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- PDB-2qel: Crystal structure of the highly amyloidogenic transthyretin mutan... -

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Basic information

Entry
Database: PDB / ID: 2qel
TitleCrystal structure of the highly amyloidogenic transthyretin mutant TTR G53S/E54D/L55S- heated protein
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Greek key / Beta barrel / Beta-slip / Protein heating
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/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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsKarlsson, A. / Sauer-Eriksson, A.E.
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Heating of proteins as a means of improving crystallization: a successful case study on a highly amyloidogenic triple mutant of human transthyretin
Authors: Karlsson, A. / Sauer-Eriksson, A.E.
#1: Journal: Mol.Cell / Year: 2000
Title: The beta-slip: a new concept in transthyretin amyloidosis
Authors: Eneqvist, T. / Andersson, K. / Olofsson, A. / Lundgren, E. / Sauer-Eriksson, A.E.
#2: Journal: J.Mol.Biol. / Year: 2000
Title: A comparative analysis of 23 structures of the amyloidogenic protein transthyretin
Authors: Hornberg, A. / Eneqvist, T. / Olofsson, A. / Lundgren, E. / Sauer-Eriksson, A.E.
History
DepositionJun 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Transthyretin
B: Transthyretin
C: Transthyretin
D: Transthyretin


Theoretical massNumber of molelcules
Total (without water)55,0694
Polymers55,0694
Non-polymers00
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.360, 58.360, 229.160
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 13767.280 Da / Num. of mol.: 4 / Mutation: G53S,E54D,L55S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Plasmid: pET3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P02766
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.04 Å3/Da / Density % sol: 39.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris, 2.4M Ammonium sulphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.115 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 14, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115 Å / Relative weight: 1
ReflectionResolution: 2.29→76.472 Å / Num. obs: 20038 / % possible obs: 93.9 % / Observed criterion σ(I): 0 / Redundancy: 9.9 % / Rmerge(I) obs: 0.114 / Rsym value: 0.114 / Net I/σ(I): 3.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.29-2.428.90.5541.42477327970.55492
2.42-2.569.50.4551.62071421910.45576.3
2.56-2.7410.20.3212.22753227050.321100
2.74-2.9610.30.213.42628625520.21100
2.96-3.2410.40.1395.12452323570.139100
3.24-3.6310.40.16.52244921520.1100
3.63-4.199.70.1922.11644617000.19288.7
4.19-5.1310.40.04315.31550514980.04392.2
5.13-7.2510.10.03916.61335513170.039100
7.25-29.188.90.03119.768697690.03198

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.74 Å29.18 Å
Translation2.74 Å29.18 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1g1o

1g1o


Resolution: 2.29→15 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.864 / SU B: 16.671 / SU ML: 0.218 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.289 1018 5.1 %RANDOM
Rwork0.231 ---
obs0.234 19892 93.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.065 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20.34 Å20 Å2
2--0.68 Å20 Å2
3----1.02 Å2
Refinement stepCycle: LAST / Resolution: 2.29→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3472 0 0 150 3622
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223577
X-RAY DIFFRACTIONr_angle_refined_deg1.5671.9364891
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7585457
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.27723.286140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.11815517
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2461516
X-RAY DIFFRACTIONr_chiral_restr0.1050.2562
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022715
X-RAY DIFFRACTIONr_nbd_refined0.2170.21376
X-RAY DIFFRACTIONr_nbtor_refined0.3080.22275
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2238
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2850.210
X-RAY DIFFRACTIONr_mcbond_it2.5191.52346
X-RAY DIFFRACTIONr_mcangle_it4.44323699
X-RAY DIFFRACTIONr_scbond_it3.25531425
X-RAY DIFFRACTIONr_scangle_it4.4714.51191
LS refinement shellResolution: 2.29→2.351 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 73 -
Rwork0.251 1199 -
obs-1272 83.52 %
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)
10.57290.52010.67492.5628-0.46021.58370.00480.17320.02410.2017-0.1923-0.2102-0.17190.39350.18750.0191-0.0252-0.0020.04940.0277-0.0506-14.0849.105-25.741
21.10210.00121.4131.1232-1.85754.8885-0.0227-0.038-0.00250.07750.13660.036-0.1514-0.1093-0.1139-0.06210.04040.0173-0.0324-0.0224-0.0894-33.6388.909-23.89
31.01890.06850.08791.9529-0.45645.4561-0.0217-0.0649-0.13520.01730.0042-0.13460.66850.82930.01750.06140.0965-0.00540.0763-0.0114-0.0633-13.827-11.543-10.429
41.53980.146-1.61290.04050.14354.98020.02070.0042-0.0171-0.029-0.0386-0.02540.306-0.18340.01790.0524-0.0324-0.0022-0.0134-0.0123-0.1123-32.756-14.227-14.805
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA11 - 12511 - 125
2X-RAY DIFFRACTION2BB11 - 12411 - 124
3X-RAY DIFFRACTION3CC12 - 12512 - 125
4X-RAY DIFFRACTION4DD10 - 12510 - 125

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