5WER | pdb_00005wer

Crystal Structure of TAPBPR and H2-Dd complex

• PDB DOI: https://doi.org/10.2210/pdb5WER/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Escherichia coli BL21(DE3), Drosophila acanthoptera
• Mutation(s): Yes 


• Deposited: 2017-07-10 Released: 2017-10-18 
• Deposition Author(s): Jiang, J.S., Natarajan, K., Boyd, L.F., Margulies, D.H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.41 Å
• R-Value Free: 
  0.269 (Depositor), 0.273 (DCC) 
• R-Value Work: 
  0.239 (Depositor), 0.239 (DCC) 
• R-Value Observed: 
  0.243 (Depositor) 

Literature

Crystal structure of a TAPBPR-MHC I complex reveals the mechanism of peptide editing in antigen presentation.

Jiang, J., Natarajan, K., Boyd, L.F., Morozov, G.I., Mage, M.G., Margulies, D.H.

(2017) Science 358: 1064-1068

• PubMed: 29025991 
• DOI: https://doi.org/10.1126/science.aao5154
• Primary Citation Related Structures: 
  5WER, 5WES, 5WET, 5WEU


• PubMed Abstract: 
  

  Central to CD8 ⁺ T cell-mediated immunity is the recognition of peptide-major histocompatibility complex class I (p-MHC I) proteins displayed by antigen-presenting cells. Chaperone-mediated loading of high-affinity peptides onto MHC I is a key step in the MHC I antigen presentation pathway. However, the structure of MHC I with a chaperone that facilitates peptide loading has not been determined. We report the crystal structure of MHC I in complex with the peptide editor TAPBPR (TAP-binding protein-related), a tapasin homolog. TAPBPR remodels the peptide-binding groove of MHC I, resulting in the release of low-affinity peptide. Changes include groove relaxation, modifications of key binding pockets, and domain adjustments. This structure captures a peptide-receptive state of MHC I and provides insights into the mechanism of peptide editing by TAPBPR and, by analogy, tapasin.

---

Organizational Affiliation: 
• Molecular Biology Section, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
Hebrew University of Jerusalem, Robert H. Smith Faculty of Agriculture, Food and Environment, Rehovot 76100, Israel.
Molecular Biology Section, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 346.59 kDa 
• Atom Count: 20,155 
• Modeled Residue Count: 2,706 
• Deposited Residue Count: 3,084 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H-2 class I histocompatibility antigen, D-D alpha chain	A, D, G, J	277	Mus musculus	Mutation(s): 1  Gene Names: H2-D1
UniProt
Find proteins for P01900 (Mus musculus) Explore P01900  Go to UniProtKB:  P01900

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B, E, H, K	100	Homo sapiens	Mutation(s): 0  Gene Names: B2M, CDABP0092, HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769
PHAROS:  P61769 GTEx:  ENSG00000166710

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
TAP binding protein related	C, F, I, L	394	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BX59 (Homo sapiens) Explore Q9BX59  Go to UniProtKB:  Q9BX59
PHAROS:  Q9BX59 GTEx:  ENSG00000139192

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PE	Q [auth J]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
CIT	R [auth L]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
GOL	N [auth C], P [auth F], S [auth L]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	M [auth A], O [auth E]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.41 Å
• R-Value Free:  0.269 (Depositor), 0.273 (DCC) 
• R-Value Work:  0.239 (Depositor), 0.239 (DCC) 
• R-Value Observed: 0.243 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 169.05	α = 90
b = 169.05	β = 90
c = 139.41	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-10-18 
Deposition Author(s): Jiang, J.S., Natarajan, K., Boyd, L.F., Margulies, D.H.

Revision History  

• Version 1.0: 2017-10-18
  Type: Initial release
  
• Version 1.1: 2017-10-25
  Changes: Database references
• Version 1.2: 2017-12-06
  Changes: Database references
• Version 1.3: 2017-12-13
  Changes: Database references
• Version 1.4: 2019-08-28
  Changes: Data collection, Database references
• Version 1.5: 2024-12-25
  Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary