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- PDB-8w2w: Structure of transthyretin synthetic mutation A120L -

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Basic information

Entry
Database: PDB / ID: 8w2w
TitleStructure of transthyretin synthetic mutation A120L
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Tetramer
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsYang, K. / Sun, X. / Ferguson, J.A. / Stanfield, R.L. / Wright, P.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)DK34909 United States
CitationJournal: Protein Sci. / Year: 2024
Title: Mispacking of the F87 sidechain drives aggregation-promoting conformational fluctuations in the subunit interfaces of the transthyretin tetramer.
Authors: Sun, X. / Ferguson, J.A. / Yang, K. / Stanfield, R.L. / Dyson, H.J. / Wright, P.E.
History
DepositionFeb 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2024Group: Database references / Category: citation / citation_author
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 / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transthyretin


Theoretical massNumber of molelcules
Total (without water)15,9471
Polymers15,9471
Non-polymers00
Water23413
1
A: Transthyretin

A: Transthyretin

A: Transthyretin

A: Transthyretin


  • defined by author&software
  • Evidence: NMR Distance Restraints, TTR is well established in the literature as a functional tetramer. However, NMR experiments in this paper show this synthetic mutant to have both monomeric and tetrameric states.
  • 63.8 kDa, 4 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)63,7884
Polymers63,7884
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area6300 Å2
ΔGint-39 kcal/mol
Surface area19030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.141, 64.069, 84.633
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 15947.064 Da / Num. of mol.: 1 / Mutation: A120L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P02766
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 1.79 Å3/Da / Density % sol: 31.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M sodium cacodylate (pH 6.5), 1M sodium chloride, 10% (v/v) glycerol, and 30% (v/v) PEG 600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.07→32.03 Å / Num. obs: 7206 / % possible obs: 99.7 % / Redundancy: 5.6 % / Biso Wilson estimate: 40.59 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.022 / Rrim(I) all: 0.075 / Net I/σ(I): 15.1
Reflection shellResolution: 2.07→2.14 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.628 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 361 / CC1/2: 0.889 / Rpim(I) all: 0.31 / Rrim(I) all: 0.703 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5127refinement
HKL-2000data scaling
PHENIXphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→32.03 Å / SU ML: 0.2279 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 29.2866
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2355 712 9.91 %
Rwork0.2098 6476 -
obs0.2124 7188 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.23 Å2
Refinement stepCycle: LAST / Resolution: 2.07→32.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms901 0 0 13 914
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046924
X-RAY DIFFRACTIONf_angle_d0.54831259
X-RAY DIFFRACTIONf_chiral_restr0.0514144
X-RAY DIFFRACTIONf_plane_restr0.0065159
X-RAY DIFFRACTIONf_dihedral_angle_d13.0962326
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.230.31191170.31311233X-RAY DIFFRACTION94.08
2.23-2.450.28121360.26921274X-RAY DIFFRACTION99.37
2.45-2.810.32891410.27371299X-RAY DIFFRACTION99.72
2.81-3.540.27231740.21921286X-RAY DIFFRACTION99.86
3.54-32.030.17481440.16911384X-RAY DIFFRACTION100
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)
12.122514375947.56316199903-5.639015606097.95143670172-6.039532264135.10327521919-0.1205479084230.27413056206-2.48606509514-0.314877072084-0.0403013234409-1.331536231130.8919041530390.1202354598330.4991011383620.2969106148760.041155676850.01017402082380.4567765598970.02069617263460.5747300571290.19417639294216.42180807428.04591493918
21.211985205972.86039745031-3.304093026628.30822962192-8.577877232232.053066958520.957983169836-0.5051794804480.07623160724951.40096447711-0.764070837846-0.885921964308-0.6876488914822.703078921060.3920680747670.1422128419270.05881418932970.1028933653060.642877175043-0.1888198371490.45255115611112.017625156121.48639046863.33833522154
37.67398236375-0.0175420427774-0.5018738245086.157170994770.7402041584687.23042715267-0.219746488278-2.043454449740.07592717878651.124068613620.1018074018170.449265940814-0.6827106271520.33099245086-0.01213349121830.49830977647-0.0138334791003-0.04335950268230.494129569052-0.06475991633860.303803370554-1.3287439212622.13038550823.6267453692
47.530882040681.21698143714-2.849903104592.92777799962-1.001930940096.73725113128-0.168594339106-0.225591112264-0.1369949132690.244069773010.179185297216-0.1856847489280.06133397271250.991330698207-0.06186117199580.2370089381230.006490626888-0.05423747017630.343497949328-0.01583807935240.2108549097212.3708348419718.948402253814.1832133787
56.56595862132-3.21664856729-0.417315455683.6557248404-3.093496752125.20301473935-0.05155944969891.325335688541.343927382921.297539933170.002178211119-0.837294995965-0.9819200414911.2383911512-0.1250330712680.799296705729-0.289901677354-0.04787555872580.899971408251-0.1321472796450.93837691944613.483046847432.421862769811.0875111434
64.707838001890.981868908384-6.16720553857.44870097677-2.225871810658.51852469851.19473056368-0.01420100834720.3621025328620.0895478337671-0.3136883973030.246452616683-0.936136662780.167751378423-0.8651494169570.5460047860030.0007631111373490.09062792647210.327698938851-0.01071277996410.329367086056-5.1632772457426.420085984515.348400723
75.08559068221-0.3509521029380.4692403587557.830001632487.793787089777.88633300746-1.033404415080.922110943576-1.24132202304-0.869328376741-2.658527024141.089343122850.17778076705-2.184130225052.643628615131.09746664835-0.2579256257750.1892982698261.233017236120.1319997228331.10375257153-16.786331583516.061052968613.2812453581
84.431758664193.03827580079-3.864503120555.06430026784-4.434303216465.49964243686-0.4867993525950.6157935740920.309269812337-0.4062665205981.093986303730.4332361261590.240672998426-0.708943546546-0.4989362943390.247712052936-0.002217182530540.02438063852080.3440672515150.009331003448670.405883320573-1.3132096413224.49211718066.44480041405
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 9 through 18 )9 - 181 - 10
22chain 'A' and (resid 19 through 28 )19 - 2811 - 20
33chain 'A' and (resid 29 through 48 )29 - 4821 - 40
44chain 'A' and (resid 49 through 81 )49 - 8141 - 73
55chain 'A' and (resid 82 through 90 )82 - 9074 - 82
66chain 'A' and (resid 91 through 97 )91 - 9783 - 89
77chain 'A' and (resid 98 through 103 )98 - 10390 - 95
88chain 'A' and (resid 104 through 124 )104 - 12496 - 116

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