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

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Basic information

Entry
Database: PDB / ID: 5akv
TitleTransthyretin binding heterogeneity and anti-amyloidogenic activity of natural polyphenols and their metabolites: genistein-7-O- glucuronide
ComponentsTRANSTHYRETIN
KeywordsTRANSPORT PROTEIN / AMYLOID / FIBRILLOGENESIS / FIBRILLOGENESIS INHIBITORS / POLYPHENOLS / POLYPHENOL METABOLITES / TRANSTHYRETIN / NEGATIVE COOPERATIVITY
Function / homology
Function and homology information


Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / hormone binding / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / molecular sequestering activity / phototransduction, visible light / retinoid metabolic process / Retinoid metabolism and transport ...Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / hormone binding / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / molecular sequestering activity / phototransduction, visible light / retinoid metabolic process / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / protein-containing complex binding / protein-containing complex / 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
Genistein-7-O-glucuronide / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 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 1.3Mar 7, 2018Group: Data collection / Source and taxonomy / Category: diffrn_source / entity_src_gen
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.4May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5Jan 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)28,4474
Polymers27,5552
Non-polymers8932
Water4,053225
1
A: TRANSTHYRETIN
B: TRANSTHYRETIN
hetero molecules

A: TRANSTHYRETIN
B: TRANSTHYRETIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8958
Polymers55,1094
Non-polymers1,7854
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area6190 Å2
ΔGint-44.2 kcal/mol
Surface area19220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.843, 84.959, 63.636
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-1126-

G7G

21A-1126-

G7G

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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-G7G / Genistein-7-O-glucuronide


Mass: 446.361 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H18O11
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.967
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 31, 2013 / Details: KB MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.967 Å / Relative weight: 1
ReflectionResolution: 1.52→63.64 Å / Num. obs: 36372 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 6.5 % / Biso Wilson estimate: 20.08 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.8
Reflection shellResolution: 1.52→1.55 Å / Redundancy: 6 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3 / % possible all: 98.5

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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: 1.52→63.636 Å / SU ML: 0.16 / σ(F): 1.36 / Phase error: 20.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2004 1819 5 %
Rwork0.1702 --
obs0.1717 36328 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.52→63.636 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1785 0 64 225 2074
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112093
X-RAY DIFFRACTIONf_angle_d1.5152896
X-RAY DIFFRACTIONf_dihedral_angle_d14.741757
X-RAY DIFFRACTIONf_chiral_restr0.051322
X-RAY DIFFRACTIONf_plane_restr0.008376
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.52-1.56110.3021450.24072593X-RAY DIFFRACTION99
1.5611-1.60710.25231400.21312604X-RAY DIFFRACTION99
1.6071-1.6590.27381330.21712603X-RAY DIFFRACTION99
1.659-1.71830.24871390.20492620X-RAY DIFFRACTION99
1.7183-1.78710.22491280.20232640X-RAY DIFFRACTION100
1.7871-1.86840.21851270.17792634X-RAY DIFFRACTION99
1.8684-1.96690.20061420.16462616X-RAY DIFFRACTION100
1.9669-2.09010.17521430.16622641X-RAY DIFFRACTION100
2.0901-2.25150.23061270.16132691X-RAY DIFFRACTION100
2.2515-2.47810.19231300.1642668X-RAY DIFFRACTION100
2.4781-2.83670.20171540.16822673X-RAY DIFFRACTION100
2.8367-3.57390.20521480.16482699X-RAY DIFFRACTION99
3.5739-63.69130.17491630.1612827X-RAY DIFFRACTION99

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