[English] 日本語
Yorodumi
- EMDB-35017: Cryo-EM structure of human TMEM87A, gluconate-bound -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-35017
TitleCryo-EM structure of human TMEM87A, gluconate-bound
Map data
Sample
  • Organelle or cellular component: Transmembrane protein 87A with GFP tag and Twin-strep tag with gluconateTransmembrane protein
    • Protein or peptide: Transmembrane protein 87A,EGFPTransmembrane protein
  • Ligand: D-gluconic acid
Keywordsnon-selective cation channel / ion channel / membrane protein / Golgi-localized protein
Function / homology
Function and homology information


retrograde transport, endosome to Golgi / Golgi cisterna membrane / RHOA GTPase cycle / ruffle / bioluminescence / generation of precursor metabolites and energy / cellular response to mechanical stimulus / Golgi membrane / Golgi apparatus / plasma membrane / cytosol
Similarity search - Function
Transmembrane protein GPR107/GPR108-like / GOST, seven transmembrane domain / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
EGFP / Transmembrane protein 87A
Similarity search - Component
Biological speciesHomo sapiens (human) / Human adenovirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsHan A / Kim HM
Funding support Korea, Republic Of, 1 items
OrganizationGrant numberCountry
Other governmentIBS-R030-C1 Korea, Republic Of
CitationJournal: To Be Published
Title: Cryo-EM structure of human TMEM87A, PE-bound
Authors: Han A / Kim HM
History
DepositionDec 21, 2022-
Header (metadata) releaseDec 27, 2023-
Map releaseDec 27, 2023-
UpdateDec 27, 2023-
Current statusDec 27, 2023Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_35017.png

Downloads & links

-
Map

FileDownload / File: emd_35017.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.849 Å
Density
Contour LevelBy AUTHOR: 0.101
Minimum - Maximum-0.29120538 - 0.5151153
Average (Standard dev.)-0.000303486 (±0.009581631)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 271.68 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_35017_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_35017_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Transmembrane protein 87A with GFP tag and Twin-strep tag with gl...

EntireName: Transmembrane protein 87A with GFP tag and Twin-strep tag with gluconateTransmembrane protein
Components
  • Organelle or cellular component: Transmembrane protein 87A with GFP tag and Twin-strep tag with gluconateTransmembrane protein
    • Protein or peptide: Transmembrane protein 87A,EGFPTransmembrane protein
  • Ligand: D-gluconic acid

-
Supramolecule #1: Transmembrane protein 87A with GFP tag and Twin-strep tag with gl...

SupramoleculeName: Transmembrane protein 87A with GFP tag and Twin-strep tag with gluconate
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Transmembrane protein 87A with GFP tag and Twin-strep tag with gluconate purified with detergent LMNG/CHS
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Transmembrane protein 87A,EGFP

MacromoleculeName: Transmembrane protein 87A,EGFP / type: protein_or_peptide / ID: 1
Details: The chimera of Transmembrane protein 87A, Linkers, EGFP and Tags
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human adenovirus 2
Molecular weightTheoretical: 97.965617 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAAAAWLQVL PVILLLLGAH PSPLSFFSAG PATVAAADRS KWHIPIPSGK NYFSFGKILF RNTTIFLKFD GEPCDLSLNI TWYLKSADC YNEIYNFKAE EVELYLEKLK EKRGLSGKYQ TSSKLFQNCS ELFKTQTFSG DFMHRLPLLG EKQEAKENGT N LTFIGDKT ...String:
MAAAAWLQVL PVILLLLGAH PSPLSFFSAG PATVAAADRS KWHIPIPSGK NYFSFGKILF RNTTIFLKFD GEPCDLSLNI TWYLKSADC YNEIYNFKAE EVELYLEKLK EKRGLSGKYQ TSSKLFQNCS ELFKTQTFSG DFMHRLPLLG EKQEAKENGT N LTFIGDKT AMHEPLQTWQ DAPYIFIVHI GISSSKESSK ENSLSNLFTM TVEVKGPYEY LTLEDYPLMI FFMVMCIVYV LF GVLWLAW SACYWRDLLR IQFWIGAVIF LGMLEKAVFY AEFQNIRYKG ESVQGALILA ELLSAVKRSL ARTLVIIVSL GYG IVKPRL GVTLHKVVVA GALYLLFSGM EGVLRVTGAQ TDLASLAFIP LAFLDTALCW WIFISLTQTM KLLKLRRNIV KLSL YRHFT NTLILAVAAS IVFIIWTTMK FRIVTCQSDW RELWVDDAIW RLLFSMILFV IMVLWRPSAN NQRFAFSPLS EEEEE DEQK EPMLKESFEG MKMRSTKQEP NGNSKVNKAQ EDDLKWVEEN VPSSVTDVAL PALLDSDEER MITHFERSKM ELKENL YFQ GGTLEVLFQG PNPAFLYKVV DPVVSKGEEL FTGVVPILVE LDGDVNGHKF SVSGEGEGDA TYGKLTLKFI CTTGKLP VP WPTLVTTLTY GVQCFSRYPD HMKQHDFFKS AMPEGYVQER TIFFKDDGNY KTRAEVKFEG DTLVNRIELK GIDFKEDG N ILGHKLEYNY NSHNVYIMAD KQKNGIKVNF KIRHNIEDGS VQLADHYQQN TPIGDGPVLL PDNHYLSTQS ALSKDPNEK RDHMVLLEFV TAAGITLGMD ELYKEFLVPR GSSRSAWSHP QFEKGGGSGG GSGGSAWSHP QFEK

UniProtKB: Transmembrane protein 87A, EGFP

-
Macromolecule #4: D-gluconic acid

MacromoleculeName: D-gluconic acid / type: ligand / ID: 4 / Number of copies: 1 / Formula: GCO
Molecular weightTheoretical: 196.155 Da
Chemical component information

ChemComp-GCO:
D-gluconic acid / Gluconic acid

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.7 mg/mL
BufferpH: 9
Component:
ConcentrationFormulaName
50.0 mMHEPES4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
250.0 mMNaClSodium chlorideSodium Chloride
0.01 % (w/v)LMNGlauryl maltose neopentyl glycol
0.002 % (w/v)CHSCholesteryl hemisuccinate

Details: 50mM HEPES pH 7.5, 250mM NaCl, 0.01% (w/v) LMNG, 0.002% (w/v) CHS
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsThis sample was monodisperse

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated magnification: 58900 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Alignment procedureComa free - Residual tilt: 10.0 mrad
DetailsUsing Zemlin tableau in sherpa
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 13099 / Average exposure time: 6.14 sec. / Average electron dose: 68.15 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 6035205
Details: The previous model was used as a template for particle picking. 2D class average images were generated as templates for subsequent reference-based auto-picking.
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8hsi

Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 3.3.2) / Software - details: Ab-intio reconstruction
Final 3D classificationNumber classes: 6 / Avg.num./class: 513049 / Software - Name: cryoSPARC (ver. 3.3.2) / Software - details: Hetero refinement
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2) / Software - details: Non-uniform refinement
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) / Software - details: Local refinement
Details: Non-uniform refinement and CTF refinement were used to improve the particle alignment and map quality.
Number images used: 201915
FSC plot (resolution estimation)

-
Atomic model buiding 1

DetailsChimera Fit in map tool was used for initial local fitting. Then, Real-space refinement with the rigid body option in PHENIX was used for flexible fitting.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 40
Output model

PDB-8htt:
Cryo-EM structure of human TMEM87A, gluconate-bound

+
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