[English] 日本語
Yorodumi
- EMDB-74047: C3 local refinement of Urea Transporter B (SLC14A1) bound to huma... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-74047
TitleC3 local refinement of Urea Transporter B (SLC14A1) bound to human stomatin oligomer
Map dataUnsharpened map
Sample
  • Complex: Local refinement of UT-B in complex with Stomatin.
    • Protein or peptide: Urea transporter 1
  • Ligand: PHOSPHATIDYLETHANOLAMINE
KeywordsMembrane protein / solute carrier / SLC / SPFH / TRANSPORT PROTEIN
Function / homology
Function and homology information


urea channel activity / water transmembrane transporter activity / urea transport / : / urea transmembrane transport / urea transmembrane transporter activity / establishment of localization in cell / transmembrane transport / basolateral plasma membrane / plasma membrane
Similarity search - Function
Urea transporter / Urea transporter / Ammonium/urea transporter
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsVallese F / Clarke OB
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Stomatin encapsulates aquaporin-1 and urea transporter-B in the erythrocyte membrane
Authors: Vallese F / Li H / Clarke OB
History
DepositionNov 24, 2025-
Header (metadata) releaseFeb 25, 2026-
Map releaseFeb 25, 2026-
UpdateFeb 25, 2026-
Current statusFeb 25, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_74047.png

Downloads & links

-
Map

FileDownload / File: emd_74047.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 300 pix.
= 249.9 Å		0.83 Å/pix.
x 300 pix.
= 249.9 Å		0.83 Å/pix.
x 300 pix.
= 249.9 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.833 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.049696047 - 0.098318376
Average (Standard dev.)0.0015589198 (±0.0051506143)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 249.9 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_74047_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Sharpened map (B=-61.8)

Fileemd_74047_additional_1.map
AnnotationSharpened map (B=-61.8)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map A

Fileemd_74047_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map B

Fileemd_74047_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Local refinement of UT-B in complex with Stomatin.

EntireName: Local refinement of UT-B in complex with Stomatin.
Components
  • Complex: Local refinement of UT-B in complex with Stomatin.
    • Protein or peptide: Urea transporter 1
  • Ligand: PHOSPHATIDYLETHANOLAMINE

-
Supramolecule #1: Local refinement of UT-B in complex with Stomatin.

SupramoleculeName: Local refinement of UT-B in complex with Stomatin. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Urea transporter 1

MacromoleculeName: Urea transporter 1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.753828 KDa
SequenceString: FPKALGYVTG DMKELANQLK DKPVVLQFID WILRGISQVV FVNNPVSGIL ILVGLLVQNP WWALTGWLGT VVSTLMALLL SQDRSLIAS GLYGYNATLV GVLMAVFSDK GDYFWWLLLP VCAMSMTCPI FSSALNSVLS KWDLPVFTLP FNMALSMYLS A TGHYNPFF ...String:
FPKALGYVTG DMKELANQLK DKPVVLQFID WILRGISQVV FVNNPVSGIL ILVGLLVQNP WWALTGWLGT VVSTLMALLL SQDRSLIAS GLYGYNATLV GVLMAVFSDK GDYFWWLLLP VCAMSMTCPI FSSALNSVLS KWDLPVFTLP FNMALSMYLS A TGHYNPFF PAKLVIPITT APQISWSDLS ALELLKSIPV GVGQIYGCDN PWTGGIFLGA ILLSSPLMCL HAAIGSLLGI AA GLSLSAP FENIYFGLWG FNSSLACIAM GGMFMALTWQ THLLALGCAL FTAYLGVGMA NFMAEVGLPA CTWPFCLATL LFL IMTTKN SNIYKMPLSK VTYPEENRIF YLQAKKRMV

UniProtKB: Urea transporter 1

-
Macromolecule #2: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 2 / Number of copies: 6 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 258739
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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