[English] 日本語
Yorodumi
- EMDB-74040: Parus major TRPM8 with a chimeric human outer pore loops, semi-sw... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-74040
TitleParus major TRPM8 with a chimeric human outer pore loops, semi-swapped, ligand-free, cold, structure resolved in GDN
Map data
Sample
  • Complex: Homotetrameric complex of a chimeric Parus major TRPM8 determined in a cell-derived vesicles.
    • Protein or peptide: Transient receptor potential cation channel subfamily M member 8
KeywordsTRPM8 / transient receptor potential melastatin 8 / MEMBRANE PROTEIN / Human
Function / homology
Function and homology information


ligand-gated calcium channel activity / plasma membrane
Similarity search - Function
: / TRPM, SLOG domain / : / SLOG in TRPM / TRPM2-like domain / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Transient receptor potential cation channel subfamily M member 8
Similarity search - Component
Biological speciesParus major (Great Tit)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.07 Å
AuthorsChoi KY / Lin X / Cheng Y / Julius D
Funding support United States, 3 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R35NS105038 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM140847 United States
CitationJournal: Nature / Year: 2026
Title: Structural energetics of cold sensitivity
Authors: Choi KY / Lin X / Cheng Y / Julius D
History
DepositionNov 24, 2025-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_74040.png

Downloads & links

-
Map

FileDownload / File: emd_74040.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 320 pix.
= 262.048 Å		0.82 Å/pix.
x 320 pix.
= 262.048 Å		0.82 Å/pix.
x 320 pix.
= 262.048 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8189 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.0053374 - 1.9389745
Average (Standard dev.)0.004342614 (±0.06770099)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 262.048 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: #1

Fileemd_74040_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_74040_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_74040_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Homotetrameric complex of a chimeric Parus major TRPM8 determined...

EntireName: Homotetrameric complex of a chimeric Parus major TRPM8 determined in a cell-derived vesicles.
Components
  • Complex: Homotetrameric complex of a chimeric Parus major TRPM8 determined in a cell-derived vesicles.
    • Protein or peptide: Transient receptor potential cation channel subfamily M member 8

-
Supramolecule #1: Homotetrameric complex of a chimeric Parus major TRPM8 determined...

SupramoleculeName: Homotetrameric complex of a chimeric Parus major TRPM8 determined in a cell-derived vesicles.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Parus major (Great Tit)

-
Macromolecule #1: Transient receptor potential cation channel subfamily M member 8

MacromoleculeName: Transient receptor potential cation channel subfamily M member 8
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Parus major (Great Tit)
Molecular weightTheoretical: 127.130016 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPGSGSGMRH RRNGNFESSR LLYSSMSRSI DVACSDADLA NFIQENFKKR ECVFFTKDTK SMGNLCKCGY PENQHIEGTQ VNTTEKWNY KKHTKELPTD AFGDIQFENL GKRGKYIRLS CDTDSETLYD LMTQHWHLKT PNLVISVTGG AKNFALKPRM R KIFSRLIY ...String:
GPGSGSGMRH RRNGNFESSR LLYSSMSRSI DVACSDADLA NFIQENFKKR ECVFFTKDTK SMGNLCKCGY PENQHIEGTQ VNTTEKWNY KKHTKELPTD AFGDIQFENL GKRGKYIRLS CDTDSETLYD LMTQHWHLKT PNLVISVTGG AKNFALKPRM R KIFSRLIY IAQSKGAWIF TGGTHYGLMK YIGEVVRDNT ISRSSEENVV AIGIAAWGMI SNRETLIRTA DSDGSFLARY IM DDLKRDP LYCLDNNHTH LLLVDNGTHG HPTTEAKVRT QLEKYISERV IPESNYGGKI PIVCFAQGGG KETLKSINVA IKS KIPCVV VEGSGRIADV IASLVEAEGT LASSCVKESL LRFLPRTISR LSEEETESWI KWIKEVLESP HLLTVIKIEE AGDE IVSNA ISFALYKAFS TNEHDRDNWN GQLKLLLEWN QLDLASDEIF TNDRNWESAD LQDVMFTALV KDRPKFVRLF LENGL NLRK FLTTEVLREL YTNNFSSLVF KNLQIAKNSY NDALLTFVWK MVEDFRRGFK RDYKNSKDEM EIQLSEECPI TRHPLQ ALF IWSVLQNKKE LSKVIWEQTR GCTLAALGAS KLLKSMAKVK NDINAAGESE ELANEYETRA VELFTECYSN DEDLAEQ LL TYSCEAWGGS NCLELAVEAR DQQFIAQPGV QNFLSKQWYG EISRDTKNWK IIMCLFFFPL IGCGFISFRK KPVEKSKK L FLYYVSFFTS PFVVFSWNVI FYIAFLLLFA YVLLMDFQKE PTALEIILYV LVFVLLCDEV RQWYMNGSKY FSDLWNVMD TLAIFYFIAG IVFRLHSDES SWYSGRVIFC LDYIVFTLRL IHIFTVSRNL GPKIIMLQRM MIDVFFFLFL FAVWMVAFGV ARQGILRKN EHRWEWIFRS VIYEPYLAMF GQVPSDVDGT TYDFAHCTFT GNESKPLCVE LDEHNLPRFP EWITIPLVCI Y MLSTNILL VNLLVAMFGY TVGSVQENND QVWKFQRFFL VQEYCSRLTI PFPFVIFAYI FMVMRKCFKC CCNKESKEPS IC CSRNEDN EILAWEAVMK ENYLVKINTK ANDSSEEMVH RFRQLDAKLS DLKGLLKEIS SKIK

UniProtKB: Transient receptor potential cation channel subfamily M member 8

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
20.0 mMC8H18N2O4SHEPES
0.0025 mMC56H92O25glyco-diosgenin
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 4 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 19158 / Average exposure time: 2.0 sec. / Average electron dose: 47.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 1720102
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: An initial model determined ab initio from a subset of images in the same dataset. This model was used for subsequent refinement steps.
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Number images used: 73172
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4)

+
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