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- PDB-9rsr: Cryogenic crystal structure of the TTR mutant V30M at pH5. -

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Basic information

Entry
Database: PDB / ID: 9rsr
TitleCryogenic crystal structure of the TTR mutant V30M at pH5.
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Transthyretin Amyloidosis V30M mutation Familial amyloidotic polyneuropathy
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, 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: 1.25 Å
AuthorsSagot, J. / Fisher, Z.F. / Forsyth, T.V.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryogenic crystal structure of the TTR mutant V30M at pH5.
Authors: Sagot, J. / Fisher, Z.F. / Forsyth, T.V.
History
DepositionJul 1, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release

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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)25,2762
Polymers25,2762
Non-polymers00
Water3,585199
1
A: Transthyretin
B: Transthyretin

A: Transthyretin
B: Transthyretin


Theoretical massNumber of molelcules
Total (without water)50,5534
Polymers50,5534
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area6250 Å2
ΔGint-44 kcal/mol
Surface area19570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.392, 43.004, 63.685
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-2240-

HOH

21A-2295-

HOH

31B-247-

HOH

41B-288-

HOH

51B-289-

HOH

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 12638.168 Da / Num. of mol.: 2 / Mutation: V30M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P02766
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.46 Å3/Da / Density % sol: 50 % / Description: diamond shaped
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 2.15 M sodium malonate pH 5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.72932 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 14, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.72932 Å / Relative weight: 1
ReflectionResolution: 1.25→63.697 Å / Num. obs: 64266 / % possible obs: 98.9 % / Redundancy: 13.2 % / Biso Wilson estimate: 15.85 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.055 / Rrim(I) all: 0.058 / Net I/σ(I): 24.3
Reflection shellResolution: 1.25→1.3 Å / Redundancy: 13.1 % / Rmerge(I) obs: 0.643 / Mean I/σ(I) obs: 4 / Num. unique obs: 6135 / CC1/2: 0.872 / Rrim(I) all: 0.669 / % possible all: 95.7

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Processing

Software
NameVersionClassification
PHENIX1.21refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→30.3 Å / SU ML: 0.1389 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.6645
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2089 1999 3.11 %
Rwork0.1976 62256 -
obs0.198 64255 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.56 Å2
Refinement stepCycle: LAST / Resolution: 1.25→30.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1780 0 0 199 1979
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082050
X-RAY DIFFRACTIONf_angle_d1.09612826
X-RAY DIFFRACTIONf_chiral_restr0.0913313
X-RAY DIFFRACTIONf_plane_restr0.0335372
X-RAY DIFFRACTIONf_dihedral_angle_d13.4488747
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.290.31011350.26724181X-RAY DIFFRACTION94.88
1.29-1.320.30341400.26264365X-RAY DIFFRACTION98.36
1.32-1.360.24341400.24894375X-RAY DIFFRACTION98.47
1.36-1.40.24771410.23144399X-RAY DIFFRACTION98.91
1.4-1.450.21941410.23584402X-RAY DIFFRACTION98.61
1.45-1.510.23881420.22274402X-RAY DIFFRACTION99.08
1.51-1.580.2441430.21264429X-RAY DIFFRACTION99.2
1.58-1.660.21551410.21354432X-RAY DIFFRACTION99.2
1.66-1.770.23861430.20944453X-RAY DIFFRACTION99.2
1.77-1.90.20221440.1934462X-RAY DIFFRACTION99.59
1.9-2.10.21911440.18494503X-RAY DIFFRACTION99.64
2.1-2.40.20671460.18214542X-RAY DIFFRACTION99.77
2.4-3.020.19111470.20384560X-RAY DIFFRACTION99.89
3.02-30.30.1921520.18264751X-RAY DIFFRACTION99.29

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