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- PDB-8jnu: Crystal structure of V30G mutated human transthyretin -

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Basic information

Entry
Database: PDB / ID: 8jnu
TitleCrystal structure of V30G mutated human transthyretin
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / transport of thyroid hormone
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 6, 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)29,8444
Polymers29,7952
Non-polymers492
Water2,612145
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6888
Polymers59,5914
Non-polymers974
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area6520 Å2
ΔGint-62 kcal/mol
Surface area19320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.100, 85.400, 64.480
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-350-

HOH

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 14897.634 Da / Num. of mol.: 2 / Mutation: V30G
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.: 145 / 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: 1.99 Å3/Da / Density % sol: 38.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8 / 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→51.46 Å / Num. obs: 29770 / % possible obs: 99.7 % / Redundancy: 6.9 % / Biso Wilson estimate: 17.84 Å2 / CC1/2: 0.999 / Net I/σ(I): 21.5
Reflection shellResolution: 1.64→1.73 Å / Rmerge(I) obs: 0.294 / Num. unique obs: 4265 / CC1/2: 0.939

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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→35.6 Å / SU ML: 0.1345 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.0809
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2068 1467 4.93 %
Rwork0.1853 28262 -
obs0.1863 29729 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.6 Å2
Refinement stepCycle: LAST / Resolution: 1.64→35.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1769 0 2 145 1916
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00631815
X-RAY DIFFRACTIONf_angle_d0.88282473
X-RAY DIFFRACTIONf_chiral_restr0.0652280
X-RAY DIFFRACTIONf_plane_restr0.015314
X-RAY DIFFRACTIONf_dihedral_angle_d6.0022244
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.70.25661370.21182770X-RAY DIFFRACTION99.38
1.7-1.770.24211320.19892810X-RAY DIFFRACTION100
1.77-1.850.20741720.19162774X-RAY DIFFRACTION100
1.85-1.950.23741370.18222805X-RAY DIFFRACTION100
1.95-2.070.19081480.17282794X-RAY DIFFRACTION100
2.07-2.230.17981570.1732817X-RAY DIFFRACTION100
2.23-2.450.24141630.18652816X-RAY DIFFRACTION100
2.45-2.810.22241280.2032863X-RAY DIFFRACTION100
2.81-3.530.22531430.18342892X-RAY DIFFRACTION100
3.53-35.60.17391500.18022921X-RAY DIFFRACTION96.75
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)
19.360619145286.30925315533-5.08002263335.04534171731-2.592845036725.72721307708-0.4003849234130.600122866933-0.121722611517-0.7550838380870.281417161076-0.1162034268230.471869732115-0.2080761628290.1534944233040.216076376505-0.0185048737974-0.01976384865960.1691096284250.02776722613980.152946628636-26.91680738689.60526540805-34.3812615716
27.076210193173.89785826931-0.3572850644033.63743050448-1.546112559022.01293606758-0.04238434298880.1275466518970.390933091055-0.1765604216780.0268850749756-0.0148549284887-0.01522230605930.1882433826880.02519897265630.1105427916230.0257740689144-0.009157153802340.08730442876260.04873386954850.154843383638-15.44628247718.7025241715-29.9777509609
35.22168032891-1.904586500951.573607948178.26767318613-1.650817840457.570372264570.0488424064684-0.06400264905070.2829660192740.207198575577-0.0241652779010.35739554822-0.00466693615429-0.6292252747560.008978761350710.0964513211517-0.008570351294510.02151085615590.162011691278-0.007646307270280.122113473013-36.207023340311.0417011396-20.3011702984
43.83828574634-1.031246399272.373496827647.169111886360.3373570029847.781589950680.145568084739-0.0250805338527-0.2098101889810.456635379916-0.119980382163-0.438483554834-0.240691192844-0.0959548718595-0.01355751861690.131554936725-0.01845405699980.02510588354060.1257728690190.0007975096936030.093042520757-32.752172887512.378233052-14.3037821994
55.790336344876.37914537911-5.524346129287.61991462689-6.303554416757.49214591247-0.250144851395-0.3345996182710.47005934664-0.019148349740.2311487693120.2261260958140.174790254863-0.194610983099-0.0126021341980.1247124246320.00521789780076-0.006993715103070.145339116970.005024124125080.0669511159804-15.59371956215.3455021253-21.8225768675
63.505851952012.05036616835-2.795605168814.743916740691.571375914225.107358369630.0408047523225-0.761008243249-0.385699443333-0.1945511107840.496968205393-1.31612687167-0.2478613924941.14007898649-0.4153854888940.2156053028120.02596367960410.0862561224380.2963909157420.01523433670640.358237426736-4.438010480613.6955504197-30.854991626
76.384282707414.1002101139-5.83910663284.58143515222-3.771699734225.21452793403-0.4476582022140.547982487636-0.247564506612-0.347843216630.214256318045-0.2701412480430.464252254394-0.2772024245080.2116575944070.134401644373-0.0277202170393-0.006400067590860.1657478031260.01673710692150.0845797850028-19.8812166987.02344866192-26.344530951
87.946466729440.279776877586-7.554078446252.63368877288-0.09071517036668.92878067398-0.130180141370.0494994655163-0.195912938095-0.251746100652-0.093079420939-0.179151698749-0.01804309212760.06917009653160.1135191878630.134989970162-0.00441005446834-0.0191315002860.1123153497620.007722829526430.0720833706782-18.83717797986.15433819088-22.6997887588
99.19480058854-8.02148327153-7.39727866078.165712629167.511309718377.18577999607-0.61033739953-0.824569437329-0.4882728865891.036206162650.2497435017360.7249766913580.5098021892550.1988262598550.3366433159650.262338952897-0.01084636696980.03623068463680.221319194945-0.01694201196860.154776167469-19.75226654017.91437966154-1.89574683263
100.853829435151-0.477905757408-1.091876511356.243280193936.589721394128.83398430275-3.161844182E-5-0.3086305925820.03104089976930.3725448688060.1132982537-0.6617199516850.1148506674890.41158562694-0.07024073821380.2078793075590.0236646050553-0.05033296142630.1534254819770.01358241124080.149172311636-9.054932843082.69147978095-5.71988663026
118.67943184535-5.492230493221.419490206275.36610092909-1.568901621566.138745525380.05339569964830.1683302930210.9415897518470.0361696787156-0.0262608192373-0.301047975889-0.673299042735-0.4405877711970.03230631630620.241140633520.000582829886450.05171022277610.151472614315-0.002732454934460.296263220712-22.688327187725.0736243252-8.22351453423
127.17090527535-3.030633069563.528204969648.53371011127-2.736179349473.93070934101-0.375113368585-0.1868949838090.7566555459550.2824805023720.233905949504-0.148085475083-0.237867082713-0.01814699206910.1999467995940.160855434266-0.02265679392110.001734097437550.1929553429-0.03154093049080.19771779343-18.543336323722.322207075-3.77417603124
137.02409310645-3.53414945393-0.0581885932016.73826649423-1.045829069783.45046469091-0.486554320684-1.13239321267-0.05301003811351.040666542890.3242695877920.4410326018020.168594288248-0.2960091335930.2066104573630.2581159345380.0335917297131-0.04823989442950.266410045696-0.05859897699580.120716899895-15.19077645238.716029929972.26574340841
144.67765898964-2.831049334410.6144805782823.46221523950.5949541806711.137611338950.1733317722-0.1914902652780.5667970194810.1852625607030.00554289190560.0358174469045-0.143733690473-0.166793652347-0.1168557178730.188049691249-0.03149406646670.02534609239330.125583102541-0.06356793370830.161152755006-25.35344767419.2491447352-2.31598493073
158.01512537292-0.9936312400754.286104758127.02883304879-3.030399150295.108234377450.0182883653307-0.110125122680.001176246126040.0754620374692-0.131117028295-0.28997892286-0.09793024724640.2073057545830.1132784152810.0825160880656-0.008625908998870.01606799494540.1046149366670.0109860273740.0850464853295-7.224666368039.81330133316-14.7704338574
164.77202140822-2.53085409015-1.706544303452.908538203892.771325467358.57538386748-0.2078749885630.239334926843-0.07874622309830.344067082992-0.1021967461020.3922750705140.240775209514-0.3078736243770.3210370722860.2784631601290.005028882443260.06722319875650.103848213603-0.03616905836320.201514029077-30.053980804315.0402827799-6.28768596866
173.971760411650.04941226631510.6899656176082.971065962370.4768629206720.176332987736-0.247375358101-0.3372948367710.05874416371860.3083294856460.06295290711070.1561156306930.277910773741-0.08326002553290.1349642325720.158694975269-0.0042104501542-0.01871369938770.129429967784-0.004201637975920.0785490848813-22.47604193936.46706777976-8.48564449957
184.76374875465.4186226449-5.467110150886.59251528927-6.072275597196.2453471548-0.5189548654730.894848142375-0.326585928648-0.5195350735040.284831658501-0.4861750359070.435830974768-0.3020275078020.2115851404150.188593088768-0.04441839925820.02727498558130.2070991362370.00559054038420.157227967932-22.53549190158.06913178632-30.2926205973
191.190503827841.58934426426-2.047326221933.98155334417-5.896367976828.996345182770.02648035836670.1051192892880.209034823897-0.07259535497810.09902778075250.564490100680.126439597839-0.227672168794-0.2528283155150.140534957691-0.0211584527335-0.04270018516340.128826015810.01076282888390.151485187332-33.60102641314.2864710397-26.3841367252
201.394175781050.9988943818-2.453248574065.58049110227-1.768560775434.459267255960.0503718168215-0.251821864240.8204032067340.349629997502-0.0937395616389-0.231238390536-0.4037095827650.4396711410490.06637419576710.140955081763-0.0061163958829-0.03491308053680.11811547102-0.03349024763330.252829008515-16.977503945524.8788381744-24.1671683291
214.496716864591.294702090563.908115014628.617069956742.670775668577.20058862147-0.3556992512580.08339046858350.6286572728870.100488885250.06956815913120.0608967224393-0.3773104051990.1858950222420.3012130383710.1117237004990.0133307569345-0.001118343063080.1013126439580.0351558393020.144099069912-21.290710082322.574416091-28.3670494453
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 - 5840 - 49
22chain 'B' and (resid 59 through 74 )BB59 - 7450 - 65
33chain 'B' and (resid 75 through 82 )BB75 - 8266 - 73
44chain 'B' and (resid 83 through 90 )BB83 - 9074 - 81
55chain 'B' and (resid 91 through 97 )BB91 - 9782 - 88
66chain 'B' and (resid 98 through 103 )BB98 - 10389 - 94
77chain 'B' and (resid 104 through 112 )BB104 - 11295 - 103
88chain 'B' and (resid 113 through 125 )BB113 - 125104 - 116
99chain 'A' and (resid 10 through 18 )AA10 - 181 - 9
1010chain 'A' and (resid 19 through 28 )AA19 - 2810 - 19
1111chain 'A' and (resid 29 through 40 )AA29 - 4020 - 31
1212chain 'A' and (resid 41 through 48 )AA41 - 4832 - 39
1313chain 'A' and (resid 49 through 58 )AA49 - 5840 - 49
1414chain 'A' and (resid 59 through 74 )AA59 - 7450 - 65
1515chain 'A' and (resid 75 through 90 )AA75 - 9066 - 81
1616chain 'A' and (resid 91 through 103 )AA91 - 10382 - 92
1717chain 'A' and (resid 104 through 124 )AA104 - 12493 - 113
1818chain 'B' and (resid 10 through 18 )BB10 - 181 - 9
1919chain 'B' and (resid 19 through 28 )BB19 - 2810 - 19
2020chain 'B' and (resid 29 through 40 )BB29 - 4020 - 31
2121chain 'B' and (resid 41 through 48 )BB41 - 4832 - 39

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