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- PDB-9fqv: Cryo-EM structure of MmCAT1 bound with FrMLV-RBD in the lysine-bo... -

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Basic information

Entry
Database: PDB / ID: 9fqv
TitleCryo-EM structure of MmCAT1 bound with FrMLV-RBD in the lysine-bound inward-occluded state
Components
  • High affinity cationic amino acid transporter 1,Green fluorescent protein
  • Surface protein
KeywordsMEMBRANE PROTEIN / MmCAT1 / FrMLV-RBD / SLC / viral tropism
Function / homology
Function and homology information


L-ornithine transmembrane transporter activity / L-lysine transmembrane transporter activity / lysine transport / L-ornithine transmembrane transport / L-histidine import across plasma membrane / Amino acid transport across the plasma membrane / L-arginine transmembrane transport / L-histidine transmembrane transporter activity / L-arginine transmembrane transporter activity / positive regulation of T cell proliferation ...L-ornithine transmembrane transporter activity / L-lysine transmembrane transporter activity / lysine transport / L-ornithine transmembrane transport / L-histidine import across plasma membrane / Amino acid transport across the plasma membrane / L-arginine transmembrane transport / L-histidine transmembrane transporter activity / L-arginine transmembrane transporter activity / positive regulation of T cell proliferation / bioluminescence / generation of precursor metabolites and energy / virus receptor activity / basolateral plasma membrane / apical plasma membrane / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / protein-containing complex / metal ion binding / membrane
Similarity search - Function
Cationic amino acid transport permease / Cationic amino acid transporter, C-terminal / C-terminus of AA_permease / F-MuLV receptor-binding / ENV polyprotein (coat polyprotein) / TLV/ENV coat polyprotein / Amino acid/polyamine transporter I / Amino acid permease / Green fluorescent protein, GFP / Green fluorescent protein-related ...Cationic amino acid transport permease / Cationic amino acid transporter, C-terminal / C-terminus of AA_permease / F-MuLV receptor-binding / ENV polyprotein (coat polyprotein) / TLV/ENV coat polyprotein / Amino acid/polyamine transporter I / Amino acid permease / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
LYSINE / CHOLESTEROL HEMISUCCINATE / Envelope glycoprotein / Green fluorescent protein / High affinity cationic amino acid transporter 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Murine leukemia virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsYe, M. / Zhou, D. / Pike, A.C.W. / Wang, S. / Wang, D. / Bakshi, S. / Brooke, L. / Williams, E. / Elkins, J. / Stuart, D.I. / Sauer, D.B.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To Be Published
Title: Amino acid and viral binding by the high-affinity Cationic Amino acid Transporter 1 (CAT1) from Mus musculus
Authors: Ye, M. / Liang, Z. / Zhou, D. / Pike, A.C.W. / Wang, S. / Wang, D. / Bakshi, S. / Brooke, L. / Williams, E. / Elkins, J. / Kessler, B. / Stuart, D.I. / Sauer, D.B.
History
DepositionJun 17, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: High affinity cationic amino acid transporter 1,Green fluorescent protein
B: Surface protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,8408
Polymers128,9762
Non-polymers2,8646
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein High affinity cationic amino acid transporter 1,Green fluorescent protein / CAT-1 / CAT1 / Ecotropic retroviral leukemia receptor / Ecotropic retrovirus receptor / ERR / EcoR ...CAT-1 / CAT1 / Ecotropic retroviral leukemia receptor / Ecotropic retrovirus receptor / ERR / EcoR / Solute carrier family 7 member 1 / System Y+ basic amino acid transporter


Mass: 98703.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Slc7a1, Atrc1, Rec-1, GFP / Production host: Homo sapiens (human) / References: UniProt: Q09143, UniProt: P42212
#2: Protein Surface protein / SU / Glycoprotein 70 / gp70


Mass: 30272.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murine leukemia virus / Gene: env / Production host: Homo sapiens (human) / References: UniProt: P03390

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Sugars , 2 types, 3 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 2 types, 3 molecules

#5: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H50O4 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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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: MmCAT1 (lysine bound) in complex with FrMLV-RBD / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.1288 MDa / Experimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMSodium ChlorideNaCl1
210 mMHEPESC8H18N2O4S1
30.003 %Lauryl Maltose Neopentyl GlycolC47H88O221
40.0006 %Cholesteryl hemisuccinateC31H50O41
520 mMlysineC6H14N2O21
SpecimenConc.: 6.36 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2EPUimage acquisition
4cryoSPARCCTF correction
7UCSF ChimeraXmodel fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
12cryoSPARC3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2375463
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3150614 / Symmetry type: POINT
Atomic model buildingB value: 62.96 / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11AOL

1aol

11AOL1PDBexperimental model
21AlphaFoldin silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0026191
ELECTRON MICROSCOPYf_angle_d0.458464
ELECTRON MICROSCOPYf_dihedral_angle_d5.043907
ELECTRON MICROSCOPYf_chiral_restr0.0361008
ELECTRON MICROSCOPYf_plane_restr0.0051028

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