6Y29

Crystal structure of HLA-B2709 complexed with the nona-peptide mE

• PDB DOI: https://doi.org/10.2210/pdb6Y29/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli, synthetic construct
• Mutation(s): No 


• Deposited: 2020-02-15 Released: 2020-12-23 
• Deposition Author(s): Loll, B., Rueckert, C., Ziegler, B.-U., Ziegler, A.
• Funding Organization(s): German Research Foundation (DFG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.28 Å
• R-Value Free: 0.169 
• R-Value Work: 0.141 
• R-Value Observed: 0.141 

Starting Model: experimental

Literature

A CENTRAL PEPTIDE RESIDUE CAN CONTROL MHC POLYMORPHISM-DEPENDENT ANTIGEN PRESENTATION

Loll, B., Rueckert, C., Ziegler, B.-U., Ziegler, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 45.23 kDa 
• Atom Count: 4,129 
• Modelled Residue Count: 385 
• Deposited Residue Count: 385 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lymphocyte antigen HLA-B27	A	276	Homo sapiens	Mutation(s): 0  Gene Names: HLA-B
UniProt
Find proteins for A0A2R7Z5J3 (Homo sapiens) Explore A0A2R7Z5J3  Go to UniProtKB:  A0A2R7Z5J3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	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
mE	C	9	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A], E [auth A], F [auth A], G [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.28 Å
• R-Value Free: 0.169 
• R-Value Work: 0.141 
• R-Value Observed: 0.141 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data: https://doi.org/10.18430/m36y29

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.876	α = 90
b = 83.136	β = 90
c = 110.832	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
DNA	data collection

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-12-23 
Deposition Author(s): Loll, B., Rueckert, C., Ziegler, B.-U., Ziegler, A.

---

Funding Organization	Location	Grant Number
German Research Foundation (DFG)		SfB 449

Revision History  

• Version 1.0: 2020-12-23
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary