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- EMDB-51377: Cryo-EM structure of human SLC45A4 in detergent -

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Basic information

Entry
Database: EMDB / ID: EMD-51377
TitleCryo-EM structure of human SLC45A4 in detergent
Map data
Sample
  • Complex: SLC45A4
    • Protein or peptide: Solute carrier family 45 member 4
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: water
KeywordsSLC / MFS / Polyamine / Spermidine / TRANSPORT PROTEIN
Function / homologysucrose:proton symporter activity / sucrose transport / Major facilitator superfamily / Major Facilitator Superfamily / MFS transporter superfamily / membrane / Solute carrier family 45 member 4
Function and homology information
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsMarkusson S / Deme JC / Lea SM / Newstead S
Funding support United Kingdom, United States, 3 items
OrganizationGrant numberCountry
Wellcome Trust215519/Z/19/Z United Kingdom
Wellcome Trust219531/Z/19/Z United Kingdom
National Institutes of Health/National Cancer Institute (NIH/NCI)Intramural Research Program United States
CitationJournal: J Struct Biol / Year: 2020
Title: WITHDRAWN: SIMPLE 3.0. Stream single-particle cryo-EM analysis in real time.
Authors: Joseph Caesar / Cyril F Reboul / Chiara Machello / Simon Kiesewetter / Molly L Tang / Justin C Deme / Steven Johnson / Dominika Elmlund / Susan M Lea / Hans Elmlund /
History
DepositionAug 19, 2024-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51377.png

Downloads & links

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Map

FileDownload / File: emd_51377.map.gz / Format: CCP4 / Size: 229.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 392 pix.
= 286.944 Å		0.73 Å/pix.
x 392 pix.
= 286.944 Å		0.73 Å/pix.
x 392 pix.
= 286.944 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.732 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.8172057 - 2.4478252
Average (Standard dev.)-0.00036500502 (±0.030801035)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions392392392
Spacing392392392
CellA=B=C: 286.944 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51377_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_51377_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_51377_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 : SLC45A4

EntireName: SLC45A4
Components
  • Complex: SLC45A4
    • Protein or peptide: Solute carrier family 45 member 4
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: water

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Supramolecule #1: SLC45A4

SupramoleculeName: SLC45A4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Solute carrier family 45 member 4

MacromoleculeName: Solute carrier family 45 member 4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 84.750562 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MKMAPQNADP ESMQVQELSV PLPDPQKAGG AEAENCETIS EGSIDRIPMR LWVMHGAVMF GREFCYAMET ALVTPILLQI GLPEQYYSL TWFLSPILGL IFTPLIGSAS DRCTLSWGRR RPFILALCVG VLFGVALFLN GSAIGLALGD VPNRQPIGIV L TVLGVVVL ...String:
MKMAPQNADP ESMQVQELSV PLPDPQKAGG AEAENCETIS EGSIDRIPMR LWVMHGAVMF GREFCYAMET ALVTPILLQI GLPEQYYSL TWFLSPILGL IFTPLIGSAS DRCTLSWGRR RPFILALCVG VLFGVALFLN GSAIGLALGD VPNRQPIGIV L TVLGVVVL DFSADATEGP IRAYLLDVVD SEEQDMALNI HAFSAGLGGA IGYVLGGLDW TQTFLGSWFR TQNQVLFFFA AI IFTVSVA LHLFSIDEEQ YSPQQERSAE EPGALDGGEP HGVPAFPDEV QSEHELALDY PDVDIMRSKS DSALHVPDTA LDL EPELLF LHDIEPSIFH DASYPATPRS TSQELAKTKL PRLATFLKEA AKEDETLLDN HLNEAKVPNG SGSPTKDALG GYTR VDTKP SATSSSMRRR RHAFRRQASS TFSYYGKLGS HCYRYRRANA VVLIKPSRSM SDLYDMQKRQ RQHRHRNQSG ATTSS GDTE SEEGEGETTV RLLWLSMLKM PRELMRLCLC HLLTWFSVIA EAVFYTDFMG QVIFEGDPKA PSNSTAWQAY NAGVKM GCW GLVIYAATGA ICSALLQKYL DNYDLSVRVI YVLGTLGFSV GTAVMAMFPN VYVAMVTIST MGIVSMSISY CPYALLG QY HDIKQYIHHS PGNSKRGFGI DCAILSCQVY ISQILVASAL GGVVDAVGTV RVIPMVASVG SFLGFLTATF LVIYPNVS E EAKEEQKGLS SPLAGEGRAG GNSEKPTVLK LTRKEGLQGP VETESVVENL YFQ

UniProtKB: Solute carrier family 45 member 4

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Macromolecule #2: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 2 / Number of copies: 7 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Macromolecule #3: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 3 / Number of copies: 1 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

ChemComp-3PE:
1,2-Distearoyl-sn-glycerophosphoethanolamine / phospholipid*YM

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 17 / 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

Concentration0.3 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 21269 / Average electron dose: 57.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 165000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 700436
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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