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- PDB-8jqw: Crystal structure of V30I mutated human transthyretin -

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Basic information

Entry
Database: PDB / ID: 8jqw
TitleCrystal structure of V30I mutated human transthyretin
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Thyroid hormone-binding protein
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) / purine nucleobase metabolic process / molecular sequestering activity / phototransduction, visible light / Non-integrin membrane-ECM interactions / retinoid metabolic process / Retinoid metabolism and transport / hormone activity ...Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / molecular sequestering activity / phototransduction, visible light / Non-integrin membrane-ECM interactions / retinoid metabolic process / 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: 1.8 Å
AuthorsMizuguchi, M. / Yamada, S. / Obita, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP17028015 Japan
CitationJournal: Febs J. / Year: 2024
Title: Trypsin-induced aggregation of transthyretin Valine 30 variants associated with hereditary amyloidosis.
Authors: Mizuguchi, M. / Obita, T. / Yamada, S. / Nabeshima, Y.
History
DepositionJun 15, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)29,9564
Polymers29,9072
Non-polymers492
Water2,810156
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9128
Polymers59,8154
Non-polymers974
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area6560 Å2
ΔGint-60 kcal/mol
Surface area19260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.170, 85.640, 64.020
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-335-

HOH

21B-355-

HOH

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 14953.739 Da / Num. of mol.: 2 / Mutation: V30I
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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.98 Å3/Da / Density % sol: 37.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6 / Details: PEG400, MgCl2, glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→51.28 Å / Num. obs: 22870 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 18.2 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.078 / Net I/σ(I): 15.6
Reflection shellResolution: 1.8→1.89 Å / Rmerge(I) obs: 0.312 / Mean I/σ(I) obs: 5.5 / Num. unique obs: 3273 / CC1/2: 0.946

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→38.55 Å / SU ML: 0.1841 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.2964
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2216 1108 4.85 %
Rwork0.1765 21727 -
obs0.1786 22835 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.82 Å2
Refinement stepCycle: LAST / Resolution: 1.8→38.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1771 0 2 156 1929
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00691833
X-RAY DIFFRACTIONf_angle_d0.89442503
X-RAY DIFFRACTIONf_chiral_restr0.066288
X-RAY DIFFRACTIONf_plane_restr0.0076315
X-RAY DIFFRACTIONf_dihedral_angle_d5.6009249
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.880.25231460.20932678X-RAY DIFFRACTION100
1.88-1.980.22431430.17092640X-RAY DIFFRACTION100
1.98-2.10.26281510.17122663X-RAY DIFFRACTION100
2.1-2.260.19921400.16472694X-RAY DIFFRACTION100
2.26-2.490.24081200.17922709X-RAY DIFFRACTION100
2.49-2.850.22891400.18482718X-RAY DIFFRACTION99.97
2.85-3.590.19521370.1792759X-RAY DIFFRACTION100
3.59-38.550.21931310.17142866X-RAY DIFFRACTION98.98
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)
16.076567388661.14371137599-3.957261698457.75972327065-3.054227152936.87786933972-0.3627320703510.671896307424-0.386396813537-0.6007672970310.200869567279-0.03355798330890.608515555876-0.4011833969170.1254416515520.160002921481-0.0203317282936-0.0178832895420.139256608358-0.003617171553870.103867850847-26.7739630439.4302330861-34.4630459288
27.819535645113.90248508251-0.435258880233.58940435859-1.998246857472.101434026340.04613332256120.03883663215950.238371942178-0.0793121083417-0.0529011266657-0.107579465881-0.05112537397820.3024702883650.0391038657850.1060542306090.0128134749603-0.004349724507280.04878772841060.0268905205060.148385232959-15.454302790418.772589583-29.7527493744
33.546140035210.5799395616152.309966983934.251511282891.998854253637.705257753570.130616631688-0.1105963051280.02971319777370.115954659039-0.2347765704710.2173038055410.00566060198428-0.487528831310.1191023010220.09506277571580.008652865361290.02139991615830.126816089038-0.008737220100730.122351528042-34.639299776411.8081702198-17.3133824604
44.01669372985.63089569484-4.222160252059.0385949316-4.810612841518.05528126880.0525825247161-0.2768894860340.8092237518840.3134276033170.1660808643760.328736096237-0.0546598476476-0.368502869847-0.1662721250850.107226046564-0.0104525330017-0.002845618424920.137637104492-0.002053696977760.127359484659-15.767901676715.4033127002-21.6269223758
55.725097003843.86732798007-5.424637784564.75130281063-2.931186297625.70434739797-0.1565827953110.255380598133-0.0118951175601-0.3515292836990.132954476205-0.4487293093450.2043198709410.09894543545270.09953786904050.1445012730690.01901474803180.006016681652430.1271007804450.02677509198060.158030434583-13.83091172079.78958837367-28.0326840677
64.60136192547-0.911777414018-5.348317202771.975513783441.306258430956.4521636654-0.03740572366330.177561806505-0.0431263074127-0.188925832156-0.0248734848107-0.189356515143-0.0865391843601-0.070687552825-0.02012450023020.172045866958-0.00276568112196-0.009624057628150.143875380290.01735735576050.110937697626-19.04147758296.09664927343-22.4180041601
75.36737163987-6.03093013925-6.402976111668.641466373766.865842498487.55189305614-0.395118851607-0.959849950903-0.1365943728840.6931618902450.3463314361330.4197302718240.4891129387770.3566467579780.04896726814050.219953207644-0.02155384181820.004149344668560.218603955098-0.02401911692660.151446510082-19.82036451237.91693121447-1.75322165071
80.105175219173-0.155773295313-0.5440213693568.868331687486.774653774057.206764056370.00583484948527-0.1620192159890.03585489976360.1573121019550.120152692939-0.658051228184-0.09103111967710.353090448598-0.1496856542570.163957085306-0.0143832841559-0.05083258705680.1887437502710.0153347883040.168859760518-9.159679870412.53772314712-5.58746462783
98.57409494344-5.11346293297-0.07402357218284.55732504191-0.8133122266513.859914159030.2638894973820.4682766244120.637095759828-0.0240925454098-0.259043084769-0.092868443232-0.555592483055-0.08571365373470.004610862524920.210651277551-0.02550536826790.01907171665550.148334568494-0.01337543492210.24818504061-22.112584350524.151203748-7.84746293115
106.55613891229-3.758276651375.848482899957.49878215275-5.274198942119.05201150103-0.1965388172660.04886544652880.7598602634090.0725735729471-0.129383028095-0.48802054379-0.2954750688380.04775717671230.3117362374990.156016353554-0.0352064812570.01805430270480.166089033374-0.0307737336160.191826163228-18.627969232822.439160606-3.9167896385
116.76849007712-5.00842913596-2.270791961064.617241500520.9766506683286.05565479901-0.51090315581-0.532257378656-0.2180673832480.9343313154140.3283624946980.1388450709970.6484695228310.06104426873170.2044626307350.238419979222-0.0155080118613-0.01839426683750.195944825367-0.02553508680770.138167193415-15.30958286638.72473125112.39973810555
127.42921923117-3.555380022160.4237952195084.280392730151.18114846010.8657221137840.153456244595-0.09971715043790.5070284725180.115631346905-0.09422820897420.107380042431-0.121808807554-0.24003710297-0.009792805516520.187886186418-0.0504390186131-0.00136636183080.108442363989-0.02860284957440.171470122498-25.488891680419.3591947592-2.20601256554
132.0918271011-1.058119680680.7350511582995.6315880132-3.540706703867.262671115350.0393146747953-0.02502886835980.117913386291-0.0369955673361-0.254085265832-0.3695342520410.03693419819860.3775089415670.2090931820940.11141851578-0.03573627314850.005758889878260.1602919760250.000661860456610.158513293321-7.315131847729.83622038833-14.5795891373
146.84243238219-2.86630587469-0.2155322446133.529160213472.058599744427.30497455005-0.294691685796-0.07593515293080.2647135848070.527955783545-0.06759508879710.4273602807310.103232113696-0.354565573910.3538884766690.275864574598-0.003375291730780.05202914542950.153518339366-0.06854457598120.224877461004-30.103587382515.262196022-6.29973175728
157.39100190364-1.0850796054-1.966422644693.325708968541.405051514311.71532414039-0.0997788393016-0.2855639126520.04639299376760.2260337900410.02087251809890.09791550850970.0551607551816-0.0346538160370.08225719274050.156733976498-0.0174054425266-0.03664348842230.1115428249180.01509946065420.0877957615773-22.50764446086.47161990109-8.37020683787
166.198553397876.6244545189-7.06976666587.42603822879-7.713320591437.96456573259-0.3077464578740.621296732144-0.301365551404-0.5420736912180.0530739117715-0.431251231080.439321348283-0.2699545679540.2378925623420.163456753761-0.0008743927120850.009494291775150.1543354151220.01066040366770.149036699874-23.27168995997.57132271759-29.2957801367
171.159811441121.65169259295-1.289105514554.14480198246-4.531849958645.38866092871-0.1205575104160.158309051980.186459302865-0.2874074750650.2450008665620.768095912656-0.0305453136165-0.32415622611-0.2160172183920.1345910693510.0069886807429-0.05377817519860.126492142834-0.001048627643850.164581765346-33.65153195574.28541239585-26.2018900566
184.001236828562.41804835431-0.7225457384886.10795238001-0.5585560638482.860613164820.119375014609-0.2361118545940.3839691392850.225221734905-0.0494554967581-0.355849069564-0.2954078555880.26593360664-0.01075220076250.131575826622-0.0185736797782-0.000262053307530.112456180926-0.02268027836070.194223422987-17.843456168124.061272461-24.2820193341
192.794304131271.604048469941.772752453987.059569703722.21060964237.11818740996-0.469109388502-0.04872994988950.52447188677-0.3617936774680.1165665679940.305986179497-0.6496617574110.1260049673330.3241893619060.1023958258810.02254377930520.02380675788280.08601892978390.02021884134730.119770085492-21.427268481822.6129756115-28.3105416348
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 49 through 58 )BB49 - 5839 - 48
22chain 'B' and (resid 59 through 74 )BB59 - 7449 - 64
33chain 'B' and (resid 75 through 90 )BB75 - 9065 - 80
44chain 'B' and (resid 91 through 97 )BB91 - 9781 - 87
55chain 'B' and (resid 98 through 112 )BB98 - 11288 - 102
66chain 'B' and (resid 113 through 125 )BB113 - 125103 - 115
77chain 'A' and (resid 10 through 18 )AA10 - 181 - 9
88chain 'A' and (resid 19 through 28 )AA19 - 2810 - 19
99chain 'A' and (resid 29 through 40 )AA29 - 4020 - 31
1010chain 'A' and (resid 41 through 48 )AA41 - 4832 - 39
1111chain 'A' and (resid 49 through 58 )AA49 - 5840 - 49
1212chain 'A' and (resid 59 through 74 )AA59 - 7450 - 65
1313chain 'A' and (resid 75 through 90 )AA75 - 9066 - 81
1414chain 'A' and (resid 91 through 103 )AA91 - 10382 - 92
1515chain 'A' and (resid 104 through 124 )AA104 - 12493 - 113
1616chain 'B' and (resid 11 through 18 )BB11 - 181 - 8
1717chain 'B' and (resid 19 through 28 )BB19 - 289 - 18
1818chain 'B' and (resid 29 through 40 )BB29 - 4019 - 30
1919chain 'B' and (resid 41 through 48 )BB41 - 4831 - 38

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