[English] 日本語
Yorodumi
- EMDB-74433: Low-resolution electron density map of C. elegans PEZO-1 Isoform L -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-74433
TitleLow-resolution electron density map of C. elegans PEZO-1 Isoform L
Map data
Sample
  • Complex: C. elegans PEZO-1 Isoform L
    • Protein or peptide: C. elegans PEZO-1 Isoform L
KeywordsPEZO-1 / Piezo / Mechanosensation / MEMBRANE PROTEIN
Biological speciesCaenorhabditis elegans (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.1 Å
AuthorsBell B / Vasquez V
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM153208 United States
CitationJournal: To Be Published
Title: Low-resolution electron density map of PEZO-1 Isoform L
Authors: Bell B / Jaramillo-Granada A / Orlin DJ / Weng W-H / Wen H / Sotomayor M / Chesler AT / Baker ML / Cordero-Morales JF / Vasquez V
History
DepositionDec 12, 2025-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_74433.png

Downloads & links

-
Map

FileDownload / File: emd_74433.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 400 pix.
= 432. Å		1.08 Å/pix.
x 400 pix.
= 432. Å		1.08 Å/pix.
x 400 pix.
= 432. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0677
Minimum - Maximum-0.14985436 - 0.35854053
Average (Standard dev.)0.00012682987 (±0.010426695)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 432.00003 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_74433_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_74433_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : C. elegans PEZO-1 Isoform L

EntireName: C. elegans PEZO-1 Isoform L
Components
  • Complex: C. elegans PEZO-1 Isoform L
    • Protein or peptide: C. elegans PEZO-1 Isoform L

-
Supramolecule #1: C. elegans PEZO-1 Isoform L

SupramoleculeName: C. elegans PEZO-1 Isoform L / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Caenorhabditis elegans (invertebrata)

-
Macromolecule #1: C. elegans PEZO-1 Isoform L

MacromoleculeName: C. elegans PEZO-1 Isoform L / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFKYDPENDD LVEPVDSFVP EVDPKATAYD RLDPGQIMYA ATAHDLDLAK TVQQVKKGDT IKDPDSRALI AVSEPEARKP GGTEETDGDE DEDNKDSKVE STAKFIQKMI ASALDLCSVT LNKLCREHRY VGFVLSKEKQ KLKSGHSESL SNTSRKLTDI RSAVDLPSLQ ...String:
MFKYDPENDD LVEPVDSFVP EVDPKATAYD RLDPGQIMYA ATAHDLDLAK TVQQVKKGDT IKDPDSRALI AVSEPEARKP GGTEETDGDE DEDNKDSKVE STAKFIQKMI ASALDLCSVT LNKLCREHRY VGFVLSKEKQ KLKSGHSESL SNTSRKLTDI RSAVDLPSLQ LVQSANDVEK METAVSVDWQ QKSSATRLLN AVVNCIGAHT DILCYFFAIM TQVMTGGLIT LPLPLMSLFW GNLSNPRPSK FFWVTMITYT ECVIVIKFVC QFAFMPYNSI TWRTEHQMDP MSLDKLFGVS QRDSFALWDI VLLFSLFFHR YMLRKLGLWK DANLTDTFTL KEEPRSASGS DTGSPKKIAQ EPKVVVTQSD TLEGTSGGEI VIPSDPNAVS NMEELDCEPP IPEKQSGPIG RFIHQLFHPK FRYIRDLYPI MFGIDVICFL IMTFGYSAFG EGGSGNVLDD VKASRIPVTL VVMLVGMTLA IIIDRALYLR KSVVGKLIYQ VLMIAFLHIW VFLVLPNMTR RSAISNHVAQ ALYVIKSCYF LVSAWQIRNG YPELCIGNLL THSYGMTNMI AFKVFMNIPF LFELRTAIDW TWTDTSMPLF DFFNMENFYA HIFNIKCARQ FEAAYPAPRG IPKGKLVKYM MGFPIIIGVV IFIFSPLLLW SLLNQIGTIS MPEKVTLRIS IEGYPPLYEM EAQGSNHDNA ELGMIKPDQL ASLNQALTDS YTTRDTNSIL RSRMSVSYLK GYTYEDILIV RFRPESEIYW PISQDSRNAM IDKLSRNTSV NFEVSLEFTR PYDPNENAAL KHSKSWLVPI SLDMTIRAKI QSALRGDPGH PILIPQSIPA FIQVPNQGEL TLPTSIGNTI INDGNPRINT TGMEKSDEAR AWFDSLTLNL EQGKSQNEKM WIATSEHPGD QNAKLWIKTA NTTYSGRPYL QVVGFIDRAF PSFLAKVFKG GVIAVYLSVI LVVGRGLVRG IFTTSPSTVM FTELPNADHL LKICLDIYLV REAKDFMLEQ DLFAKLIFLF RSPATLIEWT RMSKKKQE

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 8.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 227008
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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