-hand containing transmembrane protein-1 F-EF-hand domain, 20 mM TRIS, 50 mM sodium chloride, 10 mM CHAPS, 100% D2Osample_3100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMHuman leucine zipper EF-hand containing transmembrane protein-1 F-EF-hand domain[U-99% 15N]1
20 mMTRISnatural abundance1
50 mMsodium chloridenatural abundance1
10 mMCHAPSnatural abundance1
1 mMHuman leucine zipper EF-hand containing transmembrane protein-1 F-EF-hand domain[U-99% 15N; U-99% 15N]2
20 mMTRISnatural abundance2
50 mMsodium chloridenatural abundance2
10 mMCHAPSnatural abundance2
1 mMHuman leucine zipper EF-hand containing transmembrane protein-1 F-EF-hand domain[U-99% 15N; U-99% 15N]3
20 mMTRISnatural abundance3
50 mMsodium chloridenatural abundance3
10 mMCHAPSnatural abundance3
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
195 mMcondition_17.81 atm308.15 K
295 mMcondition_28.2 pD1 atm308.15 K

-
NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
CARA1.9.1B12Keller and Wuthrichchemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
NMRPipe10.9Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / 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://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