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- PDB-3tct: Structure of wild-type TTR in complex with tafamidis -

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Basic information

Entry
Database: PDB / ID: 3tct
TitleStructure of wild-type TTR in complex with tafamidis
ComponentsTransthyretin
KeywordsHORMONE / BINDING PROTEIN / AMYLOID / AMYLOIDOSIS / DISEASE MUTATION / GAMMA-CARBOXYGLUTAMIC ACID / GLYCOPROTEIN / NEUROPATHY / SECRETED / THYROID HORMONE / TRANSPORT / Kinetic Stabilizer / Inhibition of the Amyloid Cascade
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/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-3MI / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsConnelly, S. / Kelly, J.W. / Wilson, I.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Tafamidis, a potent and selective transthyretin kinetic stabilizer that inhibits the amyloid cascade.
Authors: Bulawa, C.E. / Connelly, S. / Devit, M. / Wang, L. / Weigel, C. / Fleming, J.A. / Packman, J. / Powers, E.T. / Wiseman, R.L. / Foss, T.R. / Wilson, I.A. / Kelly, J.W. / Labaudiniere, R.
History
DepositionAug 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references
Revision 1.2Sep 13, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)28,1714
Polymers27,5552
Non-polymers6162
Water2,540141
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3428
Polymers55,1094
Non-polymers1,2324
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6180 Å2
ΔGint-44 kcal/mol
Surface area19290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.749, 84.994, 64.334
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-128-

3MI

21A-128-

3MI

31A-128-

3MI

41B-128-

3MI

51B-128-

3MI

61B-128-

3MI

71A-192-

HOH

81B-190-

HOH

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 13777.360 Da / Num. of mol.: 2 / Fragment: unp residues 21-147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PALB, TTR / Plasmid: PMMHA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): EPICUREAN GOLD / References: UniProt: P02766
#2: Chemical ChemComp-3MI / 2-(3,5-dichlorophenyl)-1,3-benzoxazole-6-carboxylic acid / Tafamidis


Mass: 308.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H7Cl2NO3 / Comment: medication*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.12 Å3/Da / Density % sol: 42 %
Crystal growpH: 5.5
Details: THE WT-TTR WAS CONCENTRATED TO 4 MG/ML IN 10 MM NAPI, 100 MM KCL, AT PH 7.6 AND CO-CRYSTALLIZED AT ROOM TEMPERATURE WITH INHIBITORS USING THE VAPOR-DIFFUSION SITTING DROP METHOD, CRYSTALS ...Details: THE WT-TTR WAS CONCENTRATED TO 4 MG/ML IN 10 MM NAPI, 100 MM KCL, AT PH 7.6 AND CO-CRYSTALLIZED AT ROOM TEMPERATURE WITH INHIBITORS USING THE VAPOR-DIFFUSION SITTING DROP METHOD, CRYSTALS WERE GROWN FROM 1.395 M SODIUM CITRATE, 3.5% V/V GLYCEROL AT PH 5.5. THE CRYSTALS WERE FROZEN USING A CRYO-PROTECTANT SOLUTION OF 1.395 M SODIUM CITRATE, PH 5.5, CONTAINING 10% V/V GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298.0K

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9795 / Wavelength: 0.9795 Å
Detector
TypeIDDetectorDateDetails
MARMOSAIC 325 mm CCD1CCDFeb 19, 2010FLAT MIRROR (VERTICAL FOCUSING)
2SINGLE CRYSTAL SI(111) BENT MONOCHROMATOR (HO RIZONTAL FOCUSING)
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SIDE SCATTERING BENT CUBE-ROOT I -BEAM SINGLE CRYSTALSINGLE WAVELENGTHMx-ray1
2ASYMMETRIC CUT 4.965 DEGSMx-ray1
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 58308 / % possible obs: 99.4 % / Redundancy: 7 % / Biso Wilson estimate: 16.9 Å2 / Rsym value: 0.035 / Net I/σ(I): 51.5
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.4 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.4.0077refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2FBR

2fbr


Resolution: 1.3→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.383 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.192 2940 5.1 %RANDOM
Rwork0.161 ---
obs0.163 58122 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2---0.28 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1773 0 40 141 1954
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222021
X-RAY DIFFRACTIONr_bond_other_d0.0030.021336
X-RAY DIFFRACTIONr_angle_refined_deg1.6821.9692790
X-RAY DIFFRACTIONr_angle_other_deg1.5593.0013277
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9935274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.51424.15789
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.02215327
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9731510
X-RAY DIFFRACTIONr_chiral_restr0.1090.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212306
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02408
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0781.51220
X-RAY DIFFRACTIONr_mcbond_other1.0241.5489
X-RAY DIFFRACTIONr_mcangle_it3.19822006
X-RAY DIFFRACTIONr_scbond_it4.1893801
X-RAY DIFFRACTIONr_scangle_it6.2064.5762
X-RAY DIFFRACTIONr_rigid_bond_restr2.05633357
X-RAY DIFFRACTIONr_sphericity_free9.8433143
X-RAY DIFFRACTIONr_sphericity_bonded5.34933281
LS refinement shellResolution: 1.3→1.33 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 183 -
Rwork0.264 3915 -
obs--96.13 %

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