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- PDB-8yqd: Crystal structure of human transthyretin variant A97S in complex ... -

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Basic information

Entry
Database: PDB / ID: 8yqd
TitleCrystal structure of human transthyretin variant A97S in complex with Tafamidis
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Transport thyroxine
Function / homology
Function and homology information


Defective visual phototransduction due to STRA6 loss of function / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / hormone binding / Non-integrin membrane-ECM interactions / molecular sequestering activity / Retinoid metabolism and transport / retinoid metabolic process / hormone activity / azurophil granule lumen ...Defective visual phototransduction due to STRA6 loss of function / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / hormone binding / Non-integrin membrane-ECM interactions / molecular sequestering activity / Retinoid metabolism and transport / retinoid metabolic process / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / protein-containing complex binding / protein-containing complex / : / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Transthyretin, conserved site / Transthyretin signature 2. / Transthyretin, thyroxine binding site / Transthyretin signature 1. / Transthyretin / Transthyretin/hydroxyisourate hydrolase / Transthyretin/hydroxyisourate hydrolase domain / Transthyretin/hydroxyisourate hydrolase domain superfamily / HIUase/Transthyretin family
Similarity search - Domain/homology
Chem-3MI / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsTzeng, S.R. / Huang, C.H. / Wang, Y.S. / Hsieh, M.F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Ann Clin Transl Neurol / Year: 2024
Title: Diflunisal versus tafamidis on neuropathy and cardiomyopathy in hereditary transthyretin amyloidosis.
Authors: Chao, C.C. / Tzeng, S.R. / Chiang, M.C. / Hsueh, H.W. / Hsieh, W.J. / Chao, Y.C. / Cheng, M.F. / Lin, Y.H. / Su, M.Y. / Huang, C.H. / Wang, Y.S. / Hsieh, M.F. / Tseng, P.H. / Hsieh, S.T.
History
DepositionMar 19, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4924
Polymers26,8762
Non-polymers6162
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.303, 42.606, 63.774
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-200-

3MI

21A-200-

3MI

31A-200-

3MI

41B-200-

3MI

51B-200-

3MI

61B-200-

3MI

71B-329-

HOH

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 13437.952 Da / Num. of mol.: 2 / Mutation: A97S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Production host: Escherichia coli (E. coli) / References: UniProt: P02766
#2: Chemical ChemComp-3MI / 2-(3,5-dichlorophenyl)-1,3-benzoxazole-6-carboxylic acid / Tafamidis


Mass: 308.116 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C14H7Cl2NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.11 %
Crystal growTemperature: 310 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.05 M Calcium chloride dihydrate +0.1 M Bis-Tris +25% PEG 550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 07A / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 14, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.69→27.25 Å / Num. obs: 26616 / % possible obs: 99.7 % / Redundancy: 10.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.018 / Rrim(I) all: 0.057 / Net I/σ(I): 21.1
Reflection shellResolution: 1.69→1.75 Å / Rmerge(I) obs: 0.882 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2596 / CC1/2: 0.915 / Rrim(I) all: 0.928

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.69→27.25 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2246 1330 5 %
Rwork0.1965 --
obs0.1978 26595 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.69→27.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1762 0 40 112 1914
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012
X-RAY DIFFRACTIONf_angle_d1.114
X-RAY DIFFRACTIONf_dihedral_angle_d5.502246
X-RAY DIFFRACTIONf_chiral_restr0.062282
X-RAY DIFFRACTIONf_plane_restr0.008316
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.750.34251300.34252463X-RAY DIFFRACTION99
1.75-1.820.33921310.28282486X-RAY DIFFRACTION100
1.82-1.910.26691310.22332488X-RAY DIFFRACTION100
1.91-2.010.2631310.2062500X-RAY DIFFRACTION100
2.01-2.130.22631330.20192525X-RAY DIFFRACTION100
2.13-2.30.21391300.18542466X-RAY DIFFRACTION100
2.3-2.530.24291330.19922541X-RAY DIFFRACTION100
2.53-2.890.23581350.21032538X-RAY DIFFRACTION100
2.89-3.640.221340.18422565X-RAY DIFFRACTION100
3.64-100.19421420.18032693X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 12.6457 Å / Origin y: 21.9819 Å / Origin z: 15.7253 Å
111213212223313233
T0.1811 Å2-0.0125 Å2-0.0002 Å2-0.2395 Å2-0.0105 Å2--0.215 Å2
L1.4888 °2-0.0742 °2-0.2177 °2-0.8817 °2-0.3186 °2--1.5106 °2
S-0.0238 Å °0.0052 Å °-0.002 Å °-0.0264 Å °-0.0006 Å °-0.1092 Å °0.017 Å °0.1215 Å °0.0222 Å °
Refinement TLS groupSelection details: all

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