[English] 日本語
Yorodumi
- PDB-7dt6: Crystal structure of V30M mutated transthyretin in complex with p... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7dt6
TitleCrystal structure of V30M mutated transthyretin in complex with purpurin
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Inhibitor / Complex / T4-binding / amyloidosis
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
Purpurin / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsKitakami, R. / Yokoyama, T. / Mizuguchi, M.
CitationJournal: Bioorg.Med.Chem. / Year: 2021
Title: Inhibitory activities of anthraquinone and xanthone derivatives against transthyretin amyloidogenesis.
Authors: Kitakami, R. / Inui, K. / Nakagawa, Y. / Sawai, Y. / Katayama, W. / Yokoyama, T. / Okada, T. / Kanamitsu, K. / Nakagawa, S. / Toyooka, N. / Mizuguchi, M.
History
DepositionJan 4, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9413
Polymers34,6852
Non-polymers2561
Water4,179232
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,8836
Polymers69,3704
Non-polymers5122
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Unit cell
Length a, b, c (Å)42.930, 85.430, 63.690
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-271-

HOH

21B-364-

HOH

-
Components

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


Mass: 17342.582 Da / Num. of mol.: 2
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-9TF / Purpurin / 1,2,4-Trihydroxyanthraquinone


Mass: 256.210 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H8O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 1.68 Å3/Da / Density % sol: 26.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG400, CaC2l, NaOAc

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→42.9 Å / Num. obs: 56091 / % possible obs: 96 % / Redundancy: 6.3 % / Rpim(I) all: 0.025 / Rrim(I) all: 0.076 / Net I/σ(I): 15.5
Reflection shellResolution: 1.3→1.35 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 5685 / Rpim(I) all: 0.492 / Rrim(I) all: 0.994

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1-2155_1069: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4pwe

4pwe


Resolution: 1.3→30.28 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2112 2802 5 %
Rwork0.1871 --
obs0.1882 56067 96.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→30.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1780 0 19 232 2031
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061872
X-RAY DIFFRACTIONf_angle_d0.8932560
X-RAY DIFFRACTIONf_dihedral_angle_d19.959658
X-RAY DIFFRACTIONf_chiral_restr0.097287
X-RAY DIFFRACTIONf_plane_restr0.009322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3001-1.32250.30111400.30872667X-RAY DIFFRACTION99
1.3225-1.34650.29771440.29622732X-RAY DIFFRACTION99
1.3465-1.37240.2741420.27512683X-RAY DIFFRACTION99
1.3724-1.40040.3321420.26922705X-RAY DIFFRACTION99
1.4004-1.43090.2961420.26172706X-RAY DIFFRACTION99
1.4309-1.46420.26871410.24472677X-RAY DIFFRACTION98
1.4642-1.50080.24371420.2342685X-RAY DIFFRACTION98
1.5008-1.54140.2431420.21762702X-RAY DIFFRACTION98
1.5414-1.58670.25031410.2192681X-RAY DIFFRACTION97
1.5867-1.63790.2331420.20452691X-RAY DIFFRACTION98
1.6379-1.69650.23681390.20542653X-RAY DIFFRACTION97
1.6965-1.76440.21671400.20952658X-RAY DIFFRACTION96
1.7644-1.84470.21031400.19752663X-RAY DIFFRACTION96
1.8447-1.94190.21231400.18012660X-RAY DIFFRACTION95
1.9419-2.06360.181380.1712622X-RAY DIFFRACTION95
2.0636-2.22280.17691390.16882642X-RAY DIFFRACTION95
2.2228-2.44650.22121380.17922626X-RAY DIFFRACTION94
2.4465-2.80020.19531360.18152605X-RAY DIFFRACTION93
2.8002-3.52720.22361360.17272589X-RAY DIFFRACTION91
3.5272-30.280.18351380.16452618X-RAY DIFFRACTION88
Refinement TLS params.Method: refined / Origin x: -22.6458 Å / Origin y: 13.0601 Å / Origin z: -15.8112 Å
111213212223313233
T0.1086 Å20.0023 Å20.0126 Å2-0.1298 Å20.0037 Å2--0.1306 Å2
L0.562 °2-0.0457 °20.1791 °2-0.7947 °20.0343 °2--0.911 °2
S-0.0297 Å °0.0202 Å °0.0972 Å °-0.0256 Å °-0.0193 Å °-0.0075 Å °-0.0191 Å °0.0441 Å °0.0469 Å °
Refinement TLS groupSelection details: not water and not resname PDB

+
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