8VSJ

Engineered peptide-specific binder in complex with HLA-DR1/CLIP

• PDB DOI: https://doi.org/10.2210/pdb8VSJ/pdb
• EM Map EMD-43499: EMDB EMDataResource

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Metamycoplasma arthritidis
• Expression System: Homo sapiens, Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-01-24 Released: 2024-10-02 
• Deposition Author(s): Jude, K.M., Yang, X., Du, H., Kassardjian, A., Julien, J.-P., Huang, P., Garcia, K.C.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.28 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Differentiating MHC-II antigens with a single loop

Du, H., Liu, J., Jude, K.M., Yang, X., Li, Y., Bell, B., Yang, H., Kassardjian, A., Mobedi, A., Parekh, U., Sperberg, A., Julien, J.-P., Mellins, E., Garcia, K.C., Huang, P.-S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A1B1C1D1E1F1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A2B2C1D1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 108.78 kDa 
• Atom Count: 5,832 
• Modelled Residue Count: 718 
• Deposited Residue Count: 957 
• Unique protein chains: 6

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class II histocompatibility antigen, DR alpha chain	A	184	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DRA, HLA-DRA1
UniProt & NIH Common Fund Data Resources
Find proteins for P01903 (Homo sapiens) Explore P01903  Go to UniProtKB:  P01903
PHAROS:  P01903 GTEx:  ENSG00000204287
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: P01903-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class II histocompatibility antigen DR beta chain	B	192	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DRB1
UniProt
Find proteins for D7RIG0 (Homo sapiens) Explore D7RIG0  Go to UniProtKB:  D7RIG0
Glycosylation
Glycosylation Sites: 1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Superantigen	C	129	Metamycoplasma arthritidis	Mutation(s): 18
UniProt
Find proteins for Q48898 (Metamycoplasma arthritidis) Explore Q48898  Go to UniProtKB:  Q48898

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
c44H10 Fab heavy chain	D [auth H]	223	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
c44H10 Fab light chain	E [auth L]	214	Homo sapiens	Mutation(s): 0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Class-II-associated invariant chain peptide	F [auth P]	15	Homo sapiens	Mutation(s): 0  Gene Names: CD74, DHLAG
UniProt & NIH Common Fund Data Resources
Find proteins for P04233 (Homo sapiens) Explore P04233  Go to UniProtKB:  P04233
PHAROS:  P04233 GTEx:  ENSG00000019582

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	G [auth A], H [auth A], I [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.28 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21_5207

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-02 
Deposition Author(s): Jude, K.M., Yang, X., Du, H., Kassardjian, A., Julien, J.-P., Huang, P., Garcia, K.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	r01gm147893

Revision History  

• Version 1.0: 2024-10-02
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Data collection, Structure summary