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- PDB-5uzb: Cryo-EM structure of the MAL TIR domain filament -

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Basic information

Entry
Database: PDB / ID: 5uzb
TitleCryo-EM structure of the MAL TIR domain filament
DescriptorToll/interleukin-1 receptor domain-containing adapter protein
KeywordsIMMUNE SYSTEM / TIR domain / adaptor proteins / TLR signaling / homotypic protein interactions
Specimen sourceHomo sapiens / human
MethodElectron microscopy (7 Å resolution / Filament / Helical)
AuthorsVe, T. / Vajjhala, P.R. / Hedger, A. / Croll, T. / DiMaio, F. / Horsefield, S. / Yu, X. / Lavrencic, P. / Hassan, Z. / Morgan, G.P. / Mansell, A. / Mobli, M. / O'Carrol, A. / Chauvin, B. / Gambin, Y. / Sierecki, E. / Landsberg, M.J. / Stacey, K.J. / Egelman, E.H. / Kobe, B.
CitationNat. Struct. Mol. Biol., 2017, 24, 743-751

Nat. Struct. Mol. Biol., 2017, 24, 743-751 Yorodumi Papers
Structural basis of TIR-domain-assembly formation in MAL- and MyD88-dependent TLR4 signaling.
Thomas Ve / Parimala R Vajjhala / Andrew Hedger / Tristan Croll / Frank DiMaio / Shane Horsefield / Xiong Yu / Peter Lavrencic / Zahid Hassan / Garry P Morgan / Ashley Mansell / Mehdi Mobli / Ailis O'Carroll / Brieuc Chauvin / Yann Gambin / Emma Sierecki / Michael J Landsberg / Katryn J Stacey / Edward H Egelman / Bostjan Kobe

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 25, 2017 / Release: Jul 26, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jul 26, 2017Structure modelrepositoryInitial release
1.1Aug 23, 2017Structure modelDatabase referencescitation / citation_author_citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
1.2Sep 20, 2017Structure modelData collection / Database referencescitation / em_software_citation.journal_volume / _citation.page_first / _citation.page_last / _em_software.name

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Assembly

Deposited unit
A: Toll/interleukin-1 receptor domain-containing adapter protein
B: Toll/interleukin-1 receptor domain-containing adapter protein
C: Toll/interleukin-1 receptor domain-containing adapter protein
D: Toll/interleukin-1 receptor domain-containing adapter protein
E: Toll/interleukin-1 receptor domain-containing adapter protein
F: Toll/interleukin-1 receptor domain-containing adapter protein
G: Toll/interleukin-1 receptor domain-containing adapter protein
H: Toll/interleukin-1 receptor domain-containing adapter protein
I: Toll/interleukin-1 receptor domain-containing adapter protein
J: Toll/interleukin-1 receptor domain-containing adapter protein
K: Toll/interleukin-1 receptor domain-containing adapter protein
L: Toll/interleukin-1 receptor domain-containing adapter protein
M: Toll/interleukin-1 receptor domain-containing adapter protein
N: Toll/interleukin-1 receptor domain-containing adapter protein


Theoretical massNumber of molelcules
Total (without water)275,64814
Polyers275,64814
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Polypeptide(L)
Toll/interleukin-1 receptor domain-containing adapter protein / TIR domain-containing adapter protein / Adaptor protein Wyatt / MyD88 adapter-like protein / MyD88-2


Mass: 19689.162 Da / Num. of mol.: 14 / Fragment: UNP residues 79-221 / Source: (gene. exp.) Homo sapiens / human / References: UniProt: P58753

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / Reconstruction method: HELICAL

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Sample preparation

ComponentName: MAL TIR domain filament / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens
Source (recombinant)Organism: Escherichia coli
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen 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
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 20 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) / Number of real images: 446

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Processing

EM software
IDNameCategoryImage processing IDFitting ID
1EMAN2PARTICLE SELECTION1
4CTFFIND3CTF CORRECTION1
7ChimeraMODEL FITTING1
8RosettaMODEL FITTING1
9iMDFFMODEL FITTING1
14SPIDERRECONSTRUCTION1
15IHRSRRECONSTRUCTION1
16RosettaMODEL REFINEMENT1
17iMDFFMODEL REFINEMENT1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -26.8 deg. / Axial rise/subunit: 15.5 Å / Axial symmetry: C6
3D reconstructionResolution: 7 Å / Resolution method: OTHER / Number of particles: 17175 / Symmetry type: HELICAL

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