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- PDB-9s94: Crystal structure of human TTR mutant L111M bound to tafamidis -

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Basic information

Entry
Database: PDB / ID: 9s94
TitleCrystal structure of human TTR mutant L111M bound to tafamidis
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / TTR / transthyretin / mutant
Function / homology
Function and homology information


Defective visual phototransduction due to STRA6 loss of function / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / hormone binding / Non-integrin membrane-ECM interactions / molecular sequestering activity / Retinoid metabolism and transport / retinoid metabolic process / hormone activity / azurophil granule lumen ...Defective visual phototransduction due to STRA6 loss of function / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / hormone binding / Non-integrin membrane-ECM interactions / molecular sequestering activity / Retinoid metabolism and transport / retinoid metabolic process / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / protein-containing complex binding / : / protein-containing complex / 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
Chem-3MI / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCalderone, V. / Fragai, M. / Cerofolini, L. / Russomanno, P. / Callozzo, S.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Ministry of Education Italy
CitationJournal: To Be Published
Title: Crystal structure of human TTR mutant L111M bound to tafamidis
Authors: Calderone, V. / Fragai, M. / Cerofolini, L. / Russomanno, P. / Callozzo, S.
History
DepositionAug 6, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2026Provider: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0594
Polymers25,4432
Non-polymers6162
Water1,874104
1
B: Transthyretin
hetero molecules

A: Transthyretin
hetero molecules

A: Transthyretin
hetero molecules

B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1178
Polymers50,8854
Non-polymers1,2324
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation2_355-x-2,-y,z1
Unit cell
Length a, b, c (Å)42.343, 84.816, 63.043
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

41B-201-

3MI

51B-201-

3MI

61B-201-

3MI

71A-332-

HOH

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 12721.255 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Production host: Escherichia coli (E. coli) / 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 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.23 Å3/Da / Density % sol: 44.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES, 0.4 M CaCl2, 34% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 VENTURE / Wavelength: 1.541 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Apr 11, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 1.7→42.44 Å / Num. obs: 24345 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.1 / Net I/σ(I): 9
Reflection shellResolution: 1.7→1.8 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3673 / CC1/2: 0.64

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→42.44 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.585 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23302 1211 5 %RANDOM
Rwork0.21589 ---
obs0.21677 23131 94.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.447 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20 Å2-0 Å2
2---0.86 Å20 Å2
3---0.12 Å2
Refinement stepCycle: 1 / Resolution: 1.7→42.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1805 0 20 104 1929
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0121882
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161693
X-RAY DIFFRACTIONr_angle_refined_deg1.7471.8452571
X-RAY DIFFRACTIONr_angle_other_deg0.5861.7433916
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8545231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.60658
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.59310285
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.080.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022177
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02411
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_it2.7132.102924
X-RAY DIFFRACTIONr_mcbond_other2.7032.102924
X-RAY DIFFRACTIONr_mcangle_it4.4443.7511152
X-RAY DIFFRACTIONr_mcangle_other4.4423.7561153
X-RAY DIFFRACTIONr_scbond_it3.3242.567958
X-RAY DIFFRACTIONr_scbond_other3.3222.568959
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.254.511419
X-RAY DIFFRACTIONr_long_range_B_refined8.21123.422126
X-RAY DIFFRACTIONr_long_range_B_other8.19723.192112
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.743 Å
RfactorNum. reflection% reflection
Rfree0.336 84 -
Rwork0.323 1539 -
obs--87.97 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7802-0.2166-0.44360.65290.45470.44320.05440.04260.05090.0373-0.0476-0.00510.0006-0.0482-0.00680.03290.01380.00310.0146-0.00610.0406-19.00912.3467-5.8904
20.68680.4907-0.22020.6481-0.24820.2575-0.00360.03880.08190.0365-0.02240.04730.02450.01150.02610.0137-0.00510.00750.01430.01430.0348-21.627912.7712-25.6155
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 201
2X-RAY DIFFRACTION2B10 - 201

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