4NEH Cell Adhesion date Oct 29, 2013
title An Internal Ligand-Bound, Metastable State Of A Leukocyte In Axb2
authors M.Sen, K.Yuki, T.A.Springer
compound source
Molecule: Integrin Alpha-X
Chain: A
Fragment: Cd11c
Synonym: Cd11 Antigen-Like Family Member C, Leu M5, Leukocy Adhesion Glycoprotein P150,95 Alpha Chain, Leukocyte Adhesi Receptor P150,95;
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Itgax, Cd11c
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Hek-293s Gnti --
Expression_system_vector_type: Stable Cell Lines
Expression_system_plasmid: Et10

Molecule: Integrin Beta-2
Chain: B
Fragment: Cd18
Synonym: Cell Surface Adhesion Glycoproteins Lfa-1cr3p150 Subunit Beta, Complement Receptor C3 Subunit Beta;
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Itgb2, Cd18, Mfi7
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Hek-293s Gnti --
Expression_system_vector_type: Pef-Puro
symmetry Space Group: P 21 21 21
R_factor 0.193 R_Free 0.225
crystal
cell
length a length b length c angle alpha angle beta angle gamma
126.967 131.444 190.477 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.75 Å
ligand BMA, CA, CL, MAN, MG, NA, NAG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A
  • heterotypic cell-cell adhesi...

  • B


    Primary referenceAn internal ligand-bound, metastable state of a leukocyte integrin, alphaXbeta2., Sen M, Yuki K, Springer TA, J Cell Biol. 2013 Nov 25;203(4):629-42. doi: 10.1083/jcb.201308083. PMID:24385486
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (604 Kb) [Save to disk]
  • Biological Unit Coordinates (4neh.pdb1.gz) 578 Kb
  • LPC: Ligand-Protein Contacts for 4NEH
  • CSU: Contacts of Structural Units for 4NEH
  • Structure Factors (659 Kb)
  • Retrieve 4NEH in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4NEH from S2C, [Save to disk]
  • Re-refined 4neh structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4NEH 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 4NEH
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4NEH, from MSDmotif at EBI
  • Fold representative 4neh from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4neh] [4neh_A] [4neh_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4NEH: [INB] [Int_alpha] [Integrin_B_tail] [PSI] [VWA ] by SMART
  • Other resources with information on 4NEH
  • Community annotation for 4NEH at PDBWiki (http://pdbwiki.org)

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