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- PDB-5al0: Transthyretin binding heterogeneity and anti-amyloidogenic activi... -

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Basic information

Entry
Database: PDB / ID: 5al0
TitleTransthyretin binding heterogeneity and anti-amyloidogenic activity of natural polyphenols and their metabolites: resveratrol-3-O-sulfate
ComponentsTRANSTHYRETIN
KeywordsTRANSPORT PROTEIN / AMYLOID / FIBRILLOGENESIS / FIBRILLOGENESIS INHIBITORS / POLYPHENOLS / POLYPHENOL METABOLITES / NEGATIVE COOPERATIVITY
Function / homology
Function and homology information


Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation ...Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / 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/hydroxyisourate hydrolase domain / 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 ...Transthyretin/hydroxyisourate hydrolase domain / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
RESVERATROL-3-O-SULFATE / Transthyretin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.388 Å
AuthorsFlorio, P. / Foll, C. / Cianci, M. / Del Rio, D. / Zanotti, G. / Berni, R.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Transthyretin Binding Heterogeneity and Anti-Amyloidogenic Activity of Natural Polyphenols and Their Metabolites
Authors: Florio, P. / Folli, C. / Cianci, M. / Del Rio, D. / Zanotti, G. / Berni, R.
History
DepositionMar 5, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Jan 13, 2016Group: Database references
Revision 2.0May 15, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Experimental preparation / Other
Category: atom_site / exptl_crystal_grow ...atom_site / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_struct_special_symmetry
Item: _atom_site.occupancy / _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)28,4427
Polymers27,5552
Non-polymers8875
Water4,756264
1
A: TRANSTHYRETIN
B: TRANSTHYRETIN
hetero molecules

A: TRANSTHYRETIN
B: TRANSTHYRETIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,88314
Polymers55,1094
Non-polymers1,77410
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area7570 Å2
ΔGint-106.7 kcal/mol
Surface area19480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.814, 85.569, 64.122
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-1127-

R3S

21A-1127-

R3S

31A-1127-

R3S

41A-1127-

R3S

51B-1126-

R3S

61A-2009-

HOH

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Components

#1: Protein TRANSTHYRETIN / ATTR / PREALBUMIN / TBPA


Mass: 13777.360 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 21-147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET11B / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: P02766
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-R3S / RESVERATROL-3-O-SULFATE


Mass: 308.306 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H12O6S
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O

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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: 2.3 Å3/Da / Density % sol: 46.7 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: CRYSTALS OF WT HUMAN TTR- LIGAND COMPLEXES WERE OBTAINED AT ROOM TEMPERATURE IN ABOUT ONE WEEK BY CO-CRYSTALLIZATION, USING THE HANGING-DROP VAPOR DIFFUSION METHOD. THE PROTEIN (5 MG/ML), IN ...Details: CRYSTALS OF WT HUMAN TTR- LIGAND COMPLEXES WERE OBTAINED AT ROOM TEMPERATURE IN ABOUT ONE WEEK BY CO-CRYSTALLIZATION, USING THE HANGING-DROP VAPOR DIFFUSION METHOD. THE PROTEIN (5 MG/ML), IN 20 MM SODIUM PHOSPHATE, PH 7, WAS INCUBATED WITH A FOUR-FOLD MOLAR EXCESS OF LIGANDS SOLUBILIZED IN DMSO. DROPS WERE FORMED BY MIXING EQUAL VOLUMES OF THE SOLUTION CONTAINING LIGAND-TTR COMPLEXES AND OF THE RESERVOIR/PRECIPITANT SOLUTION (2.2 M AMMONIUM SULPHATE, 0.1 M KCL, 0.03 M SODIUM PHOSPHATE, PH 7.0).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.967
DetectorType: DECTRIS PAD P2M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.967 Å / Relative weight: 1
ReflectionResolution: 1.39→42.78 Å / Num. obs: 45697 / % possible obs: 96.8 % / Observed criterion σ(I): 3.2 / Redundancy: 3.4 % / Biso Wilson estimate: 14.65 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 22.8
Reflection shellResolution: 1.39→1.46 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.2 / % possible all: 93.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F41

1f41


Resolution: 1.388→42.785 Å / SU ML: 0.13 / σ(F): 1.36 / Phase error: 20.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2089 2342 5 %
Rwork0.1711 --
obs0.173 46830 96.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.388→42.785 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1785 0 56 264 2105
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082206
X-RAY DIFFRACTIONf_angle_d1.183059
X-RAY DIFFRACTIONf_dihedral_angle_d12.827807
X-RAY DIFFRACTIONf_chiral_restr0.069328
X-RAY DIFFRACTIONf_plane_restr0.007401
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3883-1.41670.242920.22041733X-RAY DIFFRACTION66
1.4167-1.44750.26561350.26572547X-RAY DIFFRACTION96
1.4475-1.48120.34271360.27792581X-RAY DIFFRACTION96
1.4812-1.51820.24231380.2312610X-RAY DIFFRACTION98
1.5182-1.55930.28371360.21872616X-RAY DIFFRACTION98
1.5593-1.60510.21651400.18272674X-RAY DIFFRACTION100
1.6051-1.6570.22141410.18032662X-RAY DIFFRACTION100
1.657-1.71620.19861410.18262680X-RAY DIFFRACTION100
1.7162-1.78490.251410.18212689X-RAY DIFFRACTION100
1.7849-1.86610.1911410.18082663X-RAY DIFFRACTION100
1.8661-1.96450.23631370.16192612X-RAY DIFFRACTION97
1.9645-2.08760.19531410.16622664X-RAY DIFFRACTION98
2.0876-2.24880.2021410.15382672X-RAY DIFFRACTION99
2.2488-2.47510.16461410.15872710X-RAY DIFFRACTION100
2.4751-2.83310.2041450.16292733X-RAY DIFFRACTION100
2.8331-3.56920.18471460.16432779X-RAY DIFFRACTION100
3.5692-42.80480.2151500.15742863X-RAY DIFFRACTION99

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