4MXW Cytokine Immune System date Sep 26, 2013
title Structure Of Heterotrimeric Lymphotoxin Lta1b2 Bound To Lymp Beta Receptor Ltbr And Anti-Lta Fab
authors J.Sudhamsu, J.P.Yin, S.G.Hymowitz
compound source
Molecule: Tumor Necrosis Factor Receptor Superfamily Member
Chain: S, R
Synonym: Lymphotoxin-Beta Receptor, Tumor Necrosis Factor C Tumor Necrosis Factor Receptor 2-Related Protein, Tumor Nec Factor Receptor Type III, Tnf-Riii, Tnfr-III;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ltbr, D12s370, Tnfcr, Tnfr3, Tnfrsf3
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
Expression_system_vector_type: Baculovirus

Molecule: Anti-Lymphotoxin Alpha Antibody Light Chain
Chain: V, L
Fragment: Fab
Synonym: Anti-Lt-Alpha Antibody Light Chain
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Cricetulus Griseus
Expression_system_common: Chinese Hamster
Expression_system_taxid: 10029
Expression_system_cell_line: Cho

Molecule: Anti-Lymphotoxin Alpha Antibody Heavy Chain
Chain: W, H
Fragment: Fab
Synonym: Anti-Lt-Alpha Antibody Heavy Chain
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Cricetulus Griseus
Expression_system_common: Chinese Hamster
Expression_system_taxid: 10029
Expression_system_cell_line: Cho

Molecule: Lymphotoxin-Alpha
Chain: X, A
Synonym: Lt-Alpha, Tnf-Beta, Tumor Necrosis Factor Ligand S Member 1;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Lta, Tnfb, Tnfsf1
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
Expression_system_vector_type: Baculovirus

Molecule: Lymphotoxin-Beta
Chain: Y, Z, B, D
Synonym: Lt-Beta, Tumor Necrosis Factor C, Tnf-C, Tumor Nec Factor Ligand Superfamily Member 3;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ltb, Tnfc, Tnfsf3
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
Expression_system_vector_type: Baculovirus
symmetry Space Group: C 1 2 1
R_factor 0.231 R_Free 0.296
crystal
cell
length a length b length c angle alpha angle beta angle gamma
211.201 52.428 253.241 90.00 101.10 90.00
method X-Ray Diffractionresolution 3.60 Å
Gene
Ontology
ChainFunctionProcessComponent
A, X


S, R


Y, B, Z, D


Primary referenceDimerization of LTbetaR by LTalpha1beta2 is necessary and sufficient for signal transduction., Sudhamsu J, Yin J, Chiang EY, Starovasnik MA, Grogan JL, Hymowitz SG, Proc Natl Acad Sci U S A. 2013 Dec 3;110(49):19896-901. doi:, 10.1073/pnas.1310838110. Epub 2013 Nov 18. PMID:24248355
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (306 Kb) [Save to disk]
  • Biological Unit Coordinates (4mxw.pdb1.gz) 146 Kb
  • Biological Unit Coordinates (4mxw.pdb2.gz) 155 Kb
  • CSU: Contacts of Structural Units for 4MXW
  • Structure Factors (312 Kb)
  • Retrieve 4MXW in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4MXW from S2C, [Save to disk]
  • Re-refined 4mxw structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4MXW 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 4MXW
  • 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 4MXW, from MSDmotif at EBI
  • Fold representative 4mxw from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4mxw_Z] [4mxw_A] [4mxw_S] [4mxw_W] [4mxw_D] [4mxw_X] [4mxw_H] [4mxw_L] [4mxw_V] [4mxw] [4mxw_R] [4mxw_Y] [4mxw_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4MXW: [IGc1] [IGv] [TNF] [TNFR ] by SMART
  • Other resources with information on 4MXW
  • Community annotation for 4MXW at PDBWiki (http://pdbwiki.org)

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