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- EMDB-61818: AtALMT1 with LMNG and sterol mimic CHS -

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Basic information

Entry
Database: EMDB / ID: EMD-61818
TitleAtALMT1 with LMNG and sterol mimic CHS
Map data
Sample
  • Complex: AtALMT1 with LMNG and sterol mimic CHS
    • Protein or peptide: Aluminum-activated malate transporter 1
KeywordsPlant / Channel / MEMBRANE PROTEIN
Function / homologymalate transmembrane transport / malate transmembrane transporter activity / Aluminum-activated malate transporter / Aluminium activated malate transporter / response to aluminum ion / monoatomic ion transmembrane transport / plasma membrane / Aluminum-activated malate transporter 1
Function and homology information
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsLee Y / Lee S
Funding support Korea, Republic Of, 3 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2022R1A2C100988211 Korea, Republic Of
National Research Foundation (NRF, Korea)RS-2023-00223552 Korea, Republic Of
National Research Foundation (NRF, Korea)2021M3A9I4022936 Korea, Republic Of
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Real-space refinement in PHENIX for cryo-EM and crystallography.
Authors: Pavel V Afonine / Billy K Poon / Randy J Read / Oleg V Sobolev / Thomas C Terwilliger / Alexandre Urzhumtsev / Paul D Adams /
Abstract: This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast ...This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast calculation, which in turn makes it possible to identify optimal data-restraint weights as part of routine refinements with little runtime cost. Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available. In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary-structure and rotamer-specific restraints, as well as restraints or constraints on internal molecular symmetry. The re-refinement of 385 cryo-EM-derived models available in the Protein Data Bank at resolutions of 6 Å or better shows significant improvement of the models and of the fit of these models to the target maps.
History
DepositionOct 7, 2024-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateMar 12, 2025-
Current statusMar 12, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61818.png

Downloads & links

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Map

FileDownload / File: emd_61818.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 300 pix.
= 252. Å		0.84 Å/pix.
x 300 pix.
= 252. Å		0.84 Å/pix.
x 300 pix.
= 252. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.154
Minimum - Maximum-0.754256 - 1.2379686
Average (Standard dev.)0.0011912865 (±0.021908402)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 251.99998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61818_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61818_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : AtALMT1 with LMNG and sterol mimic CHS

EntireName: AtALMT1 with LMNG and sterol mimic CHS
Components
  • Complex: AtALMT1 with LMNG and sterol mimic CHS
    • Protein or peptide: Aluminum-activated malate transporter 1

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Supramolecule #1: AtALMT1 with LMNG and sterol mimic CHS

SupramoleculeName: AtALMT1 with LMNG and sterol mimic CHS / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Aluminum-activated malate transporter 1

MacromoleculeName: Aluminum-activated malate transporter 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 55.146891 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MEKVREIVRE GIRVGNEDPR RIIHAFKVGL ALVLVSSFYY YQPFGPFTDY FGINAMWAVM TVVVVFEFSV GATLGKGLNR GVATLVAGG LGIGAHQLAR LSGATVEPIL LVMLVFVQAA LSTFVRFFPW VKTKFDYGIL IFILTFALIS LSGFRDEEIM D LAESRLST ...String:
MEKVREIVRE GIRVGNEDPR RIIHAFKVGL ALVLVSSFYY YQPFGPFTDY FGINAMWAVM TVVVVFEFSV GATLGKGLNR GVATLVAGG LGIGAHQLAR LSGATVEPIL LVMLVFVQAA LSTFVRFFPW VKTKFDYGIL IFILTFALIS LSGFRDEEIM D LAESRLST VVIGGVSCIL ISIFVCPVWA GQDLHSLLAS NFDTLSHFLQ DFGDEYFEAR EKGDYKVVEK RKKNLERYKS VL DSKSDEE ALANYAEWEP PHGQFRFRHP WKQYVAVGAL LRQCAYRIDA LNSYINSDFQ IPVDIKKKLE TPLRRMSSES GNS MKEMSI SLKQMIKSSS SDIHVSNSQA ACKSLSTLLK SGILNDVEPL QMISLMTTVS MLIDIVNLTE KISESVHELA SAAR FKNKM RPTVLYEKSD SGSIGRAMPI DSHEDHHVVT VLHDVDNDRS NNVDDSRGGS SQDSCHHVAI KIVDDNSNHE KHEDG EIHV HTLSNGHLQ

UniProtKB: Aluminum-activated malate transporter 1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.84 mg/mL
BufferpH: 7.6
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
150.0 mMNaClSodium chloride
1.0 mMC9H15O6PTCEP
0.005 % (w/v)C47H88O22LMNG
0.001 % (w/v)C31H50O4CHS
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 100000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 459873
Startup modelType of model: NONE
Final reconstructionNumber classes used: 4 / Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5) / Number images used: 84451
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5) / Details: NU-refinement
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5) / Details: NU-refinement
Final 3D classificationNumber classes: 5 / Avg.num./class: 20032 / Software - Name: cryoSPARC (ver. 4.5)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7vq4


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-9jtw:
AtALMT1 with LMNG and sterol mimic CHS

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