› 6x00

X-ray diffraction
1.55Å resolution

Structure of DbNA(11) peptides bound to H-2Db MHC-I

Released:
DOI: 10.2210/pdb6x00/pdb
PDB entry 6x00 coloured by chain, front view.
PDB entry 6x00 coloured by chain, side view.
PDB entry 6x00 coloured by chain, top view.
Source organisms:
Primary publication:
Overlapping Peptides Elicit Distinct CD8+ T Cell Responses following Influenza A Virus Infection.
Assmus LM, Guan J, Wu T, Farenc C, Sng XYX, Zareie P, Nguyen A, Nguyen AT, Tscharke DC, Thomas PG, Rossjohn J, Gras S, Croft NP, Purcell AW, La Gruta NL
J Immunol 205 1731-1742 (2020)
PMID: 32868409

Function and Biology Details

Reaction catalysed: 
Hydrolysis of alpha-(2->3)-, alpha-(2->6)-, alpha-(2->8)- glycosidic linkages of terminal sialic acid residues in oligosaccharides, glycoproteins, glycolipids, colominic acid and synthetic substrates.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-135283 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
H-2 class I histocompatibility antigen, D-B alpha chain Chain: A
Molecule details ›
Chain: A
Length: 281 amino acids
Theoretical weight: 32.6 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: P01899 (Residues: 25-304; Coverage: 83%)
Gene name: H2-D1
Sequence domains:
Beta-2-microglobulin Chain: B
Molecule details ›
Chain: B
Length: 100 amino acids
Theoretical weight: 11.88 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P61769 (Residues: 21-119; Coverage: 100%)
Gene names: B2M, CDABP0092, HDCMA22P
Sequence domains: Immunoglobulin C1-set domain
Neuraminidase Chain: C
Molecule details ›
Chain: C
Length: 11 amino acids
Theoretical weight: 999 Da
Source organism: Influenza A virus
Expression system: Not provided
UniProt:
  • Canonical: P03468 (Residues: 181-191; Coverage: 2%)
Gene name: NA

Ligands and Environments

1 bound ligand:
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX2
Spacegroup: P21
Unit cell:
a: 69.01Å b: 44.751Å c: 71.657Å
α: 90° β: 98.45° γ: 90°
R-values:
R R work R free
0.186 0.184 0.215
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

Novel coronavirus mutations: Vaccine development and challenges.
Luo et al. (2022)
5 other articles

1 mention without citation

Overlapping Peptides Elicit Distinct CD8+ T Cell Responses following Influenza A Virus Infection.
Assmus et al. (2020)