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- EMDB-49571: Cryo-EM structure of Serendipita indica sulfate transporter SiSul... -

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Basic information

Entry
Database: EMDB / ID: EMD-49571
TitleCryo-EM structure of Serendipita indica sulfate transporter SiSulT in oxlate bound state
Map dataSharpened final map used for model building.
Sample
  • Complex: Sulphate transporter with oxlate
    • Protein or peptide: Probable Sulfate permease
  • Ligand: OXALATE ION
  • Ligand: water
KeywordsTransporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


sulfate import across plasma membrane / sulfate transmembrane transporter activity / membrane
Similarity search - Function
SLC26A/SulP transporter / SLC26A/SulP transporter domain / Sulfate permease family / STAS domain / STAS domain profile. / STAS domain / STAS domain superfamily
Similarity search - Domain/homology
Probable Sulfate permease
Similarity search - Component
Biological speciesSerendipita indica (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsKhandelwal NK / Kumar P / Gupta M / Finer-Moore J / Stroud RM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM024485 United States
CitationJournal: To Be Published
Title: Cryo-EM structure of Serendipita indica sulfate transporter SiSulT in oxlate bound state
Authors: Khandelwal NK / Kumar P / Gupta M / Finer-Moore J / Stroud RM
History
DepositionMar 5, 2025-
Header (metadata) releaseMar 11, 2026-
Map releaseMar 11, 2026-
UpdateMar 11, 2026-
Current statusMar 11, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49571.png

Downloads & links

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Map

FileDownload / File: emd_49571.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened final map used for model building.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 440 pix.
= 360.316 Å		0.82 Å/pix.
x 440 pix.
= 360.316 Å		0.82 Å/pix.
x 440 pix.
= 360.316 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8189 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.55
Minimum - Maximum-2.3598218 - 3.9041386
Average (Standard dev.)-0.0012548408 (±0.057850905)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 360.316 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_49571_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened final map used for model building.

Fileemd_49571_additional_1.map
AnnotationUnsharpened final map used for model building.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_49571_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_49571_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Sulphate transporter with oxlate

EntireName: Sulphate transporter with oxlate
Components
  • Complex: Sulphate transporter with oxlate
    • Protein or peptide: Probable Sulfate permease
  • Ligand: OXALATE ION
  • Ligand: water

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Supramolecule #1: Sulphate transporter with oxlate

SupramoleculeName: Sulphate transporter with oxlate / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Serendipita indica (fungus)
Molecular weightTheoretical: 206.65154 KDa

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Macromolecule #1: Probable Sulfate permease

MacromoleculeName: Probable Sulfate permease / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Serendipita indica (fungus)
Molecular weightTheoretical: 88.222195 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MASDYKDDDD KGALEVLFQG PSSPGAATVK RLAKKIVSAP EEAPPTVSSG DWIKSQLEGE TPKTAVVHYL KSLFPVIQWA PNYNIGWLY GDVVAGLTVG LVLIPQSMSY ARLATLPTEY GLYASFVGVF IYCFFATSKD VSIGPVAVMS LEVANIIKYV Q SHYGDRWG ...String:
MASDYKDDDD KGALEVLFQG PSSPGAATVK RLAKKIVSAP EEAPPTVSSG DWIKSQLEGE TPKTAVVHYL KSLFPVIQWA PNYNIGWLY GDVVAGLTVG LVLIPQSMSY ARLATLPTEY GLYASFVGVF IYCFFATSKD VSIGPVAVMS LEVANIIKYV Q SHYGDRWG NVQIAVTLSF ICGFIVLGIG LLRIGWIVEF IPTPAVAGFM TGSAITIVSS QVPGLFGIQN LLDTRTSAYK VI INTLKNL GHSKKDAAFG VTGLFALYFI RWIFDYLGRR YPNRARTFFY LSVMRNAFVL IILTLAAWGV VRYEKPDKKG NYS ISILKT VPRGFKHIGQ PTIDPELLKG LGSHLFVATL ILLLEHIAIS KSFGRINGYK INPNQELIAI GVTNTIGTLF AAYP ATGSF SRSALKSKCG VRTPAAGWVT GLVVIVALYG LTDAFFFIPT AGLSAIIVHA VADLVTPPSQ VYRFWLISPL EFLIW AAAV LVSIFSSIEN GIYTSVAASL VLLLIRVARP GGQFLGKVKV HGDDNSTSRD VFVPLEPKGG LRNPHIIVEP AAPGVF IFR LEESFTFPNS SLINSTVVDH IKEHTRRGKD VSLIRLIDRP WNDPGPRRGA AFDPKAQDTS KPLLKAVVLD FAAVGNI DT TGVQNLIDTR KELENWADGP VEFHFANILS PWVRRGLVAG GFGTGKDVDF PAEVAPVVPN QSGDYADPDH QTPHLRHR E EWISKTGTTK TDKTEADVES GDSEYRKSNS PSSSVEGPLL STLTPFFHVD LASAVRVAEA RAKRSTPGLV PRGSSAHHH HHHHHHHGA

UniProtKB: Probable Sulfate permease

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Macromolecule #2: OXALATE ION

MacromoleculeName: OXALATE ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: OXL
Molecular weightTheoretical: 88.019 Da
Chemical component information

ChemComp-OXL:
OXALATE ION

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 4 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration.9 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
300.0 mMNaClsodium chloride
50.0 mMTris-ClTris chloride

Details: 50 mM Tirs ,300mM Nacl pH7.5- LMNG0.01%+.001%CHS
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Pressure: 330.0 kPa / Details: 30 glow 30 hold at 15mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281.81 K / Instrument: FEI VITROBOT MARK IV
DetailsSult-0.9mg /ml with +100mM Potassium oxalate monohydrate

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 10668 / Average exposure time: 0.8189 sec. / Average electron dose: 47.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 5967145
CTF correctionSoftware - Name: cryoSPARC (ver. v4.2.1) / Type: NONE
Startup modelType of model: INSILICO MODEL / In silico model: Ab initio model
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.2.1) / Number images used: 376034
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.2.1)
Final 3D classificationNumber classes: 2 / Software - Name: cryoSPARC (ver. v4.2.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

9nf7


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
Details1:1
RefinementProtocol: AB INITIO MODEL / Overall B value: 89.8
Output model

PDB-9nnc:
Cryo-EM structure of Serendipita indica sulfate transporter SiSulT in oxlate bound state

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