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- PDB-5nfe: Neutron structure of human transthyretin (TTR) T119M mutant at ro... -

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Basic information

Entry
Database: PDB / ID: 5nfe
TitleNeutron structure of human transthyretin (TTR) T119M mutant at room temperature to 1.85A resolution
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / transthyretin / prealbumin / homotetramer
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, 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / NUCLEAR REACTOR / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.853 Å
AuthorsYee, A.W. / Moulin, M. / Blakeley, M.P. / Ostermann, A. / Cooper, J.B. / Haertlein, M. / Mitchell, E.P. / Forsyth, V.T.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilGR/R99393/01 United Kingdom
Engineering and Physical Sciences Research CouncilEP/C015452/1 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
DepositionMar 14, 2017Deposition 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


Theoretical massNumber of molelcules
Total (without water)28,1342
Polymers28,1342
Non-polymers00
Water68538
1
A: Transthyretin
B: Transthyretin

A: Transthyretin
B: Transthyretin


Theoretical massNumber of molelcules
Total (without water)56,2674
Polymers56,2674
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)43.710, 86.320, 65.338
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 14066.779 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 43.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 1.9M sodium malonate pD5.9, 40mg/ml protein

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12981
22931
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
NUCLEAR REACTORFRM II BIODIFF12.67
SYNCHROTRONESRF ID30B20.9763
Detector
TypeIDDetectorDate
BIODIFF1IMAGE PLATESep 8, 2016
DECTRIS PILATUS 6M-F2PIXELOct 4, 2016
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMneutron1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
12.671
20.97631
Reflection

Entry-ID: 5NFE / Num. obs: 19760

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsRpim(I) allDiffraction-IDNet I/σ(I)
1.85-43.6190.620.1640.13613.7
1.85-33.4997.34.40.0470.025227.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allDiffraction-ID% possible all
1.85-1.91.70.5261.212780.499183.7
1.85-1.954.30.06216.730590.033299.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
XDSdata reduction
HKL-2000data scaling
SCALAdata scaling
Cootmodel building
REFMACphasing
Refinement

Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: 5CM1

5cm1

Resolution (Å)Refine-IDRfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection obs% reflection Rfree (%)% reflection obs (%)SU MLσ(F)Phase error
1.853-43.16X-RAY DIFFRACTION0.19410.16480.167720912089610.0196.340.161.9917.58
1.85-33.485NEUTRON DIFFRACTION0.25360.21320.21731975197441090.690.2322.81
Refinement stepCycle: LAST / Resolution: 1.853→43.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1794 0 0 38 1832
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144043
X-RAY DIFFRACTIONf_angle_d1.5487226
X-RAY DIFFRACTIONf_dihedral_angle_d13.3371959
X-RAY DIFFRACTIONf_chiral_restr0.082288
X-RAY DIFFRACTIONf_plane_restr0.009780
NEUTRON DIFFRACTIONf_bond_d0.0144043
NEUTRON DIFFRACTIONf_angle_d1.5487226
NEUTRON DIFFRACTIONf_dihedral_angle_d13.3371959
NEUTRON DIFFRACTIONf_chiral_restr0.082288
NEUTRON DIFFRACTIONf_plane_restr0.009780
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8529-1.8960.23571370.17271237X-RAY DIFFRACTION97
1.896-1.94340.21591400.15471246X-RAY DIFFRACTION99
1.9434-1.9960.19381390.14741253X-RAY DIFFRACTION98
1.996-2.05470.18231370.14421252X-RAY DIFFRACTION97
2.0547-2.1210.17541350.14691211X-RAY DIFFRACTION95
2.121-2.19680.20491410.1471272X-RAY DIFFRACTION99
2.1968-2.28480.17261410.15111257X-RAY DIFFRACTION99
2.2848-2.38880.19181380.15131252X-RAY DIFFRACTION98
2.3888-2.51470.20711410.16461255X-RAY DIFFRACTION97
2.5147-2.67220.18631410.16981280X-RAY DIFFRACTION98
2.6722-2.87850.22031400.17141254X-RAY DIFFRACTION96
2.8785-3.16810.23981340.18061209X-RAY DIFFRACTION93
3.1681-3.62630.20311410.16051276X-RAY DIFFRACTION96
3.6263-4.5680.16451420.15021271X-RAY DIFFRACTION96
4.568-43.17170.18481440.19321280X-RAY DIFFRACTION90
1.8503-1.89660.34691280.31591151NEUTRON DIFFRACTION84
1.8966-1.94790.28821310.25991175NEUTRON DIFFRACTION86
1.9479-2.00520.29351300.25191180NEUTRON DIFFRACTION85
2.0052-2.06990.29251320.23031187NEUTRON DIFFRACTION87
2.0699-2.14390.26451360.21691215NEUTRON DIFFRACTION89
2.1439-2.22970.2431370.21951232NEUTRON DIFFRACTION89
2.2297-2.33120.25321370.21911239NEUTRON DIFFRACTION89
2.3312-2.4540.24521420.21691283NEUTRON DIFFRACTION93
2.454-2.60770.24671470.20421311NEUTRON DIFFRACTION94
2.6077-2.8090.24711460.19931333NEUTRON DIFFRACTION96
2.809-3.09150.30131550.20131381NEUTRON DIFFRACTION97
3.0915-3.53840.21761520.18571372NEUTRON DIFFRACTION97
3.5384-4.45630.19861510.15661355NEUTRON DIFFRACTION94
4.4563-33.49060.20511510.19471355NEUTRON DIFFRACTION89

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