1ICT

MONOCLINIC FORM OF HUMAN TRANSTHYRETIN COMPLEXED WITH THYROXINE (T4)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.229 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of a new polymorphic monoclinic form of human transthyretin at 3 A resolution reveals a mixed complex between unliganded and T4-bound tetramers of TTR.

Wojtczak, A.Neumann, P.Cody, V.

(2001) Acta Crystallogr D Biol Crystallogr 57: 957-967

  • DOI: 10.1107/s0907444901006047
  • Primary Citation of Related Structures:  
    1ICT

  • PubMed Abstract: 
  • The crystal structure of a new polymorphic form of human transthyretin (hTTR) with a lattice containing a unique assembly of apo hTTR and TTR-T(4) complex has been determined to 3 A resolution. The monoclinic form of human TTR reported here crystallizes in space group P2(1), with unit-cell parameters a = 76 ...

    The crystal structure of a new polymorphic form of human transthyretin (hTTR) with a lattice containing a unique assembly of apo hTTR and TTR-T(4) complex has been determined to 3 A resolution. The monoclinic form of human TTR reported here crystallizes in space group P2(1), with unit-cell parameters a = 76.7 (6), b = 96.7 (8), c = 81.7 (4) A, beta = 106.8 (4) degrees. The asymmetric unit contains two tetramers of transthyretin related by the non-crystallographic symmetry (NCS) operation of a 90.28 degrees rotation between two hTTR molecules around an axis close to crystallographic z. The r.m.s. difference between the two tetramers calculated from their C(alpha) positions is 0.48 A. The structure was refined using 15.0-3.0 A resolution data to R = 22.9% and R(free) = 28.9% for reflections F > 0.0sigma(F), and R = 19.7% and R(free) = 25.8% for reflections F > 3.0sigma(F). The intermolecular interactions involve the tips of alpha-helices and loops around Arg21, Glu61 and Ser100 of all monomers. The electron-density maps revealed residual thyroxine (T(4)) bound in only one of the two unique tetrameric TTR molecules, with an occupancy of 53%, while the second tetramer is unliganded. One thyroxine ligand is bound in a way similar to the orientations described for the orthorhombic form of the hTTR-T(4) complex. The T(4) bound in the second site is positioned similar to 3',5'-dinitro-N-acetyl-L-thyronine in its hTTR complex. Differences in the size of the central channel defined by the D, A, G and H beta-strands of two monomeric subunits are observed between the apo TTR and T(4)-bound tetramer. The averaged distances between Ala108 C(alpha) and its equivalent measured across each binding site are 12.34 A for the T(4)-bound and 10.96 A for the unliganded TTR tetramer, respectively. The observed differences might reflect the mechanics of the ligand binding in the channel and possibly explain the observed negative cooperativity effect for ligand binding.


    Related Citations: 
    • STRUCTURAL ASPECTS OF INOTROPIC BIPYRIDINE BINDING. CRYSTAL STRUCTURE DETERMINATION TO 1.9 A OF THE HUMAN SERUM TRANSTHYRETIN-MILRINONE COMPLEX
      WOJTCZAK, A., LUFT, J.R., CODY, V.
      (1993) J Biol Chem 268: 6202
    • MECHANISM OF MOLECULAR RECOGNITION. STRUCTURAL ASPECTS OF 3,3'-DIIODO-L-THYRONINE BINDING TO HUMAN SERUM TRANSTHYRETIN
      WOJTCZAK, A., LUFT, J.R., CODY, V.
      (1992) J Biol Chem 267: 353
    • STRUCTURES OF HUMAN TRANSTHYRETIN COMPLEXED WITH THYROXINE AT 2.0 A RESOLUTION AND 3',5'-DINITRO-N-ACETYL-L-THYRONINE AT 2.2 A RESOLUTION
      WOJTCZAK, A., CODY, V., LUFT, J.R., PANGBORN, W.
      (1996) Acta Crystallogr D Biol Crystallogr 52: 758

    Organizational Affiliation

    Institute of Chemistry, Nicolas Copernicus University, 87-100 Torun, Poland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TRANSTHYRETINABCDEFGH127Homo sapiensMutation(s): 0 
Gene Names: TTRPALB
Find proteins for P02766 (Homo sapiens)
Explore P02766 
Go to UniProtKB:  P02766
NIH Common Fund Data Resources
PHAROS  P02766
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
T44
Query on T44

Download CCD File 
C, D
3,5,3',5'-TETRAIODO-L-THYRONINE
C15 H11 I4 N O4
XUIIKFGFIJCVMT-LBPRGKRZSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
T44IC50:  2200   nM  BindingDB
T44IC50:  2188   nM  BindingDB
T44IC50:  10500   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.229 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.69α = 90
b = 96.66β = 106.84
c = 81.74γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
CNSrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-04-03
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description