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
Gene
Ontology
ChainFunctionProcessComponent
A, B, C, D


F, E, H, G


J, K, I, L


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 (304 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.
  • 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_C] [3kfd_L] [3kfd_J] [3kfd_A] [3kfd_E] [3kfd_H] [3kfd_B] [3kfd_G] [3kfd_D] [3kfd_F] [3kfd_K] [3kfd_I] [3kfd]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3KFD: [TGFB ] by SMART
  • Other resources with information on 3KFD
  • Community annotation for 3KFD at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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