[English] 日本語
Yorodumi
- PDB-7d65: Cryo-EM Structure of human CALHM5 in the presence of Ca2+ -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7d65
TitleCryo-EM Structure of human CALHM5 in the presence of Ca2+
ComponentsCalcium homeostasis modulator protein 5
KeywordsTRANSPORT PROTEIN / large pore channel
Function / homologyCalcium homeostasis modulator family / Calcium homeostasis modulator / ATP export / monoatomic cation channel activity / plasma membrane / 1,2-DIOCTANOYL-SN-GLYCERO-3-PHOSPHATE / Calcium homeostasis modulator protein 5
Function and homology information
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.94 Å
AuthorsLiu, J. / Guan, F.H. / Wu, J. / Wan, F.T. / Lei, M. / Ye, S.
Funding support China, 8items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2016YFA0500404 China
Ministry of Science and Technology (MoST, China)2018YFA0508100 China
National Natural Science Foundation of China (NSFC)31525001 China
National Natural Science Foundation of China (NSFC)31971127 China
National Natural Science Foundation of China (NSFC)31870724 China
National Natural Science Foundation of China (NSFC)31900041 China
National Natural Science Foundation of China (NSFC)31525007 China
National Natural Science Foundation of China (NSFC)31930063 China
CitationJournal: Cell Discov / Year: 2020
Title: Cryo-EM structures of human calcium homeostasis modulator 5.
Authors: Jie Liu / Futang Wan / Qiuheng Jin / Xiaoxiao Li / Eijaz Ahmed Bhat / Jiangtao Guo / Ming Lei / Fenghui Guan / Jian Wu / Sheng Ye /
History
DepositionSep 29, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-30589
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Calcium homeostasis modulator protein 5
B: Calcium homeostasis modulator protein 5
C: Calcium homeostasis modulator protein 5
D: Calcium homeostasis modulator protein 5
E: Calcium homeostasis modulator protein 5
F: Calcium homeostasis modulator protein 5
G: Calcium homeostasis modulator protein 5
H: Calcium homeostasis modulator protein 5
I: Calcium homeostasis modulator protein 5
J: Calcium homeostasis modulator protein 5
K: Calcium homeostasis modulator protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)385,42566
Polymers362,13411
Non-polymers23,29055
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein
Calcium homeostasis modulator protein 5 / Protein FAM26E


Mass: 32921.305 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALHM5, C6orf188, FAM26E / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q8N5C1
#2: Chemical...
ChemComp-PA8 / 1,2-DIOCTANOYL-SN-GLYCERO-3-PHOSPHATE


Mass: 423.458 Da / Num. of mol.: 55 / Source method: obtained synthetically / Formula: C19H36O8P
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Calcium homeostasis modulator protein 5 / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human) / Cellular location: membrane
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293 / Plasmid: pEZT
Buffer solutionpH: 7.5
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

CTF correctionType: NONE
3D reconstructionResolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 392239 / Symmetry type: POINT

+
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