8YV6 | pdb_00008yv6

Crystal structure of LC3B in complex with Influenza A virus M2 peptide

PDB DOI: https://doi.org/10.2210/pdb8YV6/pdb

Classification: VIRUS
Organism(s): Homo sapiens, Influenza A virus
Expression System: Escherichia phage EcSzw-2
Mutation(s): No

Deposited: 2024-03-28 Released: 2024-11-13
Deposition Author(s): Murata, D., Novoa, C., Beale, R., Akutsu, M.
Funding Organization(s): The Francis Crick Institute

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.250 (Depositor), 0.253 (DCC)
R-Value Work:
0.210 (Depositor), 0.213 (DCC)
R-Value Observed:
0.212 (Depositor)

Starting Model: experimental
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This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of LC3B in complex with Influenza A virus M2 peptide

Murata, D., Novoa, C., Beale, R., Akutsu, M.

To be published.

Macromolecule Content

Total Structure Weight: 18.01 kDa
Atom Count: 1,094
Modeled Residue Count: 127
Deposited Residue Count: 153
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Microtubule-associated proteins 1A/1B light chain 3B	A	125	Homo sapiens	Mutation(s): 0 Gene Names: MAP1LC3B, MAP1ALC3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9GZQ8 (Homo sapiens) Explore Q9GZQ8 Go to UniProtKB: Q9GZQ8
PHAROS: Q9GZQ8 GTEx: ENSG00000140941
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9GZQ8
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Matrix protein 2	B	28	Influenza A virus	Mutation(s): 0 Gene Names: M2
UniProt
Find proteins for A0A3S8TIH3 (Influenza A virus) Explore A0A3S8TIH3 Go to UniProtKB: A0A3S8TIH3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A3S8TIH3
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.250 (Depositor), 0.253 (DCC)
R-Value Work: 0.210 (Depositor), 0.213 (DCC)
R-Value Observed: 0.212 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.681	α = 90
b = 38.462	β = 90
c = 93.774	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-11-13

Deposition Author(s):

Funding Organization	Location	Grant Number
The Francis Crick Institute	United Kingdom	--

Revision History (Full details and data files)

Version 1.0: 2024-11-13
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.