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- PDB-9fqu: Cryo-EM structure of MmCAT1 bound with FrMLV-RBD in the arginine-... -

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Basic information

Entry
Database: PDB / ID: 9fqu
TitleCryo-EM structure of MmCAT1 bound with FrMLV-RBD in the arginine-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-amino acid transport / L-histidine import across plasma membrane / ornithine transport / L-arginine import across plasma membrane / Amino acid transport across the plasma membrane / basic amino acid transmembrane transporter activity ...L-ornithine transmembrane transporter activity / L-lysine transmembrane transporter activity / lysine transport / L-ornithine transmembrane transport / L-amino acid transport / L-histidine import across plasma membrane / ornithine transport / L-arginine import across plasma membrane / Amino acid transport across the plasma membrane / basic amino acid transmembrane transporter activity / L-arginine transmembrane transport / L-histidine transmembrane transporter activity / L-arginine transmembrane transporter activity / amino acid import across plasma membrane / regulation of TOR signaling / amino acid transmembrane transporter activity / positive regulation of T cell proliferation / basal plasma membrane / 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 / plasma 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
ARGININE / 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: 2.79 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: Nat Commun / Year: 2026
Title: Amino acid and viral binding by the high-affinity Cationic Amino acid Transporter 1 (CAT1) from Mus musculus.
Authors: Mingda Ye / Zhu Liang / Daming Zhou / Ashley C W Pike / SiYi Wang / Dong Wang / Souvika Bakshi / Laurent Brooke / Eleanor P Williams / Jonathan M Elkins / Benedikt M Kessler / David I Stuart / David B Sauer /
Abstract: Arginine, lysine, and ornithine are critical to several fundamental aspects of organismal physiology, including protein structure and function, the urea cycle, and intracellular signaling. These ...Arginine, lysine, and ornithine are critical to several fundamental aspects of organismal physiology, including protein structure and function, the urea cycle, and intracellular signaling. These cationic amino acids are imported by several membrane transporters, most notably the Cationic Amino acid Transporters (CATs) in the SLC7 family. Of these, CAT1 is also the receptor for two orthoretroviruses, and determines the host tropism for these viruses. Here, using a combination of CryoEM and in vitro biochemical techniques, we characterize the substrate recognition and transport of CAT1 from Mus musculus. Further, by determining the structures of MmCAT1 in complex with the receptor binding domain from the Friend Murine Leukemia Virus, we identify the key structural interactions that determine the virus' rodent-specific tropism.
History
DepositionJun 17, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)132,2519
Polymers128,9762
Non-polymers3,2767
Water181
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 , 4 types, 4 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: obtained synthetically
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 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: 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.: 1
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
#6: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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

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Non-polymers , 3 types, 4 molecules

#7: Chemical ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H50O4 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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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 (arginine 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
534 mMarginineC6H14N4O21
SpecimenConc.: 6.36 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
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: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 386193 / Symmetry type: POINT
Atomic model buildingB value: 61.64 / 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_d0.0026218
ELECTRON MICROSCOPYf_angle_d0.4498501
ELECTRON MICROSCOPYf_dihedral_angle_d4.768924
ELECTRON MICROSCOPYf_chiral_restr0.0381018
ELECTRON MICROSCOPYf_plane_restr0.0031030

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