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- PDB-6fft: Neutron structure of human transthyretin (TTR) S52P mutant in com... -

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Basic information

Entry
Database: PDB / ID: 6fft
TitleNeutron structure of human transthyretin (TTR) S52P mutant in complex with tafamidis at room temperature to 2A resolution (quasi-Laue)
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / homotetramer / prealbumin / mutant-drug complex
Function / homology
Function and homology information


Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / 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 / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / 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, 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 / NEUTRON DIFFRACTION / NUCLEAR REACTOR / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYee, A.W. / Moulin, M. / Blakeley, M.P. / Haertlein, M. / Mitchell, E.P. / Forsyth, V.T.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/C015452/1 United Kingdom
Engineering and Physical Sciences Research CouncilGR/R99393/01 United Kingdom
CitationJournal: Nat Commun / Year: 2019
Title: A molecular mechanism for transthyretin amyloidogenesis.
Authors: Yee, A.W. / Aldeghi, M. / Blakeley, M.P. / Ostermann, A. / Mas, P.J. / Moulin, M. / de Sanctis, D. / Bowler, M.W. / Mueller-Dieckmann, C. / Mitchell, E.P. / Haertlein, M. / de Groot, B.L. / ...Authors: Yee, A.W. / Aldeghi, M. / Blakeley, M.P. / Ostermann, A. / Mas, P.J. / Moulin, M. / de Sanctis, D. / Bowler, M.W. / Mueller-Dieckmann, C. / Mitchell, E.P. / Haertlein, M. / de Groot, B.L. / Boeri Erba, E. / Forsyth, V.T.
History
DepositionJan 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 2, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)28,7104
Polymers28,0932
Non-polymers6162
Water46826
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4198
Polymers56,1874
Non-polymers1,2324
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)43.901, 85.703, 65.540
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

31B-201-

3MI

41B-201-

3MI

51B-201-

3MI

61B-201-

3MI

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 14046.725 Da / Num. of mol.: 2 / Mutation: P52S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Plasmid: pET-M11 / Production host: Escherichia coli BL21(DE3) (bacteria) / 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.: 26 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.3M sodium malonate pD 5.9

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
22931
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
NUCLEAR REACTORILL LADI III12.7-3.6
SYNCHROTRONESRF ID30B20.9763
Detector
TypeIDDetectorDate
LADI III1IMAGE PLATEMar 1, 2017
DECTRIS PILATUS 6M-F2PIXELMar 1, 2017
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1LAUELneutron1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
12.71
23.61
30.97631
Reflection

Entry-ID: 6FFT

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Biso Wilson estimate (Å2)Rmerge(I) obsRpim(I) allDiffraction-IDNet I/σ(I)
2-43.91722571.92.623.280.1210.0716
2-35.851210398.74.619.340.0410.021231
Reflection shell

Resolution: 2→2.11 Å

Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allDiffraction-ID% possible all
2.20.208413640.151156.3
4.70.04623.324730.023299.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
LAUEGENdata reduction
XDSdata reduction
LSCALEdata scaling
SCALAdata scaling
REFMACphasing
Cootmodel building
Refinement

SU ML: 0.16 / Cross valid method: NONE / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 18.94 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: 5CLX

5clx

Resolution (Å)Refine-IDRfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection obs% reflection Rfree (%)% reflection obs (%)σ(F)
2-42.852X-RAY DIFFRACTION0.19470.15740.16121718171929.9999.242.06
2-35.866NEUTRON DIFFRACTION0.28010.23130.236312111209710.0169.83
Refinement stepCycle: LAST / Resolution: 2→42.852 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1794 0 40 26 1860
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0174052
X-RAY DIFFRACTIONf_angle_d1.9757247
X-RAY DIFFRACTIONf_dihedral_angle_d14.6351949
X-RAY DIFFRACTIONf_chiral_restr0.088286
X-RAY DIFFRACTIONf_plane_restr0.01780
NEUTRON DIFFRACTIONf_bond_d0.0174052
NEUTRON DIFFRACTIONf_angle_d1.9757247
NEUTRON DIFFRACTIONf_dihedral_angle_d14.6351949
NEUTRON DIFFRACTIONf_chiral_restr0.088286
NEUTRON DIFFRACTIONf_plane_restr0.01780
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.0590.20461400.14341254X-RAY DIFFRACTION100
2.059-2.12550.22921410.14411276X-RAY DIFFRACTION100
2.1255-2.20140.22521420.14491269X-RAY DIFFRACTION99
2.2014-2.28960.16281360.14191234X-RAY DIFFRACTION97
2.2896-2.39380.21011430.14361284X-RAY DIFFRACTION100
2.3938-2.51990.21291410.16841276X-RAY DIFFRACTION100
2.5199-2.67780.23431430.15811284X-RAY DIFFRACTION100
2.6778-2.88450.19721440.17031289X-RAY DIFFRACTION100
2.8845-3.17470.22571440.18281302X-RAY DIFFRACTION100
3.1747-3.63390.18911440.16081297X-RAY DIFFRACTION99
3.6339-4.57750.15951450.14111299X-RAY DIFFRACTION98
4.5775-42.86130.18271550.16551410X-RAY DIFFRACTION100
1.9998-2.07990.3895970.3654864NEUTRON DIFFRACTION51
2.0799-2.17460.35251070.3484977NEUTRON DIFFRACTION58
2.1746-2.28920.38131190.32121066NEUTRON DIFFRACTION62
2.2892-2.43260.36231230.30471107NEUTRON DIFFRACTION65
2.4326-2.62030.29941290.29221162NEUTRON DIFFRACTION68
2.6203-2.88390.32071350.25951209NEUTRON DIFFRACTION71
2.8839-3.3010.30721520.24231374NEUTRON DIFFRACTION79
3.301-4.15790.26351730.19521549NEUTRON DIFFRACTION88
4.1579-35.87160.21061760.17051578NEUTRON DIFFRACTION85

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