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- PDB-6e76: Structure of Human Transthyretin Asp38Ala/Thr119Met Mutant -

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Basic information

Entry
Database: PDB / ID: 6.0E+76
TitleStructure of Human Transthyretin Asp38Ala/Thr119Met 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, 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
ACETATE ION / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsSaelices, L. / Chung, K. / Sawaya, M.R. / Cascio, D. / Eisenberg, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)AG048120 United States
CitationJournal: To Be Published
Title: Structural Variants of Transthyretin
Authors: Saelices, L. / Chung, K. / Esswein, S. / Chou, J. / Liang, W. / Li, J.H. / Sawaya, M.R. / Cascio, D. / Eisenberg, D.
History
DepositionJul 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 2, 2025Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)25,6797
Polymers25,2802
Non-polymers3985
Water63135
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,35714
Polymers50,5614
Non-polymers79710
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
Buried area8450 Å2
ΔGint-92 kcal/mol
Surface area18750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.330, 85.330, 63.510
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 10 through 33 or resid 35...
21(chain B and (resid 10 through 33 or resid 35...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11OCSOCSPHEPHE(chain A and (resid 10 through 33 or resid 35...AA10 - 331 - 24
12LYSLYSVALVAL(chain A and (resid 10 through 33 or resid 35...AA35 - 7126 - 62
13ILEILETYRTYR(chain A and (resid 10 through 33 or resid 35...AA73 - 11464 - 105
14TYRTYRASNASN(chain A and (resid 10 through 33 or resid 35...AA116 - 124107 - 115
21OCSOCSPHEPHE(chain B and (resid 10 through 33 or resid 35...BB10 - 331 - 24
22LYSLYSVALVAL(chain B and (resid 10 through 33 or resid 35...BB35 - 7126 - 62
23ILEILETYRTYR(chain B and (resid 10 through 33 or resid 35...BB73 - 11464 - 105
24TYRTYRASNASN(chain B and (resid 10 through 33 or resid 35...BB116 - 124107 - 115

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 12640.183 Da / Num. of mol.: 2 / Mutation: D38A, T119M
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 47.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 50% (w/v) PEG-400, 0.2M Lithium Sulfate, 0.1M Sodium 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: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.6→63.51 Å / Num. obs: 31882 / % possible obs: 99.8 % / Redundancy: 12.865 % / Biso Wilson estimate: 28.48 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rrim(I) all: 0.051 / Χ2: 1.059 / Net I/σ(I): 25.84
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.6-1.6412.561.0112.4922610.7971.05497.9
1.64-1.6813.3030.8263.3522600.8650.859100
1.68-1.7313.1210.6444.4722070.9260.67100
1.73-1.7912.940.4336.821450.9710.451100
1.79-1.8412.5840.2879.7320690.9870.29999.8
1.84-1.9112.1770.18113.8820080.9930.18999.4
1.91-1.9813.5740.1320.0719720.9960.135100
1.98-2.0613.5370.10124.7618710.9980.105100
2.06-2.1513.3730.08228.5517930.9980.085100
2.15-2.2613.0960.06933.5717410.9990.072100
2.26-2.3812.1160.06434.7916390.9980.06799.9
2.38-2.5313.2290.05739.1315630.9990.05999.7
2.53-2.713.5990.05143.7714730.9990.053100
2.7-2.9213.250.04746.9813860.9990.049100
2.92-3.1912.6440.04449.6612850.9990.046100
3.19-3.5711.3460.0451.611560.9990.04299.9
3.57-4.1213.0130.03958.2110310.9990.04100
4.12-5.0512.6290.03758.4489210.039100
5.05-7.1410.9660.03952.17090.9980.0499.7
7.14-63.5111.5870.03853.44210.9990.04100

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementResolution: 1.6→63.51 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 21.93
RfactorNum. reflection% reflection
Rfree0.2159 3185 9.99 %
Rwork0.191 --
obs0.1935 31868 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 113.84 Å2 / Biso mean: 38.2846 Å2 / Biso min: 20.3 Å2
Refinement stepCycle: final / Resolution: 1.6→63.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1780 0 25 35 1840
Biso mean--66.12 39.2 -
Num. residues----230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051883
X-RAY DIFFRACTIONf_angle_d0.8232571
X-RAY DIFFRACTIONf_chiral_restr0.065287
X-RAY DIFFRACTIONf_plane_restr0.007326
X-RAY DIFFRACTIONf_dihedral_angle_d16.7561109
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A992X-RAY DIFFRACTION6.533TORSIONAL
12B992X-RAY DIFFRACTION6.533TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5974-1.62120.31161280.27141155128396
1.6212-1.64660.30371360.257312231359100
1.6466-1.67360.28331400.241412621402100
1.6736-1.70240.26311330.241411951328100
1.7024-1.73340.28661390.256712521391100
1.7334-1.76670.29521370.255912331370100
1.7667-1.80280.25051370.231912351372100
1.8028-1.8420.22691340.198212051339100
1.842-1.88480.21721400.18761257139799
1.8848-1.9320.24181360.182112301366100
1.932-1.98420.20151390.177512431382100
1.9842-2.04260.22041360.178912281364100
2.0426-2.10850.18441360.171912271363100
2.1085-2.18390.17961400.173512591399100
2.1839-2.27140.22211390.180112511390100
2.2714-2.37470.20631370.177912351372100
2.3747-2.49990.22781390.188712511390100
2.4999-2.65660.21951410.18612651406100
2.6566-2.86170.20451400.187512631403100
2.8617-3.14970.2181410.190612621403100
3.1497-3.60540.18671430.165112881431100
3.6054-4.54220.19891440.178812981442100
4.5422-63.56020.23811500.22191366151699
Refinement TLS params.Method: refined / Origin x: 44.0412 Å / Origin y: 29.7237 Å / Origin z: 79.2216 Å
111213212223313233
T0.2012 Å2-0.0119 Å2-0.0046 Å2-0.2123 Å20.0009 Å2--0.2373 Å2
L0.0711 °2-0.1609 °2-0.4353 °2-0.9353 °2-0.1781 °2--1.7798 °2
S-0.0543 Å °0.0252 Å °-0.1093 Å °-0.0193 Å °-0.0324 Å °0.0247 Å °0.075 Å °-0.0379 Å °0.0865 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA10 - 124
2X-RAY DIFFRACTION1allB10 - 124
3X-RAY DIFFRACTION1allC1 - 29
4X-RAY DIFFRACTION1allC30 - 40

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