6HJP

Structure of Influenza Hemagglutinin ectodomain (A/duck/Alberta/35/76) in complex with FISW84 Fab Fragment


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Influenza hemagglutinin membrane anchor.

Benton, D.J.Nans, A.Calder, L.J.Turner, J.Neu, U.Lin, Y.P.Ketelaars, E.Kallewaard, N.L.Corti, D.Lanzavecchia, A.Gamblin, S.J.Rosenthal, P.B.Skehel, J.J.

(2018) Proc Natl Acad Sci U S A 115: 10112-10117

  • DOI: 10.1073/pnas.1810927115
  • Primary Citation of Related Structures:  
    6HJQ, 6HJP, 6HJR, 6HJN, 6HKG

  • PubMed Abstract: 
  • Viruses with membranes fuse them with cellular membranes, to transfer their genomes into cells at the beginning of infection. For Influenza virus, the membrane glycoprotein involved in fusion is the hemagglutinin (HA), the 3D structure of which is known from X-ray crystallographic studies ...

    Viruses with membranes fuse them with cellular membranes, to transfer their genomes into cells at the beginning of infection. For Influenza virus, the membrane glycoprotein involved in fusion is the hemagglutinin (HA), the 3D structure of which is known from X-ray crystallographic studies. The soluble ectodomain fragments used in these studies lacked the "membrane anchor" portion of the molecule. Since this region has a role in membrane fusion, we have determined its structure by analyzing the intact, full-length molecule in a detergent micelle, using cryo-EM. We have also compared the structures of full-length HA-detergent micelles with full-length HA-Fab complex detergent micelles, to describe an infectivity-neutralizing monoclonal Fab that binds near the ectodomain membrane anchor junction. We determine a high-resolution HA structure which compares favorably in detail with the structure of the ectodomain seen by X-ray crystallography; we detect, clearly, all five carbohydrate side chains of HA; and we find that the ectodomain is joined to the membrane anchor by flexible, eight-residue-long, linkers. The linkers extend into the detergent micelle to join a central triple-helical structure that is a major component of the membrane anchor.


    Organizational Affiliation

    Structural Biology of Disease Processes Laboratory, Francis Crick Institute, NW1 1AT London, United Kingdom; Donald.Benton@crick.ac.uk Peter.Rosenthal@crick.ac.uk John.Skehel@crick.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HemagglutininA, C, E324Influenza A virus (A/mallard/Alberta/35/1976(H1N1))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for P26562 (Influenza A virus (strain A/Duck/Alberta/35/1976 H1N1))
Explore P26562 
Go to UniProtKB:  P26562
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HemagglutininB, D, F174Influenza A virus (A/mallard/Alberta/35/1976(H1N1))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for P26562 (Influenza A virus (strain A/Duck/Alberta/35/1976 H1N1))
Explore P26562 
Go to UniProtKB:  P26562
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Heavy chain of FISW84 Fab FragmentG, I, J [auth K]216Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Light chain of FISW84 Fab FragmentH, K [auth J], L214Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseM, P, R, U, W, Z2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseN, S, X4N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G32152BH
GlyCosmos:  G32152BH
GlyGen:  G32152BH
Entity ID: 7
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseO, T, Y5N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Entity ID: 8
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseAA [auth a], Q, V3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UPL
Query on UPL

Download Ideal Coordinates CCD File 
BA [auth B], CA [auth D], DA [auth F]UNKNOWN BRANCHED FRAGMENT OF PHOSPHOLIPID
C34 H70
QPCSNFPFMCVVAI-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomFC001078
Cancer Research UKUnited KingdomFC001143
Medical Research Council (United Kingdom)United KingdomFC001078
Medical Research Council (United Kingdom)United KingdomFC001143
Wellcome TrustUnited KingdomFC001078
Wellcome TrustUnited KingdomFC001143
European Research CouncilUnited Kingdom629829

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-26
    Type: Initial release
  • Version 1.1: 2018-10-10
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2019-12-18
    Changes: Data collection, Other, Structure summary
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary