1ICT

MONOCLINIC FORM OF HUMAN TRANSTHYRETIN COMPLEXED WITH THYROXINE (T4)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.289 
  • R-Value Work: 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.,Sect.D 57: 957-967


  • 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 crystalli ...

    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: 
    • 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.,Sect.D 52: 758
    • 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
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRANSTHYRETIN
A, B, C, D, E, F, G, H
127Homo sapiensGene Names: TTR (PALB)
Find proteins for P02766 (Homo sapiens)
Go to Gene View: TTR
Go to UniProtKB:  P02766
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
T44
Query on T44

Download SDF File 
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: 10500 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.229 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 76.690α = 90.00
b = 96.660β = 106.84
c = 81.740γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
X-PLORmodel building
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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