3KFD Cytokine Cytokine Receptor date Oct 27, 2009
title Ternary Complex Of Tgf-B1 Reveals Isoform-Specific Ligand Re And Receptor Recruitment In The Superfamily
authors S.Radaev, P.D.Sun
compound source
Molecule: Transforming Growth Factor Beta-1
Chain: A, B, C, D
Synonym: Tgf-Beta-1, Latency-Associated Peptide, Lap
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tgfb1, Tgfb
Expression_system: Cricetulus Griseus
Expression_system_common: Chinese Hamster
Expression_system_taxid: 10029
Expression_system_strain: Cho-Lec3.2.8.1
Expression_system_organ: Ovary Cells

Molecule: Tgf-Beta Receptor Type-2
Chain: E, F, G, H
Fragment: Extracellular Domain
Synonym: Transforming Growth Factor-Beta Receptor Type II, Receptor Type II, Tgf-Beta Type II Receptor, Tbetar-II, Tgf
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tgfbr2
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Tgf-Beta Receptor Type-1
Chain: I, J, K, L
Fragment: Extracellular Domain
Synonym: Transforming Growth Factor-Beta Receptor Type I, T Receptor Type I, Tgf-Beta Type I Receptor, Tbetar-I, Tgfr-1 Serinethreonine-Protein Kinase Receptor R4, Skr4, Activin Like Kinase 5, Alk-5;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tgfbr1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1
R_factor 0.217 R_Free 0.268
crystal
cell
length a length b length c angle alpha angle beta angle gamma
37.700 99.350 102.700 64.01 84.47 84.34
method X-Ray Diffractionresolution 3.00 Å
Primary referenceTernary complex of transforming growth factor-beta1 reveals isoform-specific ligand recognition and receptor recruitment in the superfamily., Radaev S, Zou Z, Huang T, Lafer EM, Hinck AP, Sun PD, J Biol Chem. 2010 May 7;285(19):14806-14. Epub 2010 Mar 5. PMID:20207738
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (195 Kb) [Save to disk]
  • Biological Unit Coordinates (3kfd.pdb1.gz) 96 Kb
  • Biological Unit Coordinates (3kfd.pdb2.gz) 97 Kb
  • Biological Unit Coordinates (3kfd.pdb3.gz) 188 Kb
  • CSU: Contacts of Structural Units for 3KFD
  • Structure Factors (309 Kb)
  • Retrieve 3KFD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3KFD from S2C, [Save to disk]
  • Re-refined 3kfd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3KFD 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.
  • On AstexViewer, from MSD-EBI (viewer documentation).
  • On RasMol (Install RasMol freeware) Here's help on how to use RasMol.
    • Visual 3D analysis of 3KFD
  • 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 3KFD, from MSDmotif at EBI
  • Fold representative 3kfd from FSSP and Dali (Families of Structurally Similar Proteins)
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3kfd_A] [3kfd_B] [3kfd_C] [3kfd_D] [3kfd_E] [3kfd_F] [3kfd_G] [3kfd_H] [3kfd_I] [3kfd_J] [3kfd_K] [3kfd_L]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Alignments of the sequence of 3KFD with the sequences similar proteins can be viewed for 3KFD's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.
    • Other resources with information on 3KFD
  • Community annotation for 3KFD at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
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  • Images from IMB Jena Image Library of Biological Macromolecules.

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