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- PDB-8yv6: Crystal structure of LC3B in complex with Influenza A virus M2 peptide -

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Basic information

Entry
Database: PDB / ID: 8yv6
TitleCrystal structure of LC3B in complex with Influenza A virus M2 peptide
Components
  • Matrix protein 2
  • Microtubule-associated proteins 1A/1B light chain 3B
KeywordsVIRUS / Influenza A virus / Complex / LC3
Function / homology
Function and homology information


SARS-CoV-2 modulates autophagy / ceramide binding / phosphatidylethanolamine binding / Translation of Replicase and Assembly of the Replication Transcription Complex / TBC/RABGAPs / cellular response to nitrogen starvation / Receptor Mediated Mitophagy / Macroautophagy / organelle membrane / proton transmembrane transporter activity ...SARS-CoV-2 modulates autophagy / ceramide binding / phosphatidylethanolamine binding / Translation of Replicase and Assembly of the Replication Transcription Complex / TBC/RABGAPs / cellular response to nitrogen starvation / Receptor Mediated Mitophagy / Macroautophagy / organelle membrane / proton transmembrane transporter activity / autophagosome membrane / axoneme / autophagosome assembly / autophagosome maturation / mitophagy / endomembrane system / autophagosome / Pexophagy / cellular response to starvation / PINK1-PRKN Mediated Mitophagy / macroautophagy / mitochondrial membrane / autophagy / KEAP1-NFE2L2 pathway / channel activity / Translation of Replicase and Assembly of the Replication Transcription Complex / microtubule binding / cytoplasmic vesicle / microtubule / ubiquitin protein ligase binding / host cell plasma membrane / virion membrane / mitochondrion / membrane / cytosol
Similarity search - Function
Influenza virus matrix protein 2 / Influenza Matrix protein (M2) / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Matrix protein 2 / Microtubule-associated protein 1 light chain 3 beta
Similarity search - Component
Biological speciesHomo sapiens (human)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsMurata, D. / Novoa, C. / Beale, R. / Akutsu, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
The Francis Crick Institute United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of LC3B in complex with Influenza A virus M2 peptide
Authors: Murata, D. / Novoa, C. / Beale, R. / Akutsu, M.
History
DepositionMar 28, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Microtubule-associated proteins 1A/1B light chain 3B
B: Matrix protein 2


Theoretical massNumber of molelcules
Total (without water)18,0132
Polymers18,0132
Non-polymers00
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.681, 38.462, 93.774
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Microtubule-associated proteins 1A/1B light chain 3B / Autophagy-related protein LC3 B / Autophagy-related ubiquitin-like modifier LC3 B / MAP1 light ...Autophagy-related protein LC3 B / Autophagy-related ubiquitin-like modifier LC3 B / MAP1 light chain 3-like protein 2 / MAP1A/MAP1B light chain 3 B / MAP1A/MAP1B LC3 B / Microtubule-associated protein 1 light chain 3 beta


Mass: 14710.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP1LC3B, MAP1ALC3 / Production host: Escherichia phage EcSzw-2 (virus) / References: UniProt: Q9GZQ8
#2: Protein/peptide Matrix protein 2


Mass: 3302.561 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: M2 / Production host: Escherichia phage EcSzw-2 (virus) / References: UniProt: A0A3S5G6R9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.79 Å3/Da / Density % sol: 31.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 30% Jeffamine, 0.1M HEPES, pH 7.0

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jul 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→46.89 Å / Num. obs: 13649 / % possible obs: 100 % / Redundancy: 12.8 % / CC1/2: 1 / Net I/σ(I): 27.9
Reflection shellResolution: 1.75→1.84 Å / Num. unique obs: 1935 / CC1/2: 0.92

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→46.887 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.25 666 4.9 %
Rwork0.2098 --
obs0.2118 13599 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→46.887 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1047 0 0 22 1069
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121093
X-RAY DIFFRACTIONf_angle_d1.1831473
X-RAY DIFFRACTIONf_dihedral_angle_d6.619917
X-RAY DIFFRACTIONf_chiral_restr0.077163
X-RAY DIFFRACTIONf_plane_restr0.007192
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7501-1.88520.28181190.27862538X-RAY DIFFRACTION100
1.8852-2.07490.29591390.25582522X-RAY DIFFRACTION100
2.0749-2.37510.30851310.25352567X-RAY DIFFRACTION100
2.3751-2.99240.26751310.23872594X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -3.195 Å / Origin y: 5.2474 Å / Origin z: -10.3603 Å
111213212223313233
T0.1672 Å20.0271 Å2-0.0126 Å2-0.3011 Å20.0775 Å2--0.1748 Å2
L4.2242 °20.7227 °2-0.439 °2-2.5721 °20.9748 °2--3.9686 °2
S-0.1169 Å °-0.6693 Å °-0.1318 Å °-0.0331 Å °0.0545 Å °0.0421 Å °0.0803 Å °0.1703 Å °0.0525 Å °
Refinement TLS groupSelection details: all

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