[English] 日本語
Yorodumi
- PDB-5e4o: Human transthyretin (TTR) complexed with (Z)-((3,4-Dichloro-pheny... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5e4o
TitleHuman transthyretin (TTR) complexed with (Z)-((3,4-Dichloro-phenyl)-methyleneaminooxy)-acetic acid
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Fluorenone based Fibrillogenesis inhibitor
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/hydroxyisourate hydrolase domain / 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 ...Transthyretin/hydroxyisourate hydrolase domain / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-L57 / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsCiccone, L. / Savko, M. / Nencetti, S. / Rossello, A. / Orlandini, E. / Stura, E.A.
Funding support Italy, 1items
OrganizationGrant numberCountry
Ministero dell'IstruzionePRIN 20109MXHMR_007 Italy
CitationJournal: J Enzyme Inhib Med Chem / Year: 2016
Title: Synthesis and structural analysis of halogen substituted fibril formation inhibitors of Human Transthyretin (TTR).
Authors: Ciccone, L. / Nencetti, S. / Rossello, A. / Stura, E.A. / Orlandini, E.
History
DepositionOct 6, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references
Revision 1.2Dec 7, 2016Group: Database references
Revision 2.0May 8, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry
Item: _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3134
Polymers25,6652
Non-polymers6482
Water2,846158
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6268
Polymers51,3304
Non-polymers1,2974
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)43.470, 84.930, 63.890
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-201-

L57

21A-201-

L57

31A-201-

L57

41B-201-

L57

51B-201-

L57

61B-201-

L57

71A-301-

HOH

-
Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 12832.397 Da / Num. of mol.: 2 / Fragment: UNP residues 30-146 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02766
#2: Chemical ChemComp-L57 / ({(Z)-[(3,4-dichlorophenyl)(phenyl)methylidene]amino}oxy)acetic acid


Mass: 324.159 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C15H11Cl2NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.47 % / Description: Long jagged crystal
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Protein: 5mg/ml TTR and 1 milli-M inhibitor. Precipitant: 25% PEG4K, 0.2M imidazole malate, pH 6.0. Slow dessication over 18 months, rehydrated over 4 hours. Cryoprotectant: 40% CryoSol SM1, ...Details: Protein: 5mg/ml TTR and 1 milli-M inhibitor. Precipitant: 25% PEG4K, 0.2M imidazole malate, pH 6.0. Slow dessication over 18 months, rehydrated over 4 hours. Cryoprotectant: 40% CryoSol SM1, 25% MPEG 5K, 0.1M (Na acetate, ADA, Bicine, 80% pH 4.0/20% pH 9.0)
PH range: 5-6 / Temp details: cooled incubator

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryo-nozzle
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 1, 2015
Details: a convex prefocussing mirror and a Kirkpatrick-Baez pair of focussing mirrors
RadiationMonochromator: cryogenically cooled channel-cut Si[111] monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.5→43.467 Å / Num. all: 38665 / Num. obs: 38419 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.93 % / Rmerge(I) obs: 0.063 / Rsym value: 0.056 / Net I/σ(I): 15.19
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 4.849 % / Rmerge(I) obs: 1.2 / Mean I/σ(I) obs: 1.63 / % possible all: 98.7

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
REFMACRigid bodyphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→38.696 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2071 1920 5 %Random selection
Rwork0.1928 ---
obs0.1935 38397 99.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→38.696 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1786 0 0 158 1944
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172129
X-RAY DIFFRACTIONf_angle_d2.0222938
X-RAY DIFFRACTIONf_dihedral_angle_d18.17780
X-RAY DIFFRACTIONf_chiral_restr0.117314
X-RAY DIFFRACTIONf_plane_restr0.014395
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.53750.31651320.33672517X-RAY DIFFRACTION98
1.5375-1.57910.33811350.31052557X-RAY DIFFRACTION99
1.5791-1.62560.31340.28242557X-RAY DIFFRACTION99
1.6256-1.6780.30181380.2732604X-RAY DIFFRACTION100
1.678-1.7380.33311360.25292590X-RAY DIFFRACTION99
1.738-1.80760.26531350.23582570X-RAY DIFFRACTION100
1.8076-1.88990.22381370.20952607X-RAY DIFFRACTION100
1.8899-1.98950.21271370.19632591X-RAY DIFFRACTION100
1.9895-2.11410.18931360.18462590X-RAY DIFFRACTION100
2.1141-2.27730.19161380.17722616X-RAY DIFFRACTION100
2.2773-2.50650.21051380.18412626X-RAY DIFFRACTION100
2.5065-2.86910.20391400.18092649X-RAY DIFFRACTION100
2.8691-3.61430.16261400.16742666X-RAY DIFFRACTION100
3.6143-38.70870.19751440.18082737X-RAY DIFFRACTION97

+
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