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- PDB-8w48: Neutron and X-ray joint structure of WT-TTR in complex with picea... -

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Basic information

Entry
Database: PDB / ID: 8w48
TitleNeutron and X-ray joint structure of WT-TTR in complex with piceatannol
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Amyloidogenesis / Inhibitor / Neutron / Thyroid hormone
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, 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
DEUTERATED WATER / PICEATANNOL / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 Å
AuthorsYokoyama, T. / Kusaka, K. / Fujiwara, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2023
Title: Resveratrol Derivatives Inhibit Transthyretin Fibrillization: Structural Insights into the Interactions between Resveratrol Derivatives and Transthyretin.
Authors: Yokoyama, T. / Kusaka, K. / Mizuguchi, M. / Nabeshima, Y. / Fujiwara, S.
History
DepositionAug 23, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)35,1104
Polymers34,6212
Non-polymers4882
Water1,838102
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2198
Polymers69,2424
Non-polymers9774
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Unit cell
Length a, b, c (Å)43.670, 85.014, 65.353
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-201-

PIT

21A-201-

PIT

31B-201-

PIT

41B-201-

PIT

51B-343-

DOD

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 17310.518 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-PIT / PICEATANNOL / 4-[(E)-2-(3,5-DIHYDROXYPHENYL)ETHENYL]BENZENE-1,2-DIOL


Mass: 244.243 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H12O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: D2O
Has ligand of interestY

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.75 Å3/Da / Density % sol: 29.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Disodium malonate, 0.1M NaOAc pH 4.6

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
12931N
22931N
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-17A10.98
SPALLATION SOURCEJPARC MLF BL-03J-PARC MLF BEAMLINE BL-0322.8-5.7
Detector
TypeIDDetectorDate
DECTRIS EIGER X 16M1PIXELJun 19, 2022
iBIX2DIFFRACTOMETERMay 13, 2022
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2LAUELneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
22.81
35.71
Reflection

Entry-ID: 8W48

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Rpim(I) allRrim(I) allDiffraction-IDNet I/σ(I)
1.19-42.517855599.86.30.9990.0160.04123.8
1.9-22.331961398.86.970.9940.0620.153214.9
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allDiffraction-ID
1.19-1.232.376380.7740.3520.8761
1.9-1.972.718450.5560.3150.6462

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Processing

Refinement

SU ML: 0.12 / Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 21.36 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Stereochemistry target values: ML / Solvent model: FLAT BULK SOLVENT MODEL

Resolution (Å)Refine-IDRfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection obs% reflection Rfree (%)% reflection obs (%)σ(F)Diffraction-ID
1.19-42.507X-RAY DIFFRACTION0.20180.17930.1804392778550599.771.36
1.9-21.784NEUTRON DIFFRACTION0.20640.17830.1797977195794.9998.8701
Refinement stepCycle: LAST / Resolution: 1.19→42.507 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1771 0 36 102 1909
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0294040
X-RAY DIFFRACTIONf_angle_d0.9177160
X-RAY DIFFRACTIONf_dihedral_angle_d19.1211128
X-RAY DIFFRACTIONf_chiral_restr0.096284
X-RAY DIFFRACTIONf_plane_restr0.005776
NEUTRON DIFFRACTIONf_bond_d0.0294040
NEUTRON DIFFRACTIONf_angle_d0.9177160
NEUTRON DIFFRACTIONf_dihedral_angle_d19.1211128
NEUTRON DIFFRACTIONf_chiral_restr0.096284
NEUTRON DIFFRACTIONf_plane_restr0.005776
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.19-1.20440.30521300.30322465X-RAY DIFFRACTION96
1.2044-1.21960.29841400.2932676X-RAY DIFFRACTION100
1.2196-1.23570.29621380.29942622X-RAY DIFFRACTION100
1.2357-1.25260.26711400.27482654X-RAY DIFFRACTION100
1.2526-1.27050.24921380.25552629X-RAY DIFFRACTION100
1.2705-1.28950.26941390.24532655X-RAY DIFFRACTION100
1.2895-1.30960.26451390.24932636X-RAY DIFFRACTION100
1.3096-1.33110.25961400.24742655X-RAY DIFFRACTION100
1.3311-1.35410.25281380.24572619X-RAY DIFFRACTION100
1.3541-1.37870.2681390.23122643X-RAY DIFFRACTION100
1.3787-1.40520.26841400.22742660X-RAY DIFFRACTION100
1.4052-1.43390.23371390.22662642X-RAY DIFFRACTION100
1.4339-1.46510.26351390.2132654X-RAY DIFFRACTION100
1.4651-1.49920.22941390.21852639X-RAY DIFFRACTION100
1.4992-1.53660.21621400.21492645X-RAY DIFFRACTION100
1.5366-1.57820.23491410.20842679X-RAY DIFFRACTION100
1.5782-1.62460.22421400.20342671X-RAY DIFFRACTION100
1.6246-1.67710.21791410.20252682X-RAY DIFFRACTION100
1.6771-1.7370.18881390.19722638X-RAY DIFFRACTION100
1.737-1.80660.19151400.19012654X-RAY DIFFRACTION100
1.8066-1.88880.19041410.18392687X-RAY DIFFRACTION100
1.8888-1.98840.19181420.16852693X-RAY DIFFRACTION100
1.9884-2.11290.15671400.16192669X-RAY DIFFRACTION100
2.1129-2.27610.16771420.16032700X-RAY DIFFRACTION100
2.2761-2.50510.20231430.16432699X-RAY DIFFRACTION100
2.5051-2.86750.20851430.16832730X-RAY DIFFRACTION100
2.8675-3.61250.18181450.1622759X-RAY DIFFRACTION100
3.6125-42.5070.2031520.1652868X-RAY DIFFRACTION99
1.9-2.00010.27211350.242573NEUTRON DIFFRACTION98
2.0001-2.12530.23141360.21022601NEUTRON DIFFRACTION98
2.1253-2.28930.21131380.18472616NEUTRON DIFFRACTION99
2.2893-2.51930.20721390.1672660NEUTRON DIFFRACTION100
2.5193-2.88320.2121420.16822676NEUTRON DIFFRACTION100
2.8832-3.62980.21041420.16762707NEUTRON DIFFRACTION100
3.6298-21.7840.17351450.16432769NEUTRON DIFFRACTION98

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