› 7n9x

X-ray diffraction
3.51Å resolution

CA-targeting nanobody is a tool for studying HIV-1 capsid lattice interactions

Released:
DOI: 10.2210/pdb7n9x/pdb
PDB entry 7n9x coloured by chain, front view.
PDB entry 7n9x coloured by chain, side view.
PDB entry 7n9x coloured by chain, top view.
Source organisms:
Entry authors: Gerber EE, Digianantonio KM, Tripler TN, Smaga SS, Summers BJ, Xiong Y

Function and Biology Details

Reaction catalysed: 
Peptidylproline (omega=180) = peptidylproline (omega=0)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero octadecamer (preferred)
PDBe Complex ID:
PDB-CPX-207681 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (5 distinct):
Gag protein Chains: AAA, BBB, CCC
Molecule details ›
Chains: AAA, BBB, CCC
Length: 222 amino acids
Theoretical weight: 24.54 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: B6DRA0 (Residues: 133-354; Coverage: 55%)
Gene name: gag
Sequence domains:
Nanobody Chain: FFF
Molecule details ›
Chain: FFF
Length: 115 amino acids
Theoretical weight: 12.37 KDa
Source organism: Lama glama
Expression system: Escherichia coli BL21(DE3)
Nanobody Chain: EEE
Molecule details ›
Chain: EEE
Length: 112 amino acids
Theoretical weight: 12.12 KDa
Source organism: Lama glama
Expression system: Escherichia coli BL21(DE3)
Nanobody Chain: DDD
Molecule details ›
Chain: DDD
Length: 114 amino acids
Theoretical weight: 12.28 KDa
Source organism: Lama glama
Expression system: Escherichia coli BL21(DE3)
Peptidyl-prolyl cis-trans isomerase A Chains: GGG, HHH, III
Molecule details ›
Chains: GGG, HHH, III
Length: 165 amino acids
Theoretical weight: 18.04 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P62937 (Residues: 1-165; Coverage: 100%)
Gene names: CYPA, PPIA
Sequence domains: Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: I222
Unit cell:
a: 127.95Å b: 137.85Å c: 313.832Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.246 0.245 0.27
Expression system: Escherichia coli BL21(DE3)

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