Crystal structure of the F87M/L110M mutant of human transthyretin at pH 4.6

Experimental Data Snapshot

  • Resolution: 1.38 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 

wwPDB Validation   3D Report Full Report

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Novel Zn2+-binding sites in human transthyretin: implications for amyloidogenesis and retinol-binding protein recognition.

Palmieri, L.de.C.Lima, L.M.Freire, J.B.Bleicher, L.Polikarpov, I.Almeida, F.C.Foguel, D.

(2010) J Biol Chem 285: 31731-31741

  • DOI: https://doi.org/10.1074/jbc.M110.157206
  • Primary Citation of Related Structures:  
    3DGD, 3DID, 3GPS, 3GRB, 3GRG

  • PubMed Abstract: 

    Human transthyretin (TTR) is a homotetrameric protein involved in several amyloidoses. Zn(2+) enhances TTR aggregation in vitro, and is a component of ex vivo TTR amyloid fibrils. We report the first crystal structure of human TTR in complex with Zn(2+) at pH 4.6-7.5. All four structures reveal three tetra-coordinated Zn(2+)-binding sites (ZBS 1-3) per monomer, plus a fourth site (ZBS 4) involving amino acid residues from a symmetry-related tetramer that is not visible in solution by NMR. Zn(2+) binding perturbs loop E-α-helix-loop F, the region involved in holo-retinol-binding protein (holo-RBP) recognition, mainly at acidic pH; TTR affinity for holo-RBP decreases ∼5-fold in the presence of Zn(2+). Interestingly, this same region is disrupted in the crystal structure of the amyloidogenic intermediate of TTR formed at acidic pH in the absence of Zn(2+). HNCO and HNCA experiments performed in solution at pH 7.5 revealed that upon Zn(2+) binding, although the α-helix persists, there are perturbations in the resonances of the residues that flank this region, suggesting an increase in structural flexibility. While stability of the monomer of TTR decreases in the presence of Zn(2+), which is consistent with the tertiary structural perturbation provoked by Zn(2+) binding, tetramer stability is only marginally affected by Zn(2+). These data highlight structural and functional roles of Zn(2+) in TTR-related amyloidoses, as well as in holo-RBP recognition and vitamin A homeostasis.

  • Organizational Affiliation

    Instituto de Bioquimica Medica, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-590, Brazil.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
127Homo sapiensMutation(s): 2 
Gene Names: TTRPLAB
UniProt & NIH Common Fund Data Resources
Find proteins for P02766 (Homo sapiens)
Explore P02766 
Go to UniProtKB:  P02766
PHAROS:  P02766
GTEx:  ENSG00000118271 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02766
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on GOL

Download Ideal Coordinates CCD File 
HA [auth D],
R [auth B],
S [auth B]
C3 H8 O3
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
CA [auth D]
DA [auth D]
E [auth A]
AA [auth D],
BA [auth D],
CA [auth D],
DA [auth D],
E [auth A],
F [auth A],
G [auth A],
J [auth A],
K [auth B],
L [auth B],
M [auth B],
Q [auth B],
T [auth C],
U [auth C],
Z [auth C]
Query on ACT

Download Ideal Coordinates CCD File 
EA [auth D]
FA [auth D]
GA [auth D]
H [auth A]
I [auth A]
EA [auth D],
FA [auth D],
GA [auth D],
H [auth A],
I [auth A],
N [auth B],
O [auth B],
P [auth B],
V [auth C],
W [auth C],
X [auth C],
Y [auth C]
C2 H3 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.38 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.95α = 90
b = 60.69β = 89.98
c = 82.99γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-07-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-08-30
    Changes: Data collection, Refinement description