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- PDB-4i87: Crystal structure of TTR variant I84S in complex with CHF5074 at ... -

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Basic information

Entry
Database: PDB / ID: 4i87
TitleCrystal structure of TTR variant I84S in complex with CHF5074 at acidic pH
ComponentsTransthyretin
Keywordstransport protein/inhibitor / Transthyretin / amyloidosis / fibrillogenesis inhibitors / protein misfolding / T3 or T4 hormone / Plasma / transport protein-inhibitor complex
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 / Non-integrin membrane-ECM interactions / molecular sequestering activity / 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 / Non-integrin membrane-ECM interactions / molecular sequestering activity / 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
Chem-H50 / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsZanotti, G. / Cendron, L. / Folli, C. / Florio, P. / Imbimbo, B.P. / Berni, R.
Citation
Journal: Febs Lett. / Year: 2013
Title: Structural evidence for native state stabilization of a conformationally labile amyloidogenic transthyretin variant by fibrillogenesis inhibitors.
Authors: Zanotti, G. / Cendron, L. / Folli, C. / Florio, P. / Imbimbo, B.P. / Berni, R.
#1: Journal: J.Mol.Biol. / Year: 2007
Title: Acidic pH-induced conformational changes in amyloidogenic mutant transthyretin.
Authors: Pasquato, N. / Berni, R. / Folli, C. / Alfieri, B. / Cendron, L. / Zanotti, G.
#2: Journal: J.Biol.Chem. / Year: 2009
Title: Amyloidogenic potential of transthyretin variants: insights from structural and computational analyses.
Authors: Cendron, L. / Trovato, A. / Seno, F. / Folli, C. / Alfieri, B. / Zanotti, G. / Berni, R.
History
DepositionDec 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Aug 7, 2013Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)28,1534
Polymers27,5032
Non-polymers6502
Water5,170287
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3068
Polymers55,0054
Non-polymers1,3014
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area6220 Å2
ΔGint-43 kcal/mol
Surface area19590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.820, 84.660, 65.570
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-

H50

21B-201-

H50

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 13751.280 Da / Num. of mol.: 2 / Fragment: Transthyretin (unp residues 21-147) / Mutation: I84S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PALB, TTR / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02766
#2: Chemical ChemComp-H50 / 1-(3',4'-dichloro-2-fluorobiphenyl-4-yl)cyclopropanecarboxylic acid


Mass: 325.162 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H11Cl2FO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.16 Å3/Da / Density % sol: 43.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 15% (w/v) PEG 2000 monomethylether, 0.1 M ammonium sulfate, 0.05 M sodium acetate buffer, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 30, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.69→33.01 Å / Num. all: 27383 / Num. obs: 27383 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.7
Reflection shellResolution: 1.69→1.78 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.308 / Mean I/σ(I) obs: 5.2 / Num. unique all: 3948 / % possible all: 99.5

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F41

1f41


Resolution: 1.69→33.01 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Phase error: 18.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2115 1356 5.01 %random
Rwork0.1738 ---
obs0.1756 27083 98.72 %-
all-27383 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.807 Å2 / ksol: 0.335 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.9279 Å20 Å20 Å2
2--1.6207 Å2-0 Å2
3---0.3072 Å2
Refinement stepCycle: LAST / Resolution: 1.69→33.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1781 0 42 287 2110
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091890
X-RAY DIFFRACTIONf_angle_d1.2222589
X-RAY DIFFRACTIONf_dihedral_angle_d14.228652
X-RAY DIFFRACTIONf_chiral_restr0.091288
X-RAY DIFFRACTIONf_plane_restr0.009328
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.75040.27981270.22532456X-RAY DIFFRACTION96
1.7504-1.82050.2291370.19412487X-RAY DIFFRACTION96
1.8205-1.90330.22881320.16932501X-RAY DIFFRACTION99
1.9033-2.00370.20221330.16342562X-RAY DIFFRACTION99
2.0037-2.12920.21661190.16492567X-RAY DIFFRACTION99
2.1292-2.29350.21441200.16762578X-RAY DIFFRACTION99
2.2935-2.52430.22421430.17432598X-RAY DIFFRACTION100
2.5243-2.88940.21991320.17472606X-RAY DIFFRACTION100
2.8894-3.63950.20281540.16842631X-RAY DIFFRACTION100
3.6395-33.02020.19071590.17452741X-RAY DIFFRACTION99

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