[English] 日本語
Yorodumi
- PDB-8w2w: Structure of transthyretin synthetic mutation A120L -

+
Open data


ID or keywords:

Loading...

-
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 / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation ...Defective visual phototransduction due to STRA6 loss of function / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / 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: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more