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- EMDB-50668: Cryo-EM structure of MmCAT1 bound with FrMLV-RBD in the apo inwar... -

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Basic information

Entry
Database: EMDB / ID: EMD-50668
TitleCryo-EM structure of MmCAT1 bound with FrMLV-RBD in the apo inward-open state
Map datamain
Sample
  • Complex: MmCAT1(apo) bound with FrMLV-RBD
    • Protein or peptide: High affinity cationic amino acid transporter 1,Green fluorescent protein
  • Protein or peptide: Surface protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CHOLESTEROL HEMISUCCINATE
KeywordsMmCAT1 / FrMLV-RBD / SLC / viral tropism / MEMBRANE PROTEIN
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 transporter activity / L-histidine transmembrane transporter activity / L-arginine transmembrane transport / 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 transporter activity / L-histidine transmembrane transporter activity / L-arginine transmembrane transport / positive regulation of T cell proliferation / bioluminescence / generation of precursor metabolites and energy / virus receptor activity / basolateral plasma membrane / apical plasma membrane / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / 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
Envelope glycoprotein / Green fluorescent protein / High affinity cationic amino acid transporter 1
Similarity search - Component
Biological speciesMus musculus (house mouse) / Murine leukemia virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsYe M / Zhou D / Pike ACW / Wang S / Wang D / Bakshi S / Brooke L / Williams E / Elkins J / Stuart DI / Sauer DB
Funding support1 items
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 ACW / Wang S / Wang D / Bakshi S / Brooke L / Williams E / Elkins J / Kessler B / Stuart DI / Sauer DB
History
DepositionJun 17, 2024-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50668.png

Downloads & links

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Map

FileDownload / File: emd_50668.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 324 pix.
= 267.3 Å		0.83 Å/pix.
x 324 pix.
= 267.3 Å		0.83 Å/pix.
x 324 pix.
= 267.3 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.197
Minimum - Maximum-0.806909 - 1.2512748
Average (Standard dev.)-0.0006741997 (±0.0231109)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions324324324
Spacing324324324
CellA=B=C: 267.3 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50668_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half A

Fileemd_50668_half_map_1.map
Annotationhalf A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half B

Fileemd_50668_half_map_2.map
Annotationhalf B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : MmCAT1(apo) bound with FrMLV-RBD

EntireName: MmCAT1(apo) bound with FrMLV-RBD
Components
  • Complex: MmCAT1(apo) bound with FrMLV-RBD
    • Protein or peptide: High affinity cationic amino acid transporter 1,Green fluorescent protein
  • Protein or peptide: Surface protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CHOLESTEROL HEMISUCCINATE

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Supramolecule #1: MmCAT1(apo) bound with FrMLV-RBD

SupramoleculeName: MmCAT1(apo) bound with FrMLV-RBD / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 128.8 KDa

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Macromolecule #1: High affinity cationic amino acid transporter 1,Green fluorescent...

MacromoleculeName: High affinity cationic amino acid transporter 1,Green fluorescent protein
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 98.703758 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLRRKVVDCS REESRLSRCL NTYDLVALGV GSTLGAGVYV LAGAVARENA GPAIVISFLI AALASVLAGL CYGEFGARVP KTGSAYLYS YVTVGELWAF ITGWNLILSY IIGTSSVARA WSATFDELIG KPIGEFSRQH MALNAPGVLA QTPDIFAVII I IILTGLLT ...String:
MLRRKVVDCS REESRLSRCL NTYDLVALGV GSTLGAGVYV LAGAVARENA GPAIVISFLI AALASVLAGL CYGEFGARVP KTGSAYLYS YVTVGELWAF ITGWNLILSY IIGTSSVARA WSATFDELIG KPIGEFSRQH MALNAPGVLA QTPDIFAVII I IILTGLLT LGVKESAMVN KIFTCINVLV LCFIVVSGFV KGSIKNWQLT EKNFSCNNND TNVKYGEGGF MPFGFSGVLS GA ATCFYAF VGFDCIATTG EEVKNPQKAI PVGIVASLLI CFIAYFGVSA ALTLMMPYFC LDIDSPLPGA FKHQGWEEAK YAV AIGSLC ALSTSLLGSM FPMPRVIYAM AEDGLLFKFL AKINNRTKTP VIATVTSGAI AAVMAFLFEL KDLVDLMSIG TLLA YSLVA ACVLVLRYQP EQPNLVYQMA RTTEELDRVD QNELVSASES QTGFLPVAEK FSLKSILSPK NVEPSKFSGL IVNIS AGLL AALIITVCIV AVLGREALAE GTLWAVFVMT GSVLLCMLVT GIIWRQPESK TKLSFKVPFV PVLPVLSIFV NIYLMM QLD QGTWVRFAVW MLIGFTIYFG YGIWHSEEAS LAAGQAKTPD SNLDQCKAEN LYFQSGSAVS KGEELFTGVV PILVELD GD VNGHKFSVSG EGEGDATYGK LTLKFICTTG KLPVPWPTLV TTLTYGVQCF SRYPDHMKQH DFFKSAMPEG YVQERTIF F KDDGNYKTRA EVKFEGDTLV NRIELKGIDF KEDGNILGHK LEYNYNSHNV YIMADKQKNG IKVNFKIRHN IEDGSVQLA DHYQQNTPIG DGPVLLPDNH YLSTQSKLSK DPNEKRDHMV LLEFVTAAGI TLGMDELYKS GLRSWSHPQF EKGGGSGGGS GGSAWSHPQ FEKHHHHHHH HHH

UniProtKB: High affinity cationic amino acid transporter 1, Green fluorescent protein

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Macromolecule #2: Surface protein

MacromoleculeName: Surface protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Murine leukemia virus
Molecular weightTheoretical: 30.272078 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGILPSPGMP ALLSLVSLLS VLLMGCVAET GAAPGSSPHQ VYNITWEVTN GDRETVWAIS GNHPLWTWWP VLTPDLCMLA LSGPPHWGL EYQAPYSSPP GPPCCSGSSG SSAGCSRDCD EPLTSLTPRC NTAWNRLKLD QVTHKSSEGF YVCPGSHRPR E AKSCGGPD ...String:
MGILPSPGMP ALLSLVSLLS VLLMGCVAET GAAPGSSPHQ VYNITWEVTN GDRETVWAIS GNHPLWTWWP VLTPDLCMLA LSGPPHWGL EYQAPYSSPP GPPCCSGSSG SSAGCSRDCD EPLTSLTPRC NTAWNRLKLD QVTHKSSEGF YVCPGSHRPR E AKSCGGPD SFYCASWGCE TTGRVYWKPS SSWDYITVDN NLTTSQAVQV CKDNKWCNPL AIQFTNAGKQ VTSWTTGHYW GL RLYVSGR DPGLTFGIRL RYQNLGPRVP GTKHHHHHH

UniProtKB: Envelope glycoprotein

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #6: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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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

Concentration3.8 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClSodium Chloride
10.0 mMC8H18N2O4SHEPES
0.003 %C47H88O22Lauryl Maltose Neopentyl Glycol
0.0006 %C31H50O4Cholesteryl hemisuccinate
GridModel: Quantifoil R1.2/1.3 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2482628
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 263131
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

1aol

source_name: PDB, initial_model_type: experimental model
source_name: AlphaFold, initial_model_type: in silico model
RefinementSpace: REAL / Overall B value: 66.8
Output model

PDB-9fqt:
Cryo-EM structure of MmCAT1 bound with FrMLV-RBD in the apo inward-open state

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