6EI2 | pdb_00006ei2

Crystal Structure of HLA-A68 presenting a C-terminally extended peptide

• PDB DOI: https://doi.org/10.2210/pdb6EI2/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-09-16 Released: 2017-10-11 
• Deposition Author(s): Picaud, S., Guillaume, P., Pike, A.C.W., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Gfeller, D., Filippakopoulos, P.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 
  0.181 (Depositor), 0.191 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Starting Models: experimental

Literature

Crystal Structure of HLA-A68 presenting a C-terminally extended peptide

Picaud, S., Guillaume, P., Pike, A.C.W., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Gfeller, D., Filippakopoulos, P.

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: 45.77 kDa 
• Atom Count: 3,637 
• Modeled Residue Count: 385 
• Deposited Residue Count: 386 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I histocompatibility antigen, A-68 alpha chain	A	276	Homo sapiens	Mutation(s): 0  Gene Names: HLA-A, HLAA
UniProt & NIH Common Fund Data Resources
Find proteins for P04439 (Homo sapiens) Explore P04439  Go to UniProtKB:  P04439
PHAROS:  P04439 GTEx:  ENSG00000206503

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
G1/S-specific cyclin-D2	C	10	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P30279 (Homo sapiens) Explore P30279  Go to UniProtKB:  P30279
PHAROS:  P30279 GTEx:  ENSG00000118971

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	G [auth A], H [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
EDO	D [auth A], E [auth A], J [auth B], K [auth B], L [auth B], M [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CO	N [auth B]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N
NI	F [auth A], I [auth A], O [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free:  0.181 (Depositor), 0.191 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.061	α = 90
b = 80.247	β = 90
c = 110.88	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SCALA	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-10-11 
Deposition Author(s): Picaud, S., Guillaume, P., Pike, A.C.W., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Gfeller, D., Filippakopoulos, P.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	095751/Z/11/Z

Revision History  

• Version 1.0: 2017-10-11
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary