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- PDB-4tlk: Crystal Structure of Human Transthyretin Ser85Pro/Glu92Pro Mutant -

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Basic information

Entry
Database: PDB / ID: 4tlk
TitleCrystal Structure of Human Transthyretin Ser85Pro/Glu92Pro Mutant
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / human transthyretin / amyloid / transthyretin / mutant
Function / homology
Function and homology information


Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / hormone binding / purine nucleobase metabolic process / molecular sequestering activity / Non-integrin membrane-ECM interactions / phototransduction, visible light / retinoid metabolic process / Retinoid metabolism and transport ...Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / hormone binding / purine nucleobase metabolic process / molecular sequestering activity / Non-integrin membrane-ECM interactions / phototransduction, visible light / retinoid metabolic process / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / protein-containing complex binding / protein-containing complex / 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
DI(HYDROXYETHYL)ETHER / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.44 Å
AuthorsSaelices, L. / Cascio, D. / Sawaya, M. / Eisenberg, D.S.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Uncovering the Mechanism of Aggregation of Human Transthyretin.
Authors: Saelices, L. / Johnson, L.M. / Liang, W.Y. / Sawaya, M.R. / Cascio, D. / Ruchala, P. / Whitelegge, J. / Jiang, L. / Riek, R. / Eisenberg, D.S.
History
DepositionMay 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Dec 9, 2015Group: Database references
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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)28,1467
Polymers27,7952
Non-polymers3505
Water1,802100
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,29114
Polymers55,5904
Non-polymers70110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
Buried area8740 Å2
ΔGint-86 kcal/mol
Surface area19040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.980, 85.240, 63.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-203-

PEG

21A-305-

HOH

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 13897.609 Da / Num. of mol.: 2 / Fragment: UNP residues 29-147 / Mutation: S85P, E92P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: P02766
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 39.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% (W/V) PEG-1000, 0.1M Imidazole, 0.2M Calcium Acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 1, 2013
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.44→63.38 Å / Num. obs: 48638 / % possible obs: 99 % / Redundancy: 6.7 % / Biso Wilson estimate: 21.48 Å2 / Net I/σ(I): 13.34

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Processing

Software
NameVersionClassificationNB
PDB_EXTRACT3.14data extraction
BUSTER2.10.0refinement
XSCALEdata scaling
RefinementResolution: 1.44→63.38 Å / Cor.coef. Fo:Fc: 0.9578 / Cor.coef. Fo:Fc free: 0.9526 / SU R Cruickshank DPI: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.065 / SU Rfree Blow DPI: 0.062 / SU Rfree Cruickshank DPI: 0.062
RfactorNum. reflection% reflectionSelection details
Rfree0.2014 2105 5.03 %RANDOM
Rwork0.1886 ---
obs0.1892 41846 99.79 %-
Displacement parametersBiso max: 126.13 Å2 / Biso mean: 25.51 Å2 / Biso min: 13.12 Å2
Baniso -1Baniso -2Baniso -3
1-1.4631 Å20 Å20 Å2
2---0.5952 Å20 Å2
3----0.868 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: final / Resolution: 1.44→63.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1773 0 22 100 1895
Biso mean--66.96 33.44 -
Num. residues----230
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d613SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes35HARMONIC2
X-RAY DIFFRACTIONt_gen_planes277HARMONIC5
X-RAY DIFFRACTIONt_it1866HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion251SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2156SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1866HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2550HARMONIC21.05
X-RAY DIFFRACTIONt_omega_torsion4.07
X-RAY DIFFRACTIONt_other_torsion15.65
LS refinement shellResolution: 1.44→1.48 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2525 161 5.37 %
Rwork0.2286 2838 -
all0.2299 2999 -
obs--99.79 %
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)
10.5170.21590.22110.75250.34850.6232-0.04450.0573-0.0656-0.0857-0.01460.00930.0076-0.02360.0591-0.0232-0.00890.0013-0.0132-0.0203-0.015644.113829.890569.4463
20.6673-0.25770.21380.5296-0.28330.7825-0.0148-0.0275-0.11010.0764-0.01730.02750.01580.01370.0321-0.01720.006-0.0002-0.02280.0173-0.012541.612129.420489.0831
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A10 - 124
2X-RAY DIFFRACTION2{ B|* }B10 - 124

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