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- PDB-9cjy: CryoEM structure of NC99 hemagglutinin trimer in complex with Fab... -

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Basic information

Entry
Database: PDB / ID: 9cjy
TitleCryoEM structure of NC99 hemagglutinin trimer in complex with Fab BB798E 3-C07
Components
  • 3-C07 Heavy chain
  • 3-C07 Light chain
  • Hemagglutinin HA1 chain
  • Hemagglutinin HA2 chain
KeywordsVIRAL PROTEIN / Immune system / Hemagglutinin / Fab / Macaque
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Biological speciesInfluenza A virus
Macaca fascicularis (crab-eating macaque)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsLi, N. / Tsybovsky, Y. / Sangesland, M. / Kanekiyo, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: bioRxiv / Year: 2025
Title: Functional, Immunogenetic, and Structural Convergence in Influenza Immunity between Humans and Macaques.
Authors: Maya Sangesland / Ning Li / Yaroslav Tsybovsky / Megan D Rodgers / Julianna Han / Alesandra J Rodriguez / James A Ferguson / Amy R Henry / Sarah C Smith / Jesmine Roberts-Torres / Rebecca A ...Authors: Maya Sangesland / Ning Li / Yaroslav Tsybovsky / Megan D Rodgers / Julianna Han / Alesandra J Rodriguez / James A Ferguson / Amy R Henry / Sarah C Smith / Jesmine Roberts-Torres / Rebecca A Gillespie / Cuiping Liu / Jonah S Merriam / Tyler Stephens / Connor Williams / Emma Maestle / Martin Corcoran / Michelle Ravichandran / Adrian Creanga / Sarah F Andrews / Theodore C Pierson / Gunilla B Karlsson Hedestam / Chaim A Schramm / Douglas S Reed / Daniel C Douek / Tongqing Zhou / Andrew B Ward / Masaru Kanekiyo /
Abstract: Human B cell immunity to the influenza hemagglutinin (HA) stem region, a universal influenza vaccine target, is often stereotyped and immunogenetically restricted, posing challenges for study outside ...Human B cell immunity to the influenza hemagglutinin (HA) stem region, a universal influenza vaccine target, is often stereotyped and immunogenetically restricted, posing challenges for study outside humans. Here, we show that macaques vaccinated with a HA stem immunogen elicit human-like public B cell lineages targeting two major conserved sites of vulnerability, the central stem and anchor epitopes. Central stem antibodies were predominantly derived from V1-138, the macaque homolog of human V1-69, a V-gene preferentially used in human central stem broadly neutralizing antibodies (bnAbs). Similarly, macaques produced anchor bnAbs with the human-like NWP motif. Both bnAb lineages were functionally and structurally analogous to their human counterparts, with recognition mediated largely by germline-encoded motifs. Thus the macaque immunoglobulin repertoire supports human-like public bnAb responses to influenza HA. Moreover, this underscores the utility of homologous germline-encoded immunity, suggesting that immune repertoires of macaques and humans may have been similarly shaped during evolution.
History
DepositionJul 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
C: Hemagglutinin HA1 chain
D: Hemagglutinin HA2 chain
E: Hemagglutinin HA1 chain
F: Hemagglutinin HA2 chain
G: 3-C07 Heavy chain
H: 3-C07 Heavy chain
I: 3-C07 Light chain
J: 3-C07 Heavy chain
K: 3-C07 Light chain
L: 3-C07 Light chain


Theoretical massNumber of molelcules
Total (without water)259,08512
Polymers259,08512
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Hemagglutinin HA1 chain


Mass: 36417.867 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: Q6WG00
#2: Protein Hemagglutinin HA2 chain


Mass: 25288.090 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: Q6WG00
#3: Antibody 3-C07 Heavy chain


Mass: 13246.823 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca fascicularis (crab-eating macaque)
Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#4: Antibody 3-C07 Light chain


Mass: 11408.751 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca fascicularis (crab-eating macaque)
Cell line (production host): Expi293 / Production host: Homo sapiens (human)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: NC99 HA in complex with Fab BB798E 3-C07 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.33 MDa / Experimental value: NO
Source (natural)Organism: Influenza A virus
Source (recombinant)Organism: Homo sapiens (human) / Cell: Expi293
Buffer solutionpH: 7.4
SpecimenConc.: 0.01 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 22500 X / Nominal defocus max: 2300 nm / Nominal defocus min: 900 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1
Image scansWidth: 3840 / Height: 3712 / Movie frames/image: 40 / Used frames/image: 1-40

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Processing

EM software
IDNameVersionCategory
1Topazparticle selection
2SerialEM4.09image acquisition
4cryoSPARC4.3.1CTF correction
7UCSF Chimera1.17.3model fitting
8Coot0.9.8model fitting
9ISOLDE1.6model fitting
11cryoSPARC4.3.1initial Euler assignment
12cryoSPARC4.3.1final Euler assignment
14cryoSPARC4.3.13D reconstruction
15PHENIX1.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 371568
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 104541 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: BACKBONE TRACE
Atomic model buildingPDB-ID: 8D21

8d21


Accession code: 8D21 / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00516516
ELECTRON MICROSCOPYf_angle_d0.59722402
ELECTRON MICROSCOPYf_dihedral_angle_d4.0252201
ELECTRON MICROSCOPYf_chiral_restr0.0432423
ELECTRON MICROSCOPYf_plane_restr0.0042890

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