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- PDB-8r8q: Lysosomal peptide transporter -

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Basic information

Entry
Database: PDB / ID: 8r8q
TitleLysosomal peptide transporter
Components
  • Glycosylated lysosomal membrane protein
  • Major facilitator superfamily domain-containing protein 1
KeywordsMEMBRANE PROTEIN / MFS transporter / MFSD family / nutrition transporter / lysosomal transporter / outward open
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.08 Å
AuthorsJungnickel, K.E.J. / Loew, C.
Funding support Germany, 1items
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, K.E.J. / Guelle, O. / Iguchi, M. / Dong, W. / Kotov, V. / Gabriel, F. / Debacker, C. / Dairou, J. / McCort-Tranchepain, I. / Laqtom, N.N. / Chan, S.H. / Ejima, A. / Sato, K. / ...Authors: Jungnickel, K.E.J. / Guelle, O. / Iguchi, M. / Dong, W. / Kotov, V. / Gabriel, F. / Debacker, C. / Dairou, J. / McCort-Tranchepain, I. / Laqtom, N.N. / Chan, S.H. / Ejima, A. / Sato, K. / Massa Lopez, D. / Saftig, P. / Mehdipour, A.R. / Abu-Remaileh, M. / Gasnier, B. / Low, C. / Damme, M.
History
DepositionNov 29, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major facilitator superfamily domain-containing protein 1
B: Glycosylated lysosomal membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,9747
Polymers98,8682
Non-polymers1,1065
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area3390 Å2
ΔGint-9 kcal/mol
Surface area35260 Å2
MethodPISA

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Components

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


Mass: 55765.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mfsd1 / Production host: Homo sapiens (human) / References: UniProt: Q9DC37
#2: Protein Glycosylated lysosomal membrane protein / Lysosomal protein NCU-G1


Mass: 43102.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Glmp / Production host: Homo sapiens (human) / References: UniProt: Q9JHJ3
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: GLMP-MFSD1 / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHis-Ala1
2150 mMsodium chlorideNaClSodium chloride1
30.015 %DDM1
40.0015 %CHS1
SpecimenConc.: 3.33 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: PROPANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 81000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / C2 aperture diameter: 70 µm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3193

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2EPUimage acquisition
4CTFFINDCTF correction
7ISOLDE1.0b3model fitting
8Coot0.9.8.1model fitting
10PHENIX1.20.1-4487model refinement
11cryoSPARCinitial Euler assignment
12cryoSPARCfinal Euler assignment
13cryoSPARCclassification
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.08 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 400191 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0035855
ELECTRON MICROSCOPYf_angle_d0.6327971
ELECTRON MICROSCOPYf_dihedral_angle_d4.5801
ELECTRON MICROSCOPYf_chiral_restr0.04922
ELECTRON MICROSCOPYf_plane_restr0.004988

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