6D04 Cell Invasion date Apr 10, 2018
title Cryo-Em Structure Of A Plasmodium Vivax Invasion Complex Ess Entry Into Human Reticulocytes; Two Molecules Of Parasite L Subclass 1.
authors J.Gruszczyk, R.K.Huang, C.Hong, Z.Yu, W.H.Tham
compound source
Molecule: Transferrin Receptor Protein 1
Chain: A, B
Synonym: Trfr,T9,P90
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tfrc
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
Expression_system_cell_line: Sf21

Molecule: Serotransferrin
Chain: C, D
Synonym: Transferrin,Beta-1 Metal-Binding Globulin,Sideroph

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Reticulocyte Binding Protein 2, Putative
Chain: E, F
Engineered: Yes

Organism_scientific: Plasmodium Vivax
Organism_taxid: 126793
Strain: Salvador I
Gene: Pvx_094255
Expression_system: Escherichia Coli
Expression_system_taxid: 562
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 3.74 Å
ligand CA, CO3, FE, NAG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


D, C


Primary referenceCryo-EM structure of an essential Plasmodium vivax invasion complex., Gruszczyk J, Huang RK, Chan LJ, Menant S, Hong C, Murphy JM, Mok YF, Griffin MDW, Pearson RD, Wong W, Cowman AF, Yu Z, Tham WH, Nature. 2018 Jul;559(7712):135-139. doi: 10.1038/s41586-018-0249-1. Epub 2018 Jun, 27. PMID:29950717
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (523 Kb) [Save to disk]
  • Biological Unit Coordinates (6d04.pdb1.gz) 512 Kb
  • LPC: Ligand-Protein Contacts for 6D04
  • CSU: Contacts of Structural Units for 6D04
  • Retrieve 6D04 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6D04 from S2C, [Save to disk]
  • View 6D04 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 6D04
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6d04_D] [6d04_F] [6d04_A] [6d04_E] [6d04_B] [6d04_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6D04
  • Community annotation for 6D04 at PDBWiki (http://pdbwiki.org)

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