[English] 日本語
Yorodumi
- PDB-4xfo: Structure of an amyloid-forming segment TAVVTN from human Transth... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xfo
TitleStructure of an amyloid-forming segment TAVVTN from human Transthyretin
ComponentsAmyloid-forming peptide TAVVTN
KeywordsPROTEIN FIBRIL / amyloid / transthyretin / fibril
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.35 Å
AuthorsSaelices, L. / Sawaya, M. / Cascio, D. / Eisenberg, D.S.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Marie Curie Actions298559 Switzerland
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Uncovering the Mechanism of Aggregation of Human Transthyretin.
Authors: Saelices, L. / Johnson, L.M. / Liang, W.Y. / Sawaya, M.R. / Cascio, D. / Ruchala, P. / Whitelegge, J. / Jiang, L. / Riek, R. / Eisenberg, D.S.
History
DepositionDec 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Dec 9, 2015Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Amyloid-forming peptide TAVVTN


Theoretical massNumber of molelcules
Total (without water)6041
Polymers6041
Non-polymers00
Water00
1
A: Amyloid-forming peptide TAVVTN

A: Amyloid-forming peptide TAVVTN

A: Amyloid-forming peptide TAVVTN

A: Amyloid-forming peptide TAVVTN


Theoretical massNumber of molelcules
Total (without water)2,4154
Polymers2,4154
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation1_755x+2,y,z1
crystal symmetry operation1_855x+3,y,z1
Unit cell
Length a, b, c (Å)4.750, 10.660, 16.390
Angle α, β, γ (deg.)77.64, 87.81, 77.61
Int Tables number1
Space group name H-MP1
DetailsThe biological assembly is a pair of indefinitely long beta sheets constructed from chain A and unit cell translations along the "a" direction (that is, the "a" direction corresponds to the fiber axis) (i.e. X,Y,Z; X+1,Y,Z; X+2,Y,Z; etc.) together with a complementary sheet formed from X,Y+1,Z and its unit cell translations along the "a" direction (i.e. X+1,Y+1,Z; X+2,Y+1,Z; X+3,Y+1,Z;, etc.)

-
Components

#1: Protein/peptide Amyloid-forming peptide TAVVTN


Mass: 603.665 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence corresponds to a segment from human Transthyretin
Source: (synth.) synthetic construct (others)

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 1.35 Å3/Da / Density % sol: 6.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M Ammonium sulfate, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350, 25% Glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 9, 2012
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.35→16.01 Å / Num. obs: 629 / % possible obs: 92.6 % / Redundancy: 21.8 % / Net I/σ(I): 6.93

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementResolution: 1.35→16.01 Å / SU ML: 0.06 / Cross valid method: FREE R-VALUE / σ(F): 2.12 / Phase error: 13.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1478 63 10.1 %
Rwork0.1336 --
obs0.135 624 91.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.35→16.01 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms42 0 0 0 42
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00941
X-RAY DIFFRACTIONf_angle_d1.2757
X-RAY DIFFRACTIONf_dihedral_angle_d12.58412
X-RAY DIFFRACTIONf_chiral_restr0.05210
X-RAY DIFFRACTIONf_plane_restr0.0047

+
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://pdbjlvh1.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