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- EMDB-19006: Lysosomal peptide transporter -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-19006
TitleLysosomal peptide transporter
Map data
Sample
  • Complex: GLMP-MFSD1
    • Protein or peptide: Major facilitator superfamily domain-containing protein 1
    • Protein or peptide: Glycosylated lysosomal membrane protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsMFS transporter / MFSD family / nutrition transporter / lysosomal transporter / outward open / MEMBRANE PROTEIN
Function / homology
Function and homology information


protein localization to lysosome / transmembrane transporter activity / lysosome / protein stabilization / lysosomal membrane / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / membrane / nucleus / cytosol
Similarity search - Function
Lysosomal transcription factor, NCU-G1 / Lysosomal transcription factor, NCU-G1 / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
Major facilitator superfamily domain-containing protein 1 / Glycosylated lysosomal membrane protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.08 Å
AuthorsJungnickel KEJ / Loew C
Funding support Germany, 1 items
OrganizationGrant numberCountry
Other government05K18YEA Germany
CitationJournal: Nature Cell Biology / Year: 2024
Title: MFSD1 with its accessory subunit GLMP functions as a general dipeptide uniporter in lysosomes
Authors: Jungnickel KEJ / Guelle O / Iguchi M / Dong W / Kotov V / Gabriel F / Debacker C / Dairou J / McCort-Tranchepain I / Laqtom NN / Chan SH / Ejima A / Sato K / Massa Lopez D / Saftig P / ...Authors: Jungnickel KEJ / Guelle O / Iguchi M / Dong W / Kotov V / Gabriel F / Debacker C / Dairou J / McCort-Tranchepain I / Laqtom NN / Chan SH / Ejima A / Sato K / Massa Lopez D / Saftig P / Mehdipour AR / Abu-Remaileh M / Gasnier B / Low C / Damme M
History
DepositionNov 29, 2023-
Header (metadata) releaseMay 1, 2024-
Map releaseMay 1, 2024-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19006.png

Downloads & links

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Map

FileDownload / File: emd_19006.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.443
Minimum - Maximum-2.9615512 - 4.0634503
Average (Standard dev.)0.0010480474 (±0.053601544)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 330.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_19006_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_19006_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 : GLMP-MFSD1

EntireName: GLMP-MFSD1
Components
  • Complex: GLMP-MFSD1
    • Protein or peptide: Major facilitator superfamily domain-containing protein 1
    • Protein or peptide: Glycosylated lysosomal membrane protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: GLMP-MFSD1

SupramoleculeName: GLMP-MFSD1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Major facilitator superfamily domain-containing protein 1

MacromoleculeName: Major facilitator superfamily domain-containing protein 1
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 55.765551 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEDEDGEDRA LLGGRREADS AVHGAPRALS ALCDPSRLAH RLVVLSLMCF LGFGSYFCYD NPAALQTQVK RDMQVNTTKF MLLYAWYSW PNVVLCFLGG FLIDRIFGIR WGTVIFSCFV CIGQVIFALG GIFNAFWLME LGRFVFGIGG ESLAVAQNTY A VSWFKGKE ...String:
MEDEDGEDRA LLGGRREADS AVHGAPRALS ALCDPSRLAH RLVVLSLMCF LGFGSYFCYD NPAALQTQVK RDMQVNTTKF MLLYAWYSW PNVVLCFLGG FLIDRIFGIR WGTVIFSCFV CIGQVIFALG GIFNAFWLME LGRFVFGIGG ESLAVAQNTY A VSWFKGKE LNLVFGLQLS MARIGSTVNM NLMGWLYGKI EALLGSAGHM TLGVTLMIGC ITCIFSLICA LALAYLDRRA EK ILHKEQG KTGEVIKLRD IKDFSLPLIL VFVICVCYYV AVFPFIGLGK VFFMEKFRFS SQSASAINSI VYIISAPMSP LFG LLVDKT GKNIIWVLYA VAATLVSHMM LAFTFWNPWI AMCLLGFSYS LLACALWPMV AFIVPEHQLG TAYGFMQSIQ NLGL AVIAI LAGMILDSKG YLLLEVFFIA CVSLSLLAVV CLYLVNRAQG GNLNYSAKQR ERMKLSHPEI IILEVLFQGP SSGWS HPQF EKGGGSGGGS GGSAWSHPQF EK

UniProtKB: Major facilitator superfamily domain-containing protein 1

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Macromolecule #2: Glycosylated lysosomal membrane protein

MacromoleculeName: Glycosylated lysosomal membrane protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 43.102711 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFRCWGPHWG WVPCAPTPWL LLSLLVCSAP FGLQGEETRQ VSMEVISGWP NPQNLLHIRA VGSNSTLHYV WSSLGPPAVV LVATNTTQS VLSVNWSLLL SPDPAGALMV LPKSSIQFSS ALVFTRLLEF DSTNASEGAQ PPGKPYPPYS LAKFSWNNIT N SLDLANLS ...String:
MFRCWGPHWG WVPCAPTPWL LLSLLVCSAP FGLQGEETRQ VSMEVISGWP NPQNLLHIRA VGSNSTLHYV WSSLGPPAVV LVATNTTQS VLSVNWSLLL SPDPAGALMV LPKSSIQFSS ALVFTRLLEF DSTNASEGAQ PPGKPYPPYS LAKFSWNNIT N SLDLANLS ADFQGRPVDD PTGAFANGSL TFKVQAFSRS GRPAQPPRLL HTADVCQLEV ALVGASPRGN HSLFGLEVAT LG QGPDCPS VNERNSIDDE YAPAVFQLNQ LLWGSSPSGF MQWRPVAFSE EERARESALP CQASTLHSTL ASSLPHSPIV QAF FGSQNN FCAFNLTFGA PTGPGYWDQY YLCWSMLLGM GFPPVDIFSP LVLGIMAVAL GAPGLMFLGG GLFLLGSAGS AAGS GEF

UniProtKB: Glycosylated lysosomal membrane protein

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 5 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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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

Concentration3.33 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
20.0 mMHis-Ala
150.0 mMsodium chlorideNaClSodium chloride
0.015 %DDM
0.0015 %CHS
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec.
VitrificationCryogen name: PROPANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 3193 / Average electron dose: 55.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.08 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 400191

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8r8q:
Lysosomal peptide transporter

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