› 5esv

X-ray diffraction
3.1Å resolution

Crystal Structure of Broadly Neutralizing Antibody CH03, Isolated from Donor CH0219, in Complex with Scaffolded Trimeric HIV-1 Env V1V2 Domain from the Clade C Superinfecting Strain of Donor CAP256.

Released:
DOI: 10.2210/pdb5esv/pdb
PDB entry 5esv coloured by chain, front view.
PDB entry 5esv coloured by chain, side view.
PDB entry 5esv coloured by chain, top view.
Source organisms:
Primary publication:
Structures of HIV-1 Env V1V2 with broadly neutralizing antibodies reveal commonalities that enable vaccine design.
Gorman J, Soto C, Yang MM, Davenport TM, Guttman M, Bailer RT, Chambers M, Chuang GY, DeKosky BJ, Doria-Rose NA, Druz A, Ernandes MJ, Georgiev IS, Jarosinski MC, Joyce MG, Lemmin TM, Leung S, Louder MK, McDaniel JR, Narpala S, Pancera M, Stuckey J, Wu X, Yang Y, Zhang B, Zhou T, Program NC, Mullikin JC, Baxa U, Georgiou G, McDermott AB, Bonsignori M, Haynes BF, Moore PL, Morris L, Lee KK, Shapiro L, Mascola JR, Kwong PD
Nat Struct Mol Biol 23 81-90 (2016)
PMID: 26689967

Function and Biology Details

Reaction catalysed: 
2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol = 2-C-methyl-D-erythritol 2,4-cyclodiphosphate + CMP
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero nonamer (preferred)
PDBe Complex ID:
PDB-CPX-134652 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (8 distinct):
Ig-like domain-containing protein Chains: A, C, H
Molecule details ›
Chains: A, C, H
Length: 244 amino acids
Theoretical weight: 26.3 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: S6BGE0 (Residues: 20-117, 118-122, 123-125, 126-244; Coverage: 80%)
Sequence domains:
Structure domains: Immunoglobulins
Immunoglobulin kappa constant Chains: B, D, L
Molecule details ›
Chains: B, D, L
Length: 215 amino acids
Theoretical weight: 23.55 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P01834 (Residues: 1-107; Coverage: 100%)
Gene name: IGKC
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; Envelope glycoprotein gp160 Chains: E, F, G
Molecule details ›
Chains: E, F, G
Length: 211 amino acids
Theoretical weight: 23.14 KDa
Source organisms: Expression system: Homo sapiens
UniProt:
  • Canonical: W6ICC0 (Residues: 122-191; Coverage: 8%)
  • Canonical: P44815 (Residues: 38-158; Coverage: 73%)
Gene names: HI_0671, env, ispF
Sequence domains: YgbB family

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
2 bound ligands:
Ligand ZN 3 x ZN
Ligand NAG 1 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: C2
Unit cell:
a: 162.693Å b: 98.211Å c: 170.629Å
α: 90° β: 112.82° γ: 90°
R-values:
R R work R free
0.211 0.208 0.259
Expression system: Homo sapiens

Quick links

Citations

32 review citations

Native-like Env trimers as a platform for HIV-1 vaccine design.
Sanders et al. (2017)
31 more

6 mentions without citation

Structures of HIV-1 Env V1V2 with broadly neutralizing antibodies reveal commonalities that enable vaccine design.
Gorman et al. (2016)
5 more