6Z1V Cell Adhesion date May 14, 2020
title Structure Of The Ec2 Domain Of Cd9 In Complex With Nanobody
authors W.Oosterheert, N.M.Pearce, P.Gros
compound source
Molecule: Cd9 Antigen
Chain: A
Synonym: 5h9 Antigen,Cell Growth-Inhibiting Gene 2 Protein, Antigen Mic3,Motility-Related Protein,Mrp-1,Tetraspanin-29, P24;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cd9, Mic3, Tspan29, Gig2
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Hek293ebna
Expression_system_organ: Kidney
Expression_system_cell: Embryonic
Expression_system_plasmid: Pupe 107.03

Molecule: Nanobody 4e8
Chain: B
Engineered: Yes

Organism_scientific: Lama Glama
Organism_common: Llama
Organism_taxid: 9844
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_variant: Codon Plus
symmetry Space Group: P 21 21 2
R_factor 0.151 R_Free 0.190
length a length b length c angle alpha angle beta angle gamma
61.521 89.446 35.684 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.33 Å
ligand ACY, EDO, PGE enzyme
Primary referenceImplications for tetraspanin-enriched microdomain assembly based on structures of CD9 with EWI-F., Oosterheert W, Xenaki KT, Neviani V, Pos W, Doulkeridou S, Manshande J, Pearce NM, Kroon-Batenburg LM, Lutz M, van Bergen En Henegouwen PM, Gros P, Life Sci Alliance. 2020 Sep 21;3(11). pii: 3/11/e202000883. doi:, 10.26508/lsa.202000883. Print 2020 Nov. PMID:32958604
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (126 Kb) [Save to disk]
  • Biological Unit Coordinates (6z1v.pdb1.gz) 118 Kb
  • LPC: Ligand-Protein Contacts for 6Z1V
  • CSU: Contacts of Structural Units for 6Z1V
  • Structure Factors (354 Kb)
  • Retrieve 6Z1V in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6Z1V from S2C, [Save to disk]
  • View 6Z1V 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 6Z1V
  • 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 6z1v from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6z1v_B] [6z1v_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6Z1V
  • Community annotation for 6Z1V at PDBWiki (http://pdbwiki.org)

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