6JMR Membrane Protein Immune System date Mar 13, 2019
title Cd98hc Extracellular Domain Bound To Hbj127 Fab And Mem-108
authors Y.Lee, T.Nishizawa, T.Kusakizako, K.Oda, R.Ishitani, T.Yokoyama, T M.Shirouzu, O.Nureki
compound source
Molecule: Antibody
Chain: E
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_taxid: 10090
Expression_system: Mus Musculus
Expression_system_taxid: 10090

Molecule: Antibody
Chain: F
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_taxid: 10090
Expression_system: Mus Musculus
Expression_system_taxid: 10090

Molecule: 4f2 Cell-Surface Antigen Heavy Chain
Chain: B
Synonym: 4f2hc,4f2 Heavy Chain Antigen,Lymphocyte Activatio 4f2 Large Subunit,Solute Carrier Family 3 Member 2;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Slc3a2, Mdu1
Expression_system: Homo Sapiens
Expression_system_taxid: 9606

Molecule: Antibody
Chain: C
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_taxid: 10090
Expression_system: Mus Musculus
Expression_system_taxid: 10090

Molecule: Antibody
Chain: D
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_taxid: 10090
Expression_system: Mus Musculus
Expression_system_taxid: 10090
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 4.10 Å
ligand NAG enzyme
Gene
Ontology
ChainFunctionProcessComponent
B
  • calcium:sodium antiporter ac...


  • Primary referenceCryo-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, Nat Struct Mol Biol. 2019 Jun;26(6):510-517. doi: 10.1038/s41594-019-0237-7. Epub, 2019 Jun 3. PMID:31160781
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (182 Kb) [Save to disk]
  • Biological Unit Coordinates (6jmr.pdb1.gz) 177 Kb
  • LPC: Ligand-Protein Contacts for 6JMR
  • CSU: Contacts of Structural Units for 6JMR
  • Retrieve 6JMR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6JMR from S2C, [Save to disk]
  • View 6JMR in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 6JMR
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 6jmr from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6jmr_C] [6jmr_D] [6jmr_F] [6jmr_E] [6jmr_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6JMR
  • Community annotation for 6JMR at PDBWiki (http://pdbwiki.org)

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science