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- EMDB-41858: Structure of Apo Sialin at pH7.5 -

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Basic information

Entry
Database: EMDB / ID: EMD-41858
TitleStructure of Apo Sialin at pH7.5
Map data
Sample
  • Complex: Structure of Apo Sialin at pH7.5
    • Protein or peptide: Sialin
KeywordsTransporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


sialic acid:proton symporter activity / D-glucuronate transmembrane transporter activity / Defective SLC17A5 causes Salla disease (SD) and ISSD / Organic anion transporters / sialic acid transmembrane transporter activity / sialic acid transport / carbohydrate:proton symporter activity / Sialic acid metabolism / monoatomic anion transport / amino acid transport ...sialic acid:proton symporter activity / D-glucuronate transmembrane transporter activity / Defective SLC17A5 causes Salla disease (SD) and ISSD / Organic anion transporters / sialic acid transmembrane transporter activity / sialic acid transport / carbohydrate:proton symporter activity / Sialic acid metabolism / monoatomic anion transport / amino acid transport / monoatomic ion transport / response to bacterium / synaptic vesicle membrane / basolateral plasma membrane / lysosome / lysosomal membrane / membrane / plasma membrane / cytosol
Similarity search - Function
: / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsSchmiege P / Li X
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)135343 United States
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)110229 United States
Welch FoundationI-1957 United States
CitationJournal: To Be Published
Title: Structure of Apo Sialin at pH7.5
Authors: Schmiege P / Li X
History
DepositionSep 7, 2023-
Header (metadata) releaseMay 29, 2024-
Map releaseMay 29, 2024-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41858.png

Downloads & links

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Map

FileDownload / File: emd_41858.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.)
0.83 Å/pix.
x 300 pix.
= 249. Å		0.83 Å/pix.
x 300 pix.
= 249. Å		0.83 Å/pix.
x 300 pix.
= 249. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.668
Minimum - Maximum-2.840644 - 4.0758023
Average (Standard dev.)0.0031485297 (±0.08906626)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 249.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_41858_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_41858_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Structure of Apo Sialin at pH7.5

EntireName: Structure of Apo Sialin at pH7.5
Components
  • Complex: Structure of Apo Sialin at pH7.5
    • Protein or peptide: Sialin

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Supramolecule #1: Structure of Apo Sialin at pH7.5

SupramoleculeName: Structure of Apo Sialin at pH7.5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Sialin

MacromoleculeName: Sialin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.681137 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKR SPVRDLARND GEESTDRTPL LPGAPRAEAA PVCCSARYNL AILAFFGFFI VYALRVNLSV ALVDMVDSNT TLEDNRTSK ACPEHSAPIK VHHNQTGKKY QWDAETQGWI LGSFFYGYII TQIPGGYVAS KIGGKMLLGF GILGTAVLTL F TPIAADLG ...String:
MDYKDDDDKR SPVRDLARND GEESTDRTPL LPGAPRAEAA PVCCSARYNL AILAFFGFFI VYALRVNLSV ALVDMVDSNT TLEDNRTSK ACPEHSAPIK VHHNQTGKKY QWDAETQGWI LGSFFYGYII TQIPGGYVAS KIGGKMLLGF GILGTAVLTL F TPIAADLG VGPLIVLRAL EGLGEGVTFP AMHAMWSSWA PPLERSKLLS ISYAGAQLGT VISLPLSGII CYYMNWTYVF YF FGTIGIF WFLLWIWLVS DTPQKHKRIS HYEKEYILSS LRNQLSSQKS VPWVPILKSL PLWAIVVAHF SYNWTFYTLL TLL PTYMKE ILRFNVQENG FLSSLPYLGS WLCMILSGQA ADNLRAKWNF STLCVRRIFS LIGMIGPAVF LVAAGFIGCD YSLA VAFLT ISTTLGGFCS SGFSINHLDI APSYAGILLG ITNTFATIPG MVGPVIAKSL TPDNTVGEWQ TVFYIAAAIN VFGAI FFTL FAKGEVQNWA LNDHHGHRH

UniProtKB: Sialin

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 200101
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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