[English] 日本語
Yorodumi
- EMDB-52217: Cryo-EM structure of the Arabidopsis thaliana CAT4 transporter in... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-52217
TitleCryo-EM structure of the Arabidopsis thaliana CAT4 transporter in the outward-open apo state
Map dataSharpened EM map
Sample
  • Organelle or cellular component: Complex of Arabidopsis thaliana cationic amino acid transporter 4 with a synthetic nanobody and cholesterol
    • Protein or peptide: SybB5
    • Protein or peptide: Cationic amino acid transporter 4, vacuolar
  • Ligand: CHOLESTEROL
  • Ligand: Lauryl Maltose Neopentyl Glycol
  • Ligand: water
Keywordscationic amino acid transporter / APC fold / LeuT fold / cholesterol / outward-open state / cationic amino acids / SLC7 / MEMBRANE PROTEIN
Function / homologyCationic amino acid transporter, C-terminal / C-terminus of AA_permease / plant-type vacuole membrane / Amino acid/polyamine transporter I / Amino acid permease / plant-type vacuole / amino acid transport / transmembrane transporter activity / Cationic amino acid transporter 4, vacuolar
Function and homology information
Biological speciesArabidopsis thaliana (thale cress) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsKolokouris D / Kato T / Newstead S
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M011224/1 United Kingdom
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionNov 29, 2024-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_52217.png

Downloads & links

-
Map

FileDownload / File: emd_52217.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened EM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 212.992 Å		0.83 Å/pix.
x 256 pix.
= 212.992 Å		0.83 Å/pix.
x 256 pix.
= 212.992 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.7193589 - 2.6259632
Average (Standard dev.)0.0012260575 (±0.059999675)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.992 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Unsharpened EM map

Fileemd_52217_additional_1.map
AnnotationUnsharpened EM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_52217_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_52217_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Complex of Arabidopsis thaliana cationic amino acid transporter 4...

EntireName: Complex of Arabidopsis thaliana cationic amino acid transporter 4 with a synthetic nanobody and cholesterol
Components
  • Organelle or cellular component: Complex of Arabidopsis thaliana cationic amino acid transporter 4 with a synthetic nanobody and cholesterol
    • Protein or peptide: SybB5
    • Protein or peptide: Cationic amino acid transporter 4, vacuolar
  • Ligand: CHOLESTEROL
  • Ligand: Lauryl Maltose Neopentyl Glycol
  • Ligand: water

-
Supramolecule #1: Complex of Arabidopsis thaliana cationic amino acid transporter 4...

SupramoleculeName: Complex of Arabidopsis thaliana cationic amino acid transporter 4 with a synthetic nanobody and cholesterol
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #2, #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)

-
Macromolecule #1: Cationic amino acid transporter 4, vacuolar

MacromoleculeName: Cationic amino acid transporter 4, vacuolar / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 59.39016 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: PHQLAKKLSA VDLVAIGVGT TIGAGVYILV GTVAREHTGP ALAVSFFIAG VAAALSACCY AELASRCPSA GSAYHYAYIC LGEGIAWLV GWALVLDYTI GGSAIARGIT PNLASFFGGL DNLPVFLARQ TIPGVGIVVD PCAALLIMIV TILLCFGIKE S STVQAIVT ...String:
PHQLAKKLSA VDLVAIGVGT TIGAGVYILV GTVAREHTGP ALAVSFFIAG VAAALSACCY AELASRCPSA GSAYHYAYIC LGEGIAWLV GWALVLDYTI GGSAIARGIT PNLASFFGGL DNLPVFLARQ TIPGVGIVVD PCAALLIMIV TILLCFGIKE S STVQAIVT SVNVCTLVFI IVVGGYLACK TGWVGYDLPS GYFPFGLNGI LAGSAVVFFS YIGFDTVTST AEEVKNPQRD LP LGIGIAL LICCILYMLL SVVIVGLVPY YSLNPDTPIS SAFGDSGMQW AAYILTTGAI TALCASLLGS LLAQPRIFMA MAR DGLLPA FFSEISPRTQ VPVKSTIAIG VLAAALAFFM DVAQLSEMVS VGTLMAFTAV AVCVLVLRYV PPDGVPLSSS SQTL SDTDE SRAETENFLV DAIESSDSPL LGNETARDEK YFGKRRKIAA WSIALVCIGV LGLASAASAE RLPSFPRFTI CGVSA VILL GSLITLGYID EDEERHNFGH KGGFLCPFVP YLPVLCILIN TYLIINIGAG TWIRVLIWLL IGSMIYIFYG RSHSLL NN

UniProtKB: Cationic amino acid transporter 4, vacuolar

-
Macromolecule #2: SybB5

MacromoleculeName: SybB5 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 12.826291 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSSSQVQLVE SGGGLVQAGG SLRLSCAASG FPVNMYWMHW YRQAPGKERE WVAAIQSYGQ WTAYADSVKG RFTISRDNAK NTVYLQMNS LKPEDTAVYY CAVGVGGYYL GQGTQVTVS

-
Macromolecule #3: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 3 / Number of copies: 1 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

-
Macromolecule #4: Lauryl Maltose Neopentyl Glycol

MacromoleculeName: Lauryl Maltose Neopentyl Glycol / type: ligand / ID: 4 / Number of copies: 1 / Formula: AV0
Molecular weightTheoretical: 1.005188 KDa
Chemical component information

ChemComp-AV0:
Lauryl Maltose Neopentyl Glycol

-
Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 1 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3.4 mg/mL
BufferpH: 7.5 / Details: 20 mM Tris-HCl, 150 mM NaCl, 0.003% w/v LMNG
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsThe sample was homogeneously monodisperse.

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 3.0 sec. / 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: 1.0 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: 11166793
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 642325
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

3-f1


Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: cross-correlation coefficient
Output model

PDB-9hjk:
Cryo-EM structure of the Arabidopsis thaliana CAT4 transporter in the outward-open apo state

+
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