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- PDB-4his: The Structure of V122I Mutant Transthyretin in Complex with Tafamidis -

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Basic information

Entry
Database: PDB / ID: 4his
TitleThe Structure of V122I Mutant Transthyretin in Complex with Tafamidis
ComponentsTransthyretin
KeywordsHORMONE BINDING PROTEIN/INHIBITOR / THYROID HORMONE TRANSPORT / Thyroxine / Retinol Binding Protein / HORMONE BINDING PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / Non-integrin membrane-ECM interactions / purine nucleobase metabolic process / 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) / Non-integrin membrane-ECM interactions / purine nucleobase metabolic process / 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: 1.2 Å
AuthorsConnelly, S. / Alhamadsheh, M. / Graef, I. / Wilson, I.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: AG10 inhibits amyloidogenesis and cellular toxicity of the familial amyloid cardiomyopathy-associated V122I transthyretin.
Authors: Penchala, S.C. / Connelly, S. / Wang, Y. / Park, M.S. / Zhao, L. / Baranczak, A. / Rappley, I. / Vogel, H. / Liedtke, M. / Witteles, R.M. / Powers, E.T. / Reixach, N. / Chan, W.K. / Wilson, ...Authors: Penchala, S.C. / Connelly, S. / Wang, Y. / Park, M.S. / Zhao, L. / Baranczak, A. / Rappley, I. / Vogel, H. / Liedtke, M. / Witteles, R.M. / Powers, E.T. / Reixach, N. / Chan, W.K. / Wilson, I.A. / Kelly, J.W. / Graef, I.A. / Alhamadsheh, M.M.
History
DepositionOct 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Sep 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 / 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

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Assembly

Deposited unit
A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8913
Polymers27,5832
Non-polymers3081
Water4,125229
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7826
Polymers55,1664
Non-polymers6162
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)42.673, 84.601, 64.317
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-

3MI

21A-201-

3MI

31A-201-

3MI

41A-354-

HOH

51B-342-

HOH

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Components

#1: Protein Transthyretin / / ATTR / Prealbumin / TBPA


Mass: 13791.387 Da / Num. of mol.: 2 / Mutation: V122I
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 / Tafamidis


Mass: 308.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H7Cl2NO3 / Comment: medication*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.1 Å3/Da / Density % sol: 41.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 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 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9797 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 16, 2012 / Details: Rh coated flat mirror
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.2→64.32 Å / Num. obs: 73110 / % possible obs: 99.6 % / Redundancy: 6.2 % / Biso Wilson estimate: 13.8 Å2 / Rsym value: 0.028 / Net I/σ(I): 26

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
autoXDSdata reduction
autoXDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FBR

2fbr


Resolution: 1.2→64.32 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.97 / WRfactor Rfree: 0.1685 / WRfactor Rwork: 0.1483 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.9033 / SU B: 1.103 / SU ML: 0.023 / SU R Cruickshank DPI: 0.0393 / SU Rfree: 0.0373 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.039 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.172 3679 5 %RANDOM
Rwork0.1531 ---
obs0.1541 73015 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 169.16 Å2 / Biso mean: 20.0954 Å2 / Biso min: 8.13 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å2-0 Å2-0 Å2
2---0.15 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.2→64.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1781 0 20 229 2030
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222023
X-RAY DIFFRACTIONr_bond_other_d0.0010.021339
X-RAY DIFFRACTIONr_angle_refined_deg1.7461.9692792
X-RAY DIFFRACTIONr_angle_other_deg0.9593.0023293
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2385269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.1982490
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.19215326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7451511
X-RAY DIFFRACTIONr_chiral_restr0.1090.2309
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212301
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02422
X-RAY DIFFRACTIONr_mcbond_it2.1181.51220
X-RAY DIFFRACTIONr_mcbond_other0.6771.5486
X-RAY DIFFRACTIONr_mcangle_it3.35522006
X-RAY DIFFRACTIONr_scbond_it4.2893803
X-RAY DIFFRACTIONr_scangle_it6.4094.5766
X-RAY DIFFRACTIONr_rigid_bond_restr1.85733362
LS refinement shellResolution: 1.201→1.232 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 236 -
Rwork0.236 4959 -
all-5195 -
obs--96.71 %

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