6ML8

Crystal structure of hemagglutinin from H1N1 Influenza A virus A/Denver/57 bound to the C05 antibody

• PDB DOI: https://doi.org/10.2210/pdb6ML8/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus (A/Denver/1957(H1N1)), Homo sapiens
• Expression System: Trichoplusia ni, Homo sapiens
• Mutation(s): No 


• Deposited: 2018-09-27 Released: 2018-10-17 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.92 Å
• R-Value Free: 0.264 
• R-Value Work: 0.201 
• R-Value Observed: 0.204 

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A3B3C3D3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 107.4 kDa 
• Atom Count: 6,973 
• Modelled Residue Count: 917 
• Deposited Residue Count: 956 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A	330	Influenza A virus (A/Denver/1957(H1N1))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for Q2IBI1 (Influenza A virus) Explore Q2IBI1  Go to UniProtKB:  Q2IBI1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	B	165	Influenza A virus (A/Denver/1957(H1N1))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for Q2IBI1 (Influenza A virus) Explore Q2IBI1  Go to UniProtKB:  Q2IBI1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
C05 antibody Fab heavy chain	C [auth H]	247	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
C05 antibody Fab light chain	D [auth L]	214	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth C]	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD GlyCosmos:  G81315DD GlyGen:  G81315DD

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F [auth D]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth E]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.92 Å
• R-Value Free: 0.264 
• R-Value Work: 0.201 
• R-Value Observed: 0.204 
• Space Group: P 3 2 1
• Diffraction Data: https://doi.org/10.18430/m36ml8

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.46	α = 90
b = 118.46	β = 90
c = 162.44	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-10-17 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2018-10-17
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-05-24
  Changes: Database references, Derived calculations, Structure summary
• Version 2.2: 2023-10-25
  Changes: Data collection, Refinement description