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- PDB-8awi: Crystal structure of Human Transthyretin at 1.15 Angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 8awi
TitleCrystal structure of Human Transthyretin at 1.15 Angstrom resolution
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Transthyretin / hormone-binding protein / thyroxine / transport / fluorescence / amyloid
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 / molecular sequestering activity / Non-integrin membrane-ECM interactions / 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 / molecular sequestering activity / Non-integrin membrane-ECM interactions / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsDerbyshire, D.J. / Hammarstrom, P. / von Castelmur, E. / Begum, A.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council2019-04405 Sweden
CitationJournal: Acs Chem Neurosci / Year: 2023
Title: Transthyretin Binding Mode Dichotomy of Fluorescent trans -Stilbene Ligands.
Authors: Begum, A. / Zhang, J. / Derbyshire, D. / Wu, X. / Konradsson, P. / Hammarstrom, P. / von Castelmur, E.
History
DepositionAug 29, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 15, 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
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2274
Polymers26,1812
Non-polymers462
Water3,855214
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4558
Polymers52,3634
Non-polymers924
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area6680 Å2
ΔGint-70 kcal/mol
Surface area19430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.853, 64.325, 85.863
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-337-

HOH

21B-321-

HOH

31B-401-

HOH

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 13090.689 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Evidence for alternative conformation(s) for loop A:100-103 at crystal packing interface. Density not convincing enough to model with full occupancy.
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Production host: Escherichia coli (E. coli) / References: UniProt: P02766
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.34 Å3/Da / Density % sol: 47.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: protein at 5.2mg/ml in 10mM sodium phosphate pH7.6 and 100mM potassium chloride was mixed 1:1 with 1.3-1.6M sodium citrate and 3.5% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.97993 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97993 Å / Relative weight: 1
ReflectionResolution: 1.15→64.325 Å / Num. obs: 84053 / % possible obs: 98.8 % / Redundancy: 23.1 % / CC1/2: 0.996 / Net I/σ(I): 19.5
Reflection shellResolution: 1.15→1.17 Å / Num. unique obs: 39058 / CC1/2: 0.67

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Processing

Software
NameVersionClassification
REFMAC5.8.0349refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in-house model

Resolution: 1.15→64.325 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.1658 --RANDOM
Rwork0.1475 ---
obs0.14846 79621 98.6969 %-
Displacement parametersBiso max: 107.83 Å2 / Biso mean: 20.7441 Å2 / Biso min: 11.46 Å2
Refinement stepCycle: LAST / Resolution: 1.15→64.325 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1776 0 2 214 1992

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