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- PDB-8jok: Crystal structure of V30L mutated human transthyretin -

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Open data


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Basic information

Entry
Database: PDB / ID: 8jok
TitleCrystal structure of V30L mutated human transthyretin
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Thyroid hormone-binding protein
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, 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: 1.64 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 7, 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
Water2,594144
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 area6270 Å2
ΔGint-44 kcal/mol
Surface area19310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.160, 85.280, 64.320
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-340-

HOH

21B-352-

HOH

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 14953.739 Da / Num. of mol.: 2 / Mutation: V30L
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.: 144 / 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: 37.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.9 / 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: 1.64→51.35 Å / Num. obs: 29774 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 19.06 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.093 / Net I/σ(I): 10.7
Reflection shellResolution: 1.64→1.73 Å / Rmerge(I) obs: 0.634 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 4265 / CC1/2: 0.639

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→38.51 Å / SU ML: 0.1404 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.2354
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2148 1470 4.94 %
Rwork0.1894 28260 -
obs0.1908 29730 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.86 Å2
Refinement stepCycle: LAST / Resolution: 1.64→38.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1787 0 2 144 1933
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00661834
X-RAY DIFFRACTIONf_angle_d0.87342502
X-RAY DIFFRACTIONf_chiral_restr0.0608285
X-RAY DIFFRACTIONf_plane_restr0.0086318
X-RAY DIFFRACTIONf_dihedral_angle_d5.8258247
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.690.27981270.27142530X-RAY DIFFRACTION99.77
1.69-1.750.30521220.24412521X-RAY DIFFRACTION99.85
1.75-1.820.28921460.23022521X-RAY DIFFRACTION99.89
1.82-1.910.29091300.20942541X-RAY DIFFRACTION99.89
1.91-2.010.22741410.19462522X-RAY DIFFRACTION100
2.01-2.130.20031250.18972574X-RAY DIFFRACTION100
2.13-2.30.24721470.18462545X-RAY DIFFRACTION99.93
2.3-2.530.2441350.19242559X-RAY DIFFRACTION99.96
2.53-2.90.22831220.19612609X-RAY DIFFRACTION99.96
2.9-3.650.19781290.17792618X-RAY DIFFRACTION100
3.65-38.510.16661460.16912720X-RAY DIFFRACTION98.93
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)
17.86841234286-5.95131417154-5.491115754886.301805878154.84577037364.089238567-0.546933020972-0.940676612132-0.3470933395320.6582490168150.3390463769130.5243246158790.4600068960680.3532261059880.1685248584850.257891007647-0.004117096670690.03621802831370.262189557073-0.03347941422670.170852503444-19.84965616747.68293141116-1.68887192101
20.235161955595-0.422309067152-0.5825731530994.289013393552.105987502071.83706096209-0.0820552450998-0.2821399408680.07004747265810.2598374698640.214425581839-0.6313536555650.02444149051490.391656181277-0.09198268551080.21488200261-0.00928303449179-0.03207586981850.2067553083390.003153905710680.168069291889-9.126366273372.54058176736-5.63144147085
34.5094918679-1.6336226655-0.091153968543.681020922020.1868803609562.428989514310.1871505427170.1949904993120.722454272019-0.315843759176-0.07824114764120.165029958453-0.487407016642-0.0604514399622-0.1221801869240.285872413159-0.01687227925790.01381210270680.214340896286-0.009256025400940.326530651987-22.410419109424.713621732-8.03913769027
42.25648587359-0.6674639283872.008996730312.13865706017-2.044408013113.8275860784-0.3068212496380.2850770951330.505490957245-0.111004270176-0.0404614024111-0.243595882094-0.318969042590.2420374037150.3234974978020.265587160607-0.0365407212481-0.01465283206070.254524322778-0.0165241983430.252037020045-18.664292015622.4091459936-3.92071464031
54.18143324418-1.64071127834-1.963951141586.421339058011.591310740623.01012945698-0.309564233307-0.793490768026-0.1033326263571.10618188920.1468234850050.107996810070.234681712142-0.06658397595220.1249629637250.31212276224-0.00919512303974-0.01934244797660.274910897052-0.01840067714990.174560712237-15.40541549598.671936340052.54897055165
62.66452099116-1.472620255550.0928974245822.096689390220.8278278124611.56662913295-0.0195061084818-0.1631275587620.2221856091840.2958122750260.002289370003890.124859971764-0.141785192086-0.3400006576080.02050386007060.2349301191920.006307756618910.006452223373970.21960591179-0.04548044017170.232762274704-26.47578730219.5796216073-1.72724454351
71.370398010670.424903100271-0.115157908992.21841577038-0.5779168988822.665336789630.0491348999398-0.1669241161740.117665024783-0.0830189194434-0.149264633206-0.242516792343-0.1714141414910.3313645924550.07946595991640.161346460658-0.01711231842050.001039895443030.178518314660.003921074725370.186495336648-7.4118554340310.1461468065-14.3459485419
87.22376240162-2.992338307331.000230536264.223972729680.7569055946690.749492005730.5250521327210.6579846502220.500857002176-0.338535891866-0.2513533623420.0562972961451-0.5477378276510.310076173512-0.2546274385130.222588285695-0.001159476281010.05726481885290.235648464061-0.01918611636320.176587357599-25.46858864115.9987769369-10.3158396888
90.886260098333-0.4803939366640.1891021046261.18594604919-0.2511725528351.08015467428-0.220864928462-0.428631569233-0.3018094662640.4405158595780.5896025031240.1118300507890.429662087796-0.22384633787-0.2875848492080.61345970417-0.03156857764760.1713806860930.563545878391-0.1110941200480.59947779069-37.579419631913.426728901-0.128493986167
102.98575963528-0.1386602401320.2389429384092.159712415220.6343285161441.47491863845-0.0425417680216-0.2449986843310.09424094163980.195105871339-0.0375865871190.07315715191350.0572880351832-0.2094843369570.06409424304990.185165406168-0.0165233208051-0.009830652818340.166933422716-0.008777524081180.130815999631-22.54124696096.4918955293-8.34665172912
117.777647166545.02119209879-4.814834903664.39329916037-3.356962523443.03304507554-0.7034175548510.800223386573-0.437651510673-0.5332402977520.42285695502-0.3258037576970.558278153576-0.4437409581920.2162856724980.207677103756-0.03550695926750.01469137458480.162795581811-0.00845752093420.132114108752-22.46230890417.80070372575-30.3028922986
120.1783702075390.449742576329-0.05999511411272.9516773934-1.056708755180.711943142957-0.01729729356620.1110611495780.0313612420707-0.1553894181520.2696547894430.8118694835730.132211133793-0.211168493927-0.246352909370.166867171355-0.0184841285093-0.02213473568960.1355602147230.005785263551140.198470274761-33.62169819224.27005126221-26.2985100453
133.031136246120.53314585875-0.722683231512.16197559256-0.4162764513321.374352366060.145449341286-0.1440444274850.1761308924090.239400625591-0.0558613430028-0.311383306582-0.2860239782870.123089776236-0.1019487278930.192209333716-0.026705398117-0.01190669367110.154601725204-0.005928975544860.246439933315-17.206562492524.5205459607-24.3061629053
143.468048579861.217066739231.589882417133.472007311670.9639761623373.70969307243-0.4047393969890.06221998659610.752867794782-0.06714034456220.05002802762250.579666425607-0.4694956578010.0508485226580.2796916879070.1903367662250.02598461592150.005386228312030.1262268520730.03089358230870.209515920862-21.301464070522.6439553833-28.4087653647
153.784469951492.74014556485-2.235816569385.95715184344-1.399669836663.04432116576-0.403221419110.553035282391-0.214183552507-0.615411545630.188721956692-0.170024542230.517054117475-0.01693547075870.2088697783220.238575844636-0.01493428879250.001163365798020.1886542648050.01097230860290.186675404813-26.78391257399.4633308053-34.4401789375
164.093481746531.57921281991.900601374982.92530974004-0.1383987284153.92772651102-0.01672154678530.5431460866660.397581650529-0.309703494695-0.224877096446-0.2413972252840.2545708618310.5635274810390.2635506640710.1756287833410.00943605771510.01250764426830.1739320750730.07547400148020.251758783495-11.278448472919.3409938127-35.7206923816
179.121579329512.81102884612-0.8293771503711.21531745986-0.1473135010760.112952451470.0440875828735-0.3061901792570.7117745433120.00891208317287-0.06087817232730.200471463355-0.1373399725570.04540127973690.04031702639970.165182192795-0.0130159935285-0.002939077243030.1555262569410.01786475122720.164414008242-19.706056223818.0516250584-23.6064778766
183.88629789776-0.160629274835-0.1148975663043.06541724853-0.5765512139242.34008660170.01002341805820.007694211913930.3791578874510.251655936838-0.01694072190050.302755201735-0.0918130482537-0.441739486003-0.04110428186320.15164708017-0.005089068760280.008012173523070.210589047842-0.01261432331060.197128571961-36.219395194611.0732290468-20.2764726916
192.756849405510.4621564202560.1816330562662.88482566065-0.2966436334612.68038508390.06450537181510.234527400162-0.1364402181590.3031308274730.0365987148130.0139914418439-0.17135969159-0.107743841053-0.06437528049570.168403968292-0.01796683506990.01948150303560.170899873645-0.01978897862280.165779111733-32.79988723212.4456323796-14.2211564734
202.531445312852.69398221598-1.506518816112.94300244543-1.532481151231.63572355906-0.214578558371-0.277218570070.60745686691-0.007850883838080.2767562017870.2696088741670.0121118237134-0.189098219264-0.02988214182180.138603391644-0.00315930926632-0.004580395372840.1900893456250.02560925436070.19200274069-15.601970969815.3413859694-21.7699680081
212.747046543391.47395634001-1.066275699936.241602404764.013468410864.378687062320.220074723283-0.244750897279-0.3418209044670.06201983532370.242044310949-1.14032580254-0.3086703531650.429286645984-0.4095147478460.2319042420870.01067245671770.03990948742570.2534116121870.02294496459810.331752052599-4.5176453462113.6312847284-30.8759339843
228.035831318882.72899936683-4.745281848042.50803881441-2.275987396613.20916980114-0.3045259099690.498031491192-0.351042906361-0.1831329091880.134280482952-0.1889889142530.301667754788-0.2897292813590.1986547056580.177968219066-0.02617949992050.004361819332030.1541934078340.001188833449360.15034065173-19.84129371666.96715253253-26.2925748501
234.10705661948-0.162926685597-2.225002280071.631367574430.1096976496052.13014047817-0.1345608578030.177781567989-0.00968492439822-0.169420071323-0.0271378452534-0.1655095814450.133446296653-0.1302547521610.04492692832920.165332897736-0.009543115447670.005481965247240.1462102541650.02428104480180.132880465683-18.8565328946.13407722008-22.5971221285
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 10 through 18 )AA10 - 181 - 9
22chain 'A' and (resid 19 through 28 )AA19 - 2810 - 19
33chain 'A' and (resid 29 through 40 )AA29 - 4020 - 31
44chain 'A' and (resid 41 through 48 )AA41 - 4832 - 39
55chain 'A' and (resid 49 through 58 )AA49 - 5840 - 49
66chain 'A' and (resid 59 through 73 )AA59 - 7350 - 64
77chain 'A' and (resid 74 through 90 )AA74 - 9065 - 81
88chain 'A' and (resid 91 through 97 )AA91 - 9782 - 88
99chain 'A' and (resid 98 through 103 )AA98 - 10389 - 94
1010chain 'A' and (resid 104 through 124 )AA104 - 12495 - 115
1111chain 'B' and (resid 10 through 18 )BB10 - 181 - 9
1212chain 'B' and (resid 19 through 28 )BB19 - 2810 - 19
1313chain 'B' and (resid 29 through 40 )BB29 - 4020 - 31
1414chain 'B' and (resid 41 through 48 )BB41 - 4832 - 39
1515chain 'B' and (resid 49 through 58 )BB49 - 5840 - 49
1616chain 'B' and (resid 59 through 66 )BB59 - 6650 - 57
1717chain 'B' and (resid 67 through 74 )BB67 - 7458 - 65
1818chain 'B' and (resid 75 through 82 )BB75 - 8266 - 73
1919chain 'B' and (resid 83 through 90 )BB83 - 9074 - 81
2020chain 'B' and (resid 91 through 97 )BB91 - 9782 - 88
2121chain 'B' and (resid 98 through 103 )BB98 - 10389 - 94
2222chain 'B' and (resid 104 through 112 )BB104 - 11295 - 103
2323chain 'B' and (resid 113 through 125 )BB113 - 125104 - 116

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