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- PDB-5yud: Flagellin derivative in complex with the NLR protein NAIP5 -

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Basic information

Entry
Database: PDB / ID: 5yud
TitleFlagellin derivative in complex with the NLR protein NAIP5
DescriptorBaculoviral IAP repeat-containing protein 1e
Flagellin,Flagellin
KeywordsIMMUNE SYSTEM / Flagellin / NAIP5 / NLRC4 / Cryo-EM
Specimen sourceMus musculus / mammal / Mouse / ハツカネズミ, はつかねずみ /
Salmonella typhimurium (strain lt2 / sgsc1412 / atcc 700720) / bacteria
MethodElectron microscopy (4.28 Å resolution / Particle / Single particle)
AuthorsYang, X.R. / Yang, F. / Wang, W.G. / Lin, G.Z.
CitationCell Res., 2018, 28, 35-47

Cell Res., 2018, 28, 35-47 Yorodumi Papers
Structural basis for specific flagellin recognition by the NLR protein NAIP5.
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

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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

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Components

#1: Polypeptide(L)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 / mammal / ハツカネズミ, はつかねずみ /
References: UniProt: Q8CGT2
#2: Polypeptide(L)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
References: UniProt: P52616, UniProt: P06179
#3: ChemicalChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / ATP (energy-carrying molecule) *YM


Mass: 507.181 Da / Num. of mol.: 1 / Formula: C10H16N5O13P3

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

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

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

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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

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