7JPD | pdb_00007jpd

Crystal structure of the trimeric full length mature hemagglutinin from influenza A virus A/Fort Monmouth/1/1947


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 
    0.286 (Depositor), 0.285 (DCC) 
  • R-Value Work: 
    0.254 (Depositor), 0.253 (DCC) 
  • R-Value Observed: 
    0.255 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7JPD

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Structural characterisation of hemagglutinin from seven Influenza A H1N1 strains reveal diversity in the C05 antibody recognition site.

Ghafoori, S.M.Petersen, G.F.Conrady, D.G.Calhoun, B.M.Stigliano, M.Z.Z.Baydo, R.O.Grice, R.Abendroth, J.Lorimer, D.D.Edwards, T.E.Forwood, J.K.

(2023) Sci Rep 13: 6940-6940

  • DOI: https://doi.org/10.1038/s41598-023-33529-w
  • Primary Citation Related Structures: 
    6D8W, 6ML8, 6MYA, 6N41, 6ONA, 6OSR, 7JP4, 7JPD

  • PubMed Abstract: 

    Influenza virus (IV) causes several outbreaks of the flu each year resulting in an economic burden to the healthcare system in the billions of dollars. Several influenza pandemics have occurred during the last century and estimated to have caused 100 million deaths. There are four genera of IV, A (IVA), B (IVB), C (IVC), and D (IVD), with IVA being the most virulent to the human population. Hemagglutinin (HA) is an IVA surface protein that allows the virus to attach to host cell receptors and enter the cell. Here we have characterised the high-resolution structures of seven IVA HAs, with one in complex with the anti-influenza head-binding antibody C05. Our analysis revealed conserved receptor binding residues in all structures, as seen in previously characterised IV HAs. Amino acid conservation is more prevalent on the stalk than the receptor binding domain (RBD; also called the head domain), allowing the virus to escape from antibodies targeting the RBD. The equivalent site of C05 antibody binding to A/Denver/57 HA appears hypervariable in the other H1N1 IV HAs. Modifications within this region appear to disrupt binding of the C05 antibody, as these HAs no longer bind the C05 antibody by analytical SEC. Our study brings new insights into the structural and functional recognition of IV HA proteins and can contribute to further development of anti-influenza vaccines.


  • Organizational Affiliation
    • School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2650, Australia.

Macromolecule Content 

  • Total Structure Weight: 357.22 kDa 
  • Atom Count: 22,983 
  • Modeled Residue Count: 2,895 
  • Deposited Residue Count: 2,994 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hemagglutinin HA1 chain329Influenza A virus (A/Fort Monmouth/1/1947(H1N1))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for Q20MG8 (Influenza A virus)
Explore Q20MG8 
Go to UniProtKB:  Q20MG8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ20MG8
Glycosylation
Glycosylation Sites: 4
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Hemagglutinin HA2 chain170Influenza A virus (A/Fort Monmouth/1/1947(H1N1))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for Q20MG8 (Influenza A virus)
Explore Q20MG8 
Go to UniProtKB:  Q20MG8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ20MG8
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseM [auth G]3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
N [auth H],
O [auth I],
Q [auth K],
S [auth M],
U [auth O],
N [auth H],
O [auth I],
Q [auth K],
S [auth M],
U [auth O],
W [auth Q]
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-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-glucopyranoseP [auth J],
R [auth L],
T [auth N],
V [auth P]
5N-Glycosylation
Glycosylation Resources
GlyTouCan: G42227JK
GlyCosmos: G42227JK
GlyGen: G42227JK

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
(Subject of Investigation/LOI)

Query on NAG



Download:Ideal Coordinates CCD File
AB [auth C]
CC [auth E]
DC [auth E]
MA [auth B]
NA [auth B]
AB [auth C],
CC [auth E],
DC [auth E],
MA [auth B],
NA [auth B],
OA [auth B],
OB [auth D],
SC [auth F],
TC [auth F],
X [auth A],
ZA [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
IOD

Query on IOD



Download:Ideal Coordinates CCD File
AA [auth A]
AC [auth D]
AD [auth F]
BA [auth A]
BB [auth C]
AA [auth A],
AC [auth D],
AD [auth F],
BA [auth A],
BB [auth C],
BC [auth d],
BD [auth F],
CA [auth A],
CB [auth C],
CD [auth F],
DA [auth A],
DB [auth C],
DD [auth F],
EA [auth A],
EB [auth C],
EC [auth E],
ED [auth F],
FA [auth A],
FB [auth C],
FC [auth E],
FD [auth F],
GA [auth A],
GB [auth C],
GC [auth E],
GD [auth F],
HA [auth A],
HB [auth C],
HC [auth E],
IA [auth A],
IB [auth C],
IC [auth E],
JA [auth A],
JB [auth C],
JC [auth E],
KA [auth A],
KB [auth C],
KC [auth E],
LA [auth A],
LB [auth c],
LC [auth E],
MB [auth c],
MC [auth E],
NB [auth c],
NC [auth E],
OC [auth E],
PA [auth B],
PB [auth D],
PC [auth E],
QA [auth B],
QB [auth D],
QC [auth e],
RA [auth B],
RB [auth D],
RC [auth e],
SA [auth B],
SB [auth D],
TA [auth B],
TB [auth D],
UA [auth B],
UB [auth D],
UC [auth F],
VA [auth B],
VB [auth D],
VC [auth F],
WA [auth B],
WB [auth D],
WC [auth F],
XA [auth B],
XB [auth D],
XC [auth F],
YA [auth b],
YB [auth D],
YC [auth F],
Z [auth A],
ZB [auth D],
ZC [auth F]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
EDO

Query on EDO



Download:Ideal Coordinates CCD File
Y [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free:  0.286 (Depositor), 0.285 (DCC) 
  • R-Value Work:  0.254 (Depositor), 0.253 (DCC) 
  • R-Value Observed: 0.255 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.79α = 90
b = 142.36β = 90
c = 234.23γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-06
    Type: Initial release
  • Version 1.1: 2023-05-24
    Changes: Database references, Refinement description
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-11-20
    Changes: Structure summary