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- PDB-8w1n: Structure of transthyretin pathogenic mutation A120S -

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Basic information

Entry
Database: PDB / ID: 8w1n
TitleStructure of transthyretin pathogenic mutation A120S
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Tetramer
Function / homology
Function and homology information


Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / 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 / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsFerguson, J.A. / Stanfield, R.L. / Wright, P.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)DK34909 United States
CitationJournal: Protein Sci. / Year: 2024
Title: Mispacking of the F87 sidechain drives aggregation-promoting conformational fluctuations in the subunit interfaces of the transthyretin tetramer.
Authors: Sun, X. / Ferguson, J.A. / Yang, K. / Stanfield, R.L. / Dyson, H.J. / Wright, P.E.
History
DepositionFeb 16, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transthyretin
B: Transthyretin


Theoretical massNumber of molelcules
Total (without water)27,8492
Polymers27,8492
Non-polymers00
Water3,927218
1
A: Transthyretin
B: Transthyretin

A: Transthyretin
B: Transthyretin


Theoretical massNumber of molelcules
Total (without water)55,6984
Polymers55,6984
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)43.114, 86.280, 64.088
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
11A-287-

HOH

21B-221-

HOH

31B-271-

HOH

41B-297-

HOH

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 13924.557 Da / Num. of mol.: 2 / Mutation: A120S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P02766
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.34 Å3/Da / Density % sol: 42.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M MES at pH 6.0, 10% (v/v) glycerol, 5% (w/v) PEG 1000, and 30% (v/v) PEG 600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9765 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 1.6→38.6 Å / Num. obs: 31452 / % possible obs: 97.7 % / Redundancy: 7.6 % / Biso Wilson estimate: 20.88 Å2 / CC1/2: 0.835 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.037 / Rrim(I) all: 0.102 / Net I/σ(I): 20.7
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 2.23 / Mean I/σ(I) obs: 1 / Num. unique obs: 1493 / CC1/2: 0.333 / Rpim(I) all: 0.855 / Rrim(I) all: 2.4 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5127refinement
HKL-2000v722data scaling
PHENIX1.21phasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→38.57 Å / SU ML: 0.2608 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.3207
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.284 1605 5.16 %
Rwork0.2438 29499 -
obs0.2459 31104 96.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.99 Å2
Refinement stepCycle: LAST / Resolution: 1.6→38.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1787 0 0 218 2005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611894
X-RAY DIFFRACTIONf_angle_d0.8292602
X-RAY DIFFRACTIONf_chiral_restr0.0552298
X-RAY DIFFRACTIONf_plane_restr0.0072333
X-RAY DIFFRACTIONf_dihedral_angle_d14.8634684
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.650.38051390.3232517X-RAY DIFFRACTION92.58
1.65-1.710.36841480.31742627X-RAY DIFFRACTION96.45
1.71-1.780.35441350.31922662X-RAY DIFFRACTION96.58
1.78-1.860.33191420.32412653X-RAY DIFFRACTION96.91
1.86-1.960.53991340.45532562X-RAY DIFFRACTION91.98
1.96-2.080.30561670.25682636X-RAY DIFFRACTION97.6
2.08-2.240.27391390.26472672X-RAY DIFFRACTION96.14
2.24-2.470.32941450.27482677X-RAY DIFFRACTION96.15
2.47-2.820.29531700.22452749X-RAY DIFFRACTION98.95
2.83-3.560.21971440.20042810X-RAY DIFFRACTION98.99
3.56-38.570.22441420.19182934X-RAY DIFFRACTION98.18

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