PDB 5k9k structure summary ‹ Protein Data Bank in Europe (PDBe) ‹ EMBL-EBI

X-ray diffraction

2.97Å resolution

Crystal structure of multidonor HV6-1-class broadly neutralizing Influenza A antibody 56.a.09 in complex with Hemagglutinin Hong Kong 1968.

Released: 21 Dec 2016

DOI: 10.2210/pdb5k9k/pdb

Source organisms:

Primary publication:
Vaccine-Induced Antibodies that Neutralize Group 1 and Group 2 Influenza A Viruses.

Joyce MG, Wheatley AK, Thomas PV, Chuang GY, Soto C, Bailer RT, Druz A, Georgiev IS, Gillespie RA, Kanekiyo M, Kong WP, Leung K, Narpala SN, Prabhakaran MS, Yang ES, Zhang B, Zhang Y, Asokan M, Boyington JC, Bylund T, Darko S, Lees CR, Ransier A, Shen CH, Wang L, Whittle JR, Wu X, Yassine HM, Santos C, Matsuoka Y, Tsybovsky Y, Baxa U, Mullikin JC, Subbarao K, Douek DC, Graham BS, Koup RA, Ledgerwood JE, Roederer M, Shapiro L, Kwong PD, Mascola JR, McDermott AB

Cell 166 609-623 (2016)

PMID: 27453470

Function and Biology Details

Biochemical function:

host cell surface receptor binding

Biological process:

clathrin-dependent endocytosis of virus by host cell

Cellular component:

virion membrane

Sequence domains:

Structure analysis Details

Assembly composition:

hetero trimer (preferred)

Assembly name:

Hemagglutinin HA1 chain and IG-heavy chain and IG-light kappa chain (preferred)

PDBe Complex ID:

PDB-CPX-230388 (preferred)

Entry contents:

3 distinct polypeptide molecules

Macromolecules (9 distinct):

56.a.09 Heavy chain Chains: A, H

Molecule details ›

Chains: A, H
Length: 229 amino acids
Theoretical weight: 24.57 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens

Structure domains: Immunoglobulins

56.a.09 Light chain Chains: B, L

Molecule details ›

Chains: B, L
Length: 215 amino acids
Theoretical weight: 23.48 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens

Structure domains: Immunoglobulins

Hemagglutinin Chains: F, I

Molecule details ›

Chains: F, I
Length: 503 amino acids
Theoretical weight: 56.4 KDa
Source organism: Influenza A virus (A/Hong Kong/1/1968(H3N2))
Expression system: Homo sapiens
UniProt:

Canonical: Q91MA7 (Residues: 17-519; Coverage: 92%)

Gene name: HA
Sequence domains: Haemagglutinin
Structure domains: Hemagglutinin (Ha1 Chain); Chain: A; domain 1

Ligands and Environments

Carbohydrate polymer : NEW

Carbohydrate polymer

Carbohydrate polymer : NEW

Carbohydrate polymer

Carbohydrate polymer : NEW

Carbohydrate polymer

Carbohydrate polymer : NEW

Carbohydrate polymer

Carbohydrate polymer : NEW

Carbohydrate polymer

Carbohydrate polymer : NEW

Carbohydrate polymer

1 bound ligand:

No modified residues

Experiments and Validation Details

Entry percentile scores

X-ray source: APS BEAMLINE 22-ID

Spacegroup: C222₁

Unit cell:

a: 123.897Å b: 136.559Å c: 311.327Å

α: 90° β: 90° γ: 90°

R-values:

R R_work R_free

0.227 0.225 0.265

Expression system: Homo sapiens

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Citations

54 review citations

Passive immunotherapy of viral infections: 'super-antibodies' enter the fray.

Walker et al. (2018)

53 more

8 mentions without citation

Insights into the Structural Basis of Antibody Affinity Maturation from Next-Generation Sequencing.

Mishra et al. (2018)

7 more