[English] 日本語
Yorodumi
- PDB-5w7v: CryoEM structure of the segment, DLIIKGISVHI, assembled into a tr... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 5w7v
TitleCryoEM structure of the segment, DLIIKGISVHI, assembled into a triple-helical fibril
ComponentsTAR DNA-binding protein 43
KeywordsPROTEIN FIBRIL / Amyloid / steric zipper
Function / homologyEukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / RNA recognition motif domain / nuclear inner membrane organization / interchromatin granule / perichromatin fibrils / negative regulation by host of viral transcription / go:0001205: ...Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / RNA recognition motif domain / nuclear inner membrane organization / interchromatin granule / perichromatin fibrils / negative regulation by host of viral transcription / go:0001205: / sequence-specific double-stranded DNA binding / 3'-UTR-mediated mRNA stabilization / positive regulation of insulin secretion / response to endoplasmic reticulum stress / mRNA 3'-UTR binding / RNA splicing / single-stranded RNA binding / negative regulation of protein phosphorylation / regulation of cell cycle / ribonucleoprotein complex / mRNA processing / double-stranded DNA binding / transcription by RNA polymerase II / regulation of apoptotic process / negative regulation of gene expression / nuclear speck / DNA-binding transcription factor activity / RNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / TAR DNA-binding protein 43
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / 3.8 Å resolution
AuthorsGuenther, E.L. / Ge, P. / Eisenberg, D.S.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: Atomic-level evidence for packing and positional amyloid polymorphism by segment from TDP-43 RRM2.
Authors: Elizabeth L Guenther / Peng Ge / Hamilton Trinh / Michael R Sawaya / Duilio Cascio / David R Boyer / Tamir Gonen / Z Hong Zhou / David S Eisenberg
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 20, 2017 / Release: Mar 14, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Mar 14, 2018Structure modelrepositoryInitial release
1.1Mar 28, 2018Structure modelData collection / Database referencescitation_citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
1.2Apr 18, 2018Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last
1.3Jul 18, 2018Structure modelData collectionem_imaging_optics_em_imaging_optics.energyfilter_name

-
Structure visualization

Movie
  • Biological unit as representative helical assembly
  • Imaged by Jmol
  • Download
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-8781
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-8781
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: TAR DNA-binding protein 43
3: TAR DNA-binding protein 43
2: TAR DNA-binding protein 43
6: TAR DNA-binding protein 43
5: TAR DNA-binding protein 43
4: TAR DNA-binding protein 43
7: TAR DNA-binding protein 43
0: TAR DNA-binding protein 43
8: TAR DNA-binding protein 43


Theoretical massNumber of molelcules
Total (without water)10,8859
Polyers10,8859
Non-polymers00
Water0
1
1: TAR DNA-binding protein 43
3: TAR DNA-binding protein 43
2: TAR DNA-binding protein 43
6: TAR DNA-binding protein 43
5: TAR DNA-binding protein 43
4: TAR DNA-binding protein 43
7: TAR DNA-binding protein 43
0: TAR DNA-binding protein 43
8: TAR DNA-binding protein 43
x 30


Theoretical massNumber of molelcules
Total (without water)326,559270
Polyers326,559270
Non-polymers00
Water0
TypeNameSymmetry operationNumber
helical symmetry operation30
2


  • idetical with deposited unit in distinct coordinate
  • helical asymmetric unit
TypeNameSymmetry operationNumber
helical symmetry operation1
3


  • idetical with deposited unit in distinct coordinate
  • helical asymmetric unit, std helical frame
TypeNameSymmetry operationNumber
transform to helical frame1
Helical symmetryCircular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Number of operations: 30 / Rise per n subunits: 1.598 Å / Rotation per n subunits: -120.441 deg.

-
Components

#1: Protein/peptide
TAR DNA-binding protein 43 / TDP-43 / DLIIKGISVHI


Mass: 1209.479 Da / Num. of mol.: 9 / Fragment: RRM2 peptide (UNP residues 247-257) / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13148

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / Reconstruction method: helical reconstruction

-
Sample preparation

ComponentName: DLIIKGISVHI fibril / Type: COMPLEX / Entity ID: 1 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7
Buffer componentName: Water / Formula: H2O
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 kelvins

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / C2 aperture diameter: 70 microns / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 0.2 sec. / Electron dose: 1.2 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Number of grids imaged: 1 / Number of real images: 610
EM imaging opticsEnergyfilter name: GIF Quantum
Image scansMovie frames/image: 50 / Used frames/image: 4-20

-
Processing

SoftwareName: PHENIX / Version: 1.10.1_2155: / Classification: refinement
EM software
IDNameVersionCategoryDetails
1EMAN1.9particle selection
2Leginon3.2image acquisition
4CTFFIND4.0CTF correction
12RELION1.43D reconstruction+IHRSR implementation
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -120.441 deg. / Axial rise/subunit: 1.598 Å / Axial symmetry: C1
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.5 CUT-OFF / Number of particles: 18818 / Algorithm: FOURIER SPACE / Symmetry type: HELICAL
Atomic model buildingRef protocol: AB INITIO MODEL / Ref space: REAL
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00720370
ELECTRON MICROSCOPYf_angle_d0.77127210
ELECTRON MICROSCOPYf_dihedral_angle_d10.10612300
ELECTRON MICROSCOPYf_chiral_restr0.0633840
ELECTRON MICROSCOPYf_plane_restr0.0023060

+
About Yorodumi

-
News

-
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. See below links for details.
  • 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

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
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.

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