[English] 日本語
Yorodumi
- PDB-7qc5: Crystal structure of human wild type transthyretin in complex wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qc5
TitleCrystal structure of human wild type transthyretin in complex with (3,4-dihydroxy-5-nitrophenyl)-(3-fluoro-5-hydroxyphenyl)methanone compound
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / thyroxine (T4) binding site / stabilization compound / amyloid fibrils.
Function / homology
Function and homology information


Retinoid cycle disease events / 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 ...Retinoid cycle disease events / 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
Chem-AQI / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsVarejao, N. / Pinheiro, F. / Pallares, I. / Ventura, S. / Reverter, D.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPGC2018-098423-B-I00 Spain
CitationJournal: J.Med.Chem. / Year: 2022
Title: Development of a Highly Potent Transthyretin Amyloidogenesis Inhibitor: Design, Synthesis, and Evaluation.
Authors: Pinheiro, F. / Pallares, I. / Peccati, F. / Sanchez-Morales, A. / Varejao, N. / Bezerra, F. / Ortega-Alarcon, D. / Gonzalez, D. / Osorio, M. / Navarro, S. / Velazquez-Campoy, A. / Almeida, M. ...Authors: Pinheiro, F. / Pallares, I. / Peccati, F. / Sanchez-Morales, A. / Varejao, N. / Bezerra, F. / Ortega-Alarcon, D. / Gonzalez, D. / Osorio, M. / Navarro, S. / Velazquez-Campoy, A. / Almeida, M.R. / Reverter, D. / Busque, F. / Alibes, R. / Sodupe, M. / Ventura, S.
History
DepositionNov 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: 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)28,1414
Polymers27,5552
Non-polymers5862
Water4,252236
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2828
Polymers55,1094
Non-polymers1,1734
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Unit cell
Length a, b, c (Å)84.374, 43.818, 65.467
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-201-

AQI

21A-201-

AQI

31B-201-

AQI

41B-201-

AQI

-
Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 13777.360 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Wild type TTR / Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P02766
#2: Chemical ChemComp-AQI / (3-fluoranyl-5-oxidanyl-phenyl)-[3-nitro-4,5-bis(oxidanyl)phenyl]methanone / (3,4-dihydroxy-5-nitrophenyl)-(3-fluoro-5-hydroxyphenyl)methanone


Mass: 293.204 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H8FNO6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.16 Å3/Da / Density % sol: 43.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG 400, hepes, calcium chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.2→43.82 Å / Num. obs: 76526 / % possible obs: 99.9 % / Redundancy: 5.4 % / Biso Wilson estimate: 15.68 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.018 / Rrim(I) all: 0.042 / Net I/σ(I): 17.8
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.656 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3745 / CC1/2: 0.83 / Rpim(I) all: 0.308 / Rrim(I) all: 0.726 / Χ2: 1 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHASER1.19.2_4158phasing
PHENIX1.19.2_4158refinement
Aimless0.7.7data scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F41

1f41


Resolution: 1.2→38.89 Å / SU ML: 0.0838 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 15.746
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1746 3751 4.91 %
Rwork0.1596 72709 -
obs0.1603 76460 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.22 Å2
Refinement stepCycle: LAST / Resolution: 1.2→38.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1792 0 42 245 2079
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01221957
X-RAY DIFFRACTIONf_angle_d1.2542687
X-RAY DIFFRACTIONf_chiral_restr0.1125296
X-RAY DIFFRACTIONf_plane_restr0.0111348
X-RAY DIFFRACTIONf_dihedral_angle_d10.1856270
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.220.22891360.22132687X-RAY DIFFRACTION99.96
1.22-1.230.25771280.21342639X-RAY DIFFRACTION100
1.23-1.250.17951200.2012680X-RAY DIFFRACTION99.96
1.25-1.270.17681390.18352667X-RAY DIFFRACTION99.93
1.27-1.280.19211260.17322686X-RAY DIFFRACTION99.82
1.28-1.30.19411300.17752652X-RAY DIFFRACTION99.86
1.3-1.330.16581350.17742671X-RAY DIFFRACTION99.89
1.33-1.350.18921460.16832645X-RAY DIFFRACTION99.96
1.35-1.370.15041700.15372655X-RAY DIFFRACTION100
1.37-1.40.15761290.15352673X-RAY DIFFRACTION99.93
1.4-1.430.18161580.15692649X-RAY DIFFRACTION100
1.43-1.460.17991540.1492689X-RAY DIFFRACTION99.96
1.46-1.490.15331330.15282644X-RAY DIFFRACTION99.93
1.49-1.530.16541380.14612684X-RAY DIFFRACTION100
1.53-1.570.1691280.13652714X-RAY DIFFRACTION99.93
1.57-1.620.13521420.1352676X-RAY DIFFRACTION99.96
1.62-1.670.14431390.13622687X-RAY DIFFRACTION100
1.67-1.730.1441280.14622698X-RAY DIFFRACTION99.89
1.73-1.80.16741540.1532670X-RAY DIFFRACTION100
1.8-1.880.15271380.15632718X-RAY DIFFRACTION99.9
1.88-1.980.16331320.14822711X-RAY DIFFRACTION99.89
1.98-2.110.17221160.14942736X-RAY DIFFRACTION99.89
2.11-2.270.17591440.14672713X-RAY DIFFRACTION99.86
2.27-2.50.16471450.16062705X-RAY DIFFRACTION99.75
2.5-2.860.20091440.17422736X-RAY DIFFRACTION99.28
2.86-3.60.15531490.16362763X-RAY DIFFRACTION99.08
3.6-38.890.20231500.16472861X-RAY DIFFRACTION97.86

+
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