8Q7K | pdb_00008q7k

IRGQ LIR2 peptide in complex with LC3B

PDB DOI: https://doi.org/10.2210/pdb8Q7K/pdb

Classification: PROTEIN BINDING
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-08-16 Released: 2024-08-28
Deposition Author(s): Misra, M., Bailey, H.J., Pomirska, J., Dikic, I.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.213 (Depositor), 0.210 (DCC)
R-Value Work:
0.192 (Depositor), 0.190 (DCC)
R-Value Observed:
0.193 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

IRGQ-mediated autophagy in MHC class I quality control promotes tumor immune evasion.

Herhaus, L., Gestal-Mato, U., Eapen, V.V., Macinkovic, I., Bailey, H.J., Prieto-Garcia, C., Misra, M., Jacomin, A.C., Ammanath, A.V., Bagaric, I., Michaelis, J., Vollrath, J., Bhaskara, R.M., Bundgen, G., Covarrubias-Pinto, A., Husnjak, K., Zoller, J., Gikandi, A., Ribicic, S., Bopp, T., van der Heden van Noort, G.J., Langer, J.D., Weigert, A., Harper, J.W., Mancias, J.D., Dikic, I.

(2024) Cell 187: 7285-7302.e29

PubMed: 39481378 Search on PubMed
DOI: https://doi.org/10.1016/j.cell.2024.09.048
Primary Citation of Related Structures:
8Q7K

PubMed Abstract:
The autophagy-lysosome system directs the degradation of a wide variety of cargo and is also involved in tumor progression. Here, we show that the immunity-related GTPase family Q protein (IRGQ), an uncharacterized protein to date, acts in the quality control of major histocompatibility complex class I (MHC class I) molecules. IRGQ directs misfolded MHC class I toward lysosomal degradation through its binding mode to GABARAPL2 and LC3B. In the absence of IRGQ, free MHC class I heavy chains do not only accumulate in the cell but are also transported to the cell surface, thereby promoting an immune response. Mice and human patients suffering from hepatocellular carcinoma show improved survival rates with reduced IRGQ levels due to increased reactivity of CD8+ T cells toward IRGQ knockout tumor cells. Thus, we reveal IRGQ as a regulator of MHC class I quality control, mediating tumor immune evasion.

Organizational Affiliation

Institute of Biochemistry II, Goethe University Frankfurt, Medical Faculty, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany. Electronic address: lina.herhaus@gmail.com.

Institute of Biochemistry II, Goethe University Frankfurt, Medical Faculty, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany.

Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Institutes of Medicine, 450 Brookline Avenue, Boston, MA 02215, USA; Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.

Institute of Biochemistry II, Goethe University Frankfurt, Medical Faculty, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Institute of Biochemistry I, Goethe University School of Medicine, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany.

Institute of Biochemistry II, Goethe University Frankfurt, Medical Faculty, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Riedberg Campus, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany; Max Planck Institute of Biophysics, Goethe University Frankfurt, Riedberg Campus, 60438 Frankfurt am Main, Germany.

Institute for Immunology, University Medical Center, Johannes Gutenberg University Mainz, Mainz, Germany.

Max Planck Institute of Biophysics, Goethe University Frankfurt, Riedberg Campus, 60438 Frankfurt am Main, Germany.

Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Institutes of Medicine, 450 Brookline Avenue, Boston, MA 02215, USA.

Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands.

Institute of Biochemistry I, Goethe University School of Medicine, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany.

Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.

Macromolecule Content

Total Structure Weight: 31.78 kDa
Atom Count: 2,318
Modeled Residue Count: 250
Deposited Residue Count: 268
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Microtubule-associated proteins 1A/1B light chain 3B	A, B	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9GZQ8
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunity-related GTPase family Q protein	C, D	9	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WZA9 (Homo sapiens) Explore Q8WZA9 Go to UniProtKB: Q8WZA9
PHAROS: Q8WZA9 GTEx: ENSG00000167378
Entity Groups
UniProt Group	Q8WZA9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO (Subject of Investigation/LOI) Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]