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- PDB-6fwd: Crystal structure of human transthyretin double mutant R34G/T119M... -

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Basic information

Entry
Database: PDB / ID: 6fwd
TitleCrystal structure of human transthyretin double mutant R34G/T119M at pH 5.5
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Amyloid / Gatekeeper / Aggregation / Stability
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.576 Å
AuthorsEsperante, S. / Ventura, S. / Reverter, D. / Varejao, N.
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Disease-associated mutations impacting BC-loop flexibility trigger long-range transthyretin tetramer destabilization and aggregation.
Authors: Esperante, S.A. / Varejao, N. / Pinheiro, F. / Sant'Anna, R. / Luque-Ortega, J.R. / Alfonso, C. / Sora, V. / Papaleo, E. / Rivas, G. / Reverter, D. / Ventura, S.
History
DepositionMar 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transthyretin
B: Transthyretin


Theoretical massNumber of molelcules
Total (without water)27,4152
Polymers27,4152
Non-polymers00
Water3,855214
1
A: Transthyretin
B: Transthyretin

A: Transthyretin
B: Transthyretin


Theoretical massNumber of molelcules
Total (without water)54,8294
Polymers54,8294
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area6410 Å2
ΔGint-50 kcal/mol
Surface area19520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.127, 63.958, 85.978
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11B-298-

HOH

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 13707.311 Da / Num. of mol.: 2 / Mutation: R34G, T119M
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 41.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 7% glycerol, 1.3 M sodium citrate, pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.576→63.958 Å / Num. obs: 31271 / % possible obs: 93 % / Redundancy: 7.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.047 / Rrim(I) all: 0.122 / Net I/σ(I): 15.7 / Num. measured all: 232010
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.576-1.5817.71.33126353420.6830.5261.4332.798.3
7.31-63.9586.20.04725184090.9970.0210.05236.6100

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
Aimlessdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASER1.7.3-928phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F41

1f41


Resolution: 1.576→51.317 Å / FOM work R set: 0.8465 / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2288 1555 4.99 %
Rwork0.1972 29615 -
obs0.1987 31170 92.7 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.231 Å2 / ksol: 0.374 e/Å3
Displacement parametersBiso max: 74.58 Å2 / Biso mean: 23.28 Å2 / Biso min: 10.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.2332 Å20 Å2-0 Å2
2--5.6517 Å2-0 Å2
3----4.4185 Å2
Refinement stepCycle: final / Resolution: 1.576→51.317 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1769 0 0 214 1983
Biso mean---34.32 -
Num. residues----230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161828
X-RAY DIFFRACTIONf_angle_d1.6812495
X-RAY DIFFRACTIONf_chiral_restr0.124283
X-RAY DIFFRACTIONf_plane_restr0.011318
X-RAY DIFFRACTIONf_dihedral_angle_d15.356641
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5757-1.62660.34191600.29242830299099
1.6266-1.68470.34261620.279728242986100
1.6847-1.75220.31651510.253828723023100
1.7522-1.8320.22951480.218828362984100
1.832-1.92850.25321050.19922507261286
1.9285-2.04940.22741100.18972193230376
2.0494-2.20760.21191440.188728703014100
2.2076-2.42980.21251340.1882465259985
2.4298-2.78130.23351220.19362330245280
2.7813-3.50410.211440.18612819296395
3.5041-51.34380.21221750.1843069324499
Refinement TLS params.Method: refined / Origin x: -22.5871 Å / Origin y: -15.8698 Å / Origin z: -12.9178 Å
111213212223313233
T0.1189 Å2-0.0027 Å2-0.0026 Å2-0.1482 Å2-0.0001 Å2--0.122 Å2
L0.5615 °20.0964 °20.0778 °2-0.8627 °2-0.0164 °2--0.8793 °2
S-0.0137 Å °0.0887 Å °-0.0158 Å °-0.0311 Å °0.0364 Å °-0.0248 Å °0.0455 Å °-0.016 Å °-0.0215 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA10 - 125
2X-RAY DIFFRACTION1allB10 - 125
3X-RAY DIFFRACTION1allS1 - 214

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