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- PDB-8c85: Crystal structure of human transthyretin in complex with 3-O-meth... -

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Basic information

Entry
Database: PDB / ID: 8c85
TitleCrystal structure of human transthyretin in complex with 3-O-methyltolcapone analogue 1
ComponentsTransthyretin
KeywordsLIPID BINDING PROTEIN / AMYLOIDOSIS / TETRAMER / BINDING PROTEIN / TRANSPORT PROTEIN
Function / homology
Function and homology information


Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / Non-integrin membrane-ECM interactions / purine nucleobase metabolic process / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation ...Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / Non-integrin membrane-ECM interactions / purine nucleobase metabolic process / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / extracellular space / 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-U1F / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 Å
AuthorsPoonsiri, T. / Benini, S. / Loconte, V. / Cianci, M.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Ministry of Education Italy
CitationJournal: Int J Mol Sci / Year: 2023
Title: 3-O-Methyltolcapone and Its Lipophilic Analogues Are Potent Inhibitors of Transthyretin Amyloidogenesis with High Permeability and Low Toxicity.
Authors: Poonsiri, T. / Dell'Accantera, D. / Loconte, V. / Casnati, A. / Cervoni, L. / Arcovito, A. / Benini, S. / Ferrari, A. / Cipolloni, M. / Cacioni, E. / De Franco, F. / Giacche, N. / Rinaldo, S. ...Authors: Poonsiri, T. / Dell'Accantera, D. / Loconte, V. / Casnati, A. / Cervoni, L. / Arcovito, A. / Benini, S. / Ferrari, A. / Cipolloni, M. / Cacioni, E. / De Franco, F. / Giacche, N. / Rinaldo, S. / Folli, C. / Sansone, F. / Berni, R. / Cianci, M.
History
DepositionJan 18, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Database references / Category: citation
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Transthyretin
A: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1594
Polymers27,5552
Non-polymers6052
Water3,333185
1
B: Transthyretin
A: Transthyretin
hetero molecules

B: Transthyretin
A: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3198
Polymers55,1094
Non-polymers1,2094
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Unit cell
Length a, b, c (Å)42.059, 84.862, 64.275
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11B-201-

U1F

21A-201-

U1F

31A-201-

U1F

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Components

#1: Protein Transthyretin / / ATTR / Prealbumin / TBPA


Mass: 13777.360 Da / Num. of mol.: 2
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-U1F / (3,5-dimethylphenyl)-(3-methoxy-5-nitro-4-oxidanyl-phenyl)methanone


Mass: 302.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H16NO5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.88 Å3/Da / Density % sol: 33.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M calcium acetate hydrate, 0.1 M Tris 7.5, and 25% w/v PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.885 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 3, 2021
RadiationMonochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.885 Å / Relative weight: 1
ReflectionResolution: 1.19→42.06 Å / Num. obs: 74428 / % possible obs: 99.86 % / Observed criterion σ(I): 1.5 / Redundancy: 7.1 % / Biso Wilson estimate: 13.35 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.028 / Net I/σ(I): 11.5
Reflection shellResolution: 1.19→1.21 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.205 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3634 / CC1/2: 0.52 / Rpim(I) all: 0.533 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.19→37.68 Å / SU ML: 0.1321 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 15.8189
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1679 3746 5.03 %
Rwork0.1422 70673 -
obs0.1434 74419 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.22 Å2
Refinement stepCycle: LAST / Resolution: 1.19→37.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1792 0 44 185 2021
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01982232
X-RAY DIFFRACTIONf_angle_d1.66943131
X-RAY DIFFRACTIONf_chiral_restr0.1184349
X-RAY DIFFRACTIONf_plane_restr0.0136412
X-RAY DIFFRACTIONf_dihedral_angle_d6.3511360
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.19-1.210.30691340.26612599X-RAY DIFFRACTION99.89
1.21-1.220.27671290.2512564X-RAY DIFFRACTION100
1.22-1.240.28581210.23532626X-RAY DIFFRACTION100
1.24-1.260.25041330.21792563X-RAY DIFFRACTION100
1.26-1.270.22531370.20152614X-RAY DIFFRACTION100
1.27-1.290.25691400.20112563X-RAY DIFFRACTION100
1.29-1.320.24591450.18532622X-RAY DIFFRACTION99.96
1.32-1.340.21581380.17242542X-RAY DIFFRACTION99.96
1.34-1.360.19591310.14982626X-RAY DIFFRACTION99.86
1.36-1.390.17391490.13612574X-RAY DIFFRACTION99.96
1.39-1.420.18551350.13912593X-RAY DIFFRACTION99.89
1.42-1.450.20491350.13172601X-RAY DIFFRACTION99.85
1.45-1.480.16611430.12462592X-RAY DIFFRACTION100
1.48-1.520.16831260.12622601X-RAY DIFFRACTION99.89
1.52-1.560.16591500.12032609X-RAY DIFFRACTION99.93
1.56-1.610.14171630.11172593X-RAY DIFFRACTION100
1.61-1.660.16181360.10592597X-RAY DIFFRACTION99.96
1.66-1.720.14251200.10732635X-RAY DIFFRACTION99.96
1.72-1.780.15611410.11082629X-RAY DIFFRACTION99.96
1.78-1.870.14421410.11052597X-RAY DIFFRACTION100
1.87-1.960.15421340.11242648X-RAY DIFFRACTION99.96
1.96-2.090.14011420.11872635X-RAY DIFFRACTION99.89
2.09-2.250.13351590.11652609X-RAY DIFFRACTION99.68
2.25-2.480.1541490.13292655X-RAY DIFFRACTION99.68
2.48-2.830.18241300.14132662X-RAY DIFFRACTION99.57
2.83-3.570.15151490.14472695X-RAY DIFFRACTION99.54
3.57-37.680.17771360.16892829X-RAY DIFFRACTION99.2

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