6JMR

CD98hc extracellular domain bound to HBJ127 Fab and MEM-108 Fab


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.1 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Cryo-EM structure of the human L-type amino acid transporter 1 in complex with glycoprotein CD98hc.

Lee, Y.Wiriyasermkul, P.Jin, C.Quan, L.Ohgaki, R.Okuda, S.Kusakizako, T.Nishizawa, T.Oda, K.Ishitani, R.Yokoyama, T.Nakane, T.Shirouzu, M.Endou, H.Nagamori, S.Kanai, Y.Nureki, O.

(2019) Nat.Struct.Mol.Biol. 26: 510-517

  • DOI: 10.1038/s41594-019-0237-7
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The L-type amino acid transporter 1 (LAT1 or SLC7A5) transports large neutral amino acids across the membrane and is crucial for brain drug delivery and tumor growth. LAT1 forms a disulfide-linked heterodimer with CD98 heavy chain (CD98hc, 4F2hc or S ...

    The L-type amino acid transporter 1 (LAT1 or SLC7A5) transports large neutral amino acids across the membrane and is crucial for brain drug delivery and tumor growth. LAT1 forms a disulfide-linked heterodimer with CD98 heavy chain (CD98hc, 4F2hc or SLC3A2), but the mechanism of assembly and amino acid transport are poorly understood. Here we report the cryo-EM structure of the human LAT1-CD98hc heterodimer at 3.3-Å resolution. LAT1 features a canonical Leu T-fold and exhibits an unusual loop structure on transmembrane helix 6, creating an extended cavity that might accommodate bulky amino acids and drugs. CD98hc engages with LAT1 through the extracellular, transmembrane and putative cholesterol-mediated interactions. We also show that two anti-CD98 antibodies recognize distinct, multiple epitopes on CD98hc but not its glycans, explaining their robust reactivities. These results reveal the principles of glycoprotein-solute carrier assembly and provide templates for improving preclinical drugs and antibodies targeting LAT1 or CD98hc.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge, UK.,Department of Collaborative Research for Bio-Molecular Dynamics, Nara Medical University, Nara, Japan.,Preferred Networks, Inc., Tokyo, Japan.,J-Pharma Co., Ltd, Kanagawa, Japan.,Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt, Germany.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan. nureki@bs.s.u-tokyo.ac.jp.,Department of Bio-system Pharmacology, Graduate School of Medicine, Osaka University, Osaka, Japan.,Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Kanagawa, Japan.,Global Innovation Center, Shiseido Co., Ltd, Kanagawa, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Antibody
E
220N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Antibody
F
218N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
4F2 cell-surface antigen heavy chain
B
631Homo sapiensMutation(s): 0 
Gene Names: SLC3A2 (MDU1)
Find proteins for P08195 (Homo sapiens)
Go to Gene View: SLC3A2
Go to UniProtKB:  P08195
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Antibody
C
219N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Antibody
D
219N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
C, D
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.1 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement
phenix.real_space_refinerefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapanJP16J07405
Japan Agency for Medical Research and Development (AMED)JapanJP18am0101082
Japan Agency for Medical Research and Development (AMED)JapanJP18am0101115

Revision History 

  • Version 1.0: 2019-06-19
    Type: Initial release