[English] 日本語
Yorodumi
- PDB-5yud: Flagellin derivative in complex with the NLR protein NAIP5 -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 5yud
TitleFlagellin derivative in complex with the NLR protein NAIP5
Components
  • Baculoviral IAP repeat-containing protein 1e
  • Phase 2 flagellin,Flagellin
KeywordsIMMUNE SYSTEM / Flagellin / NAIP5 / NLRC4 / Cryo-EM
Function / homologyFlagellin, D0/D1 domain / Flagellin D3 domain / Flagellin D3 / NACHT nucleoside triphosphatase / Flagellin / BIR repeat / Leucine-rich repeat domain superfamily / Inhibitor of Apoptosis domain / Bacterial flagellin N-terminal helical region / Bacterial flagellin C-terminal helical region ...Flagellin, D0/D1 domain / Flagellin D3 domain / Flagellin D3 / NACHT nucleoside triphosphatase / Flagellin / BIR repeat / Leucine-rich repeat domain superfamily / Inhibitor of Apoptosis domain / Bacterial flagellin N-terminal helical region / Bacterial flagellin C-terminal helical region / Baculoviral IAP repeat-containing protein 1 / NACHT domain / BIR repeat. / NACHT-NTPase domain profile. / The IPAF inflammasome / MyD88 cascade initiated on plasma membrane / TLR5 cascade / NFkB and MAPK activation mediated by TRAF6 / P-loop containing nucleoside triphosphate hydrolase / BIR repeat profile. / bacterial-type flagellum filament / IPAF inflammasome complex / pyroptosis / positive regulation of interleukin-1 beta production / inhibition of cysteine-type endopeptidase activity involved in apoptotic process / bacterial-type flagellum-dependent cell motility / detection of bacterium / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / positive regulation of canonical Wnt signaling pathway / ubiquitin-protein transferase activity / perikaryon / neuron projection / defense response to Gram-negative bacterium / neuronal cell body / inflammatory response / defense response to bacterium / structural molecule activity / innate immune response / extracellular region / ATP binding / nucleus / metal ion binding / cytoplasm / Flagellin / Phase 2 flagellin / Baculoviral IAP repeat-containing protein 1e / Baculoviral IAP repeat-containing protein 1e
Function and homology information
Specimen sourceMus musculus (house mouse)
Salmonella typhimurium (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.28 Å resolution
AuthorsYang, X.R. / Yang, F. / Wang, W.G. / Lin, G.Z.
CitationJournal: Cell Res. / Year: 2018
Title: Structural basis for specific flagellin recognition by the NLR protein NAIP5.
Authors: Xinru Yang / Fan Yang / Weiguang Wang / Guangzhong Lin / Zehan Hu / Zhifu Han / Yijun Qi / Liman Zhang / Jiawei Wang / Sen-Fang Sui / Jijie Chai
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 21, 2017 / Release: Jan 3, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 3, 2018Structure modelrepositoryInitial release
1.1Jan 17, 2018Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-6845
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-6845
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Baculoviral IAP repeat-containing protein 1e
C: Phase 2 flagellin,Flagellin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,1913
Polyers167,6832
Non-polymers5071
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)7450
ΔGint (kcal/M)-39
Surface area (Å2)63030

-
Components

#1: Protein/peptide Baculoviral IAP repeat-containing protein 1e / NLR family / apoptosis inhibitory protein 5 / Neuronal apoptosis inhibitory protein 5


Mass: 160018.047 Da / Num. of mol.: 1 / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Naip5, Birc1e / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8CGT2, UniProt: Q9R016*PLUS
#2: Protein/peptide Phase 2 flagellin,Flagellin / Phase 1-I flagellin


Mass: 7665.362 Da / Num. of mol.: 1
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: fljB, H2, STM2771, fliC, flaF, hag, STM1959 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: P52616, UniProt: P06179
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

-
Sample preparation

Component
IDNameTypeEntity IDParent IDSource
1Flagellin derivative in complex with NAIP5COMPLEX1, 20RECOMBINANT
2NAIP5COMPLEX11RECOMBINANT
3FlagellinCOMPLEX21RECOMBINANT
Source (natural)
IDEntity assembly IDNcbi tax IDOrganismStrain
2110090Mus musculus (house mouse)
3199287Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)LT2 / SGSC1412 / ATCC 700720
Source (recombinant)
IDEntity assembly IDNcbi tax IDOrganismStrain
217108Spodoptera frugiperda (fall armyworm)
3183333Escherichia coli K-12 (bacteria)K-12
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
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
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

SoftwareName: PHENIX / Version: 1.10.1_2155: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.28 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 626608 / Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00810675
ELECTRON MICROSCOPYf_angle_d1.17514446
ELECTRON MICROSCOPYf_dihedral_angle_d8.9128895
ELECTRON MICROSCOPYf_chiral_restr0.0561627
ELECTRON MICROSCOPYf_plane_restr0.0061857

+
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