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- PDB-7ybr: Crystal structure of human transthyretin variant A97S complexed w... -

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Basic information

Entry
Database: PDB / ID: 7ybr
TitleCrystal structure of human transthyretin variant A97S complexed with Tolcapone
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Transport thyroxine
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
Tolcapone / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsWang, Y.S. / Huang, C.H. / Tzeng, S.R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Protein Sci. / Year: 2023
Title: A molecular basis for tetramer destabilization and aggregation of transthyretin Ala97Ser.
Authors: Wang, Y.S. / Huang, C.H. / Liou, G.G. / Hsueh, H.W. / Liang, C.T. / Tseng, H.C. / Huang, S.J. / Chao, C.C. / Hsieh, S.T. / Tzeng, S.R.
History
DepositionJun 29, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)30,5384
Polymers29,9912
Non-polymers5462
Water2,540141
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0768
Polymers59,9834
Non-polymers1,0934
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Unit cell
Length a, b, c (Å)84.925, 42.929, 64.841
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-

TCW

21A-342-

HOH

31B-339-

HOH

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 14995.710 Da / Num. of mol.: 2 / Mutation: A97S
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-TCW / Tolcapone / (3,4-dihydroxy-5-nitrophenyl)(4-methylphenyl)methanone


Mass: 273.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H11NO5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.14 Å3/Da / Density % sol: 37.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 20% PEG 400, 200 mM Calcium Chloride, 100 mM HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.71→30 Å / Num. obs: 31836 / % possible obs: 99.5 % / Redundancy: 4.1 % / Biso Wilson estimate: 17.67 Å2 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.024 / Rrim(I) all: 0.049 / Net I/σ(I): 31.57377
Reflection shellResolution: 1.71→1.77 Å / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 3 / Num. unique obs: 2555 / Rpim(I) all: 0.211 / Rrim(I) all: 0.425 / % possible all: 99

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Processing

Software
NameVersionClassification
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.18.2_3874phasing
PHENIX1.19.2_4158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QGB

2qgb


Resolution: 1.71→25.87 Å / SU ML: 0.184 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.4889
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2194 1309 5.01 %
Rwork0.1775 24839 -
obs0.1796 26148 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.85 Å2
Refinement stepCycle: LAST / Resolution: 1.71→25.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1763 0 40 141 1944
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00741900
X-RAY DIFFRACTIONf_angle_d0.95492607
X-RAY DIFFRACTIONf_chiral_restr0.0636293
X-RAY DIFFRACTIONf_plane_restr0.007333
X-RAY DIFFRACTIONf_dihedral_angle_d14.7956668
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.780.29871420.22692682X-RAY DIFFRACTION98.95
1.78-1.860.22681430.18772727X-RAY DIFFRACTION99.97
1.86-1.960.23671440.17242728X-RAY DIFFRACTION99.72
1.96-2.080.20051440.16032725X-RAY DIFFRACTION99.58
2.08-2.240.19121440.16162750X-RAY DIFFRACTION99.62
2.24-2.470.2231430.17262722X-RAY DIFFRACTION99.44
2.47-2.820.24661470.18562783X-RAY DIFFRACTION99.56
2.82-3.560.18681470.17452798X-RAY DIFFRACTION99.39
3.56-25.870.22791550.18012924X-RAY DIFFRACTION99.26

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