[English] 日本語
Yorodumi
- PDB-8w42: X-ray crystal structure of V30M-TTR in complex with resveratrol -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8w42
TitleX-ray crystal structure of V30M-TTR in complex with resveratrol
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Amyloidogenesis / thyroid hormone inhibitor
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
RESVERATROL / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsYokoyama, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2023
Title: Resveratrol Derivatives Inhibit Transthyretin Fibrillization: Structural Insights into the Interactions between Resveratrol Derivatives and Transthyretin.
Authors: Yokoyama, T. / Kusaka, K. / Mizuguchi, M. / Nabeshima, Y. / Fujiwara, S.
History
DepositionAug 23, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2023Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1655
Polymers34,6852
Non-polymers4793
Water3,135174
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,32910
Polymers69,3704
Non-polymers9596
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area8660 Å2
ΔGint-42 kcal/mol
Surface area18440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.168, 84.044, 62.691
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-200-

STL

21A-200-

STL

31A-200-

STL

41B-201-

STL

51B-201-

STL

61B-201-

STL

71A-391-

HOH

-
Components

#1: Protein Transthyretin / / ATTR / Prealbumin / TBPA


Mass: 17342.582 Da / Num. of mol.: 2 / Mutation: V30M
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-STL / RESVERATROL / Resveratrol


Mass: 228.243 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H12O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.64 Å3/Da / Density % sol: 24.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Disodium malonate, 0.1M NaOAc pH 4.6

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.45→35.55 Å / Num. obs: 41097 / % possible obs: 99.69 % / Redundancy: 7.3 % / CC1/2: 1 / Rpim(I) all: 0.015 / Rrim(I) all: 0.04 / Net I/σ(I): 24
Reflection shellResolution: 1.45→1.5 Å / Mean I/σ(I) obs: 3 / Num. unique obs: 3961 / CC1/2: 0.905 / Rpim(I) all: 0.262 / Rrim(I) all: 0.731

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→34.906 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 17.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1798 2055 5 %
Rwork0.1529 --
obs0.1542 41083 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→34.906 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1780 0 35 174 1989
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051898
X-RAY DIFFRACTIONf_angle_d0.7692584
X-RAY DIFFRACTIONf_dihedral_angle_d22.149662
X-RAY DIFFRACTIONf_chiral_restr0.091282
X-RAY DIFFRACTIONf_plane_restr0.006328
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4503-1.48410.21961320.18492513X-RAY DIFFRACTION97
1.4841-1.52120.22861350.16412568X-RAY DIFFRACTION100
1.5212-1.56230.231350.15182547X-RAY DIFFRACTION100
1.5623-1.60830.23311350.14032581X-RAY DIFFRACTION100
1.6083-1.66020.17751370.1322584X-RAY DIFFRACTION100
1.6602-1.71950.19691350.12882576X-RAY DIFFRACTION100
1.7195-1.78840.16591350.13172562X-RAY DIFFRACTION100
1.7884-1.86970.18031360.13192588X-RAY DIFFRACTION100
1.8697-1.96830.16081360.12652590X-RAY DIFFRACTION100
1.9683-2.09160.16291380.13382605X-RAY DIFFRACTION100
2.0916-2.25310.18511360.13582602X-RAY DIFFRACTION100
2.2531-2.47980.19241380.15482612X-RAY DIFFRACTION100
2.4798-2.83850.19961390.17152647X-RAY DIFFRACTION100
2.8385-3.57560.18941400.16322653X-RAY DIFFRACTION100
3.5756-34.9060.15721480.15982800X-RAY DIFFRACTION100

+
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