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

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Basic information

Entry
Database: PDB / ID: 9cjz
TitleCryoEM structure of NC99 hemagglutinin trimer in complex with Fab T009 3-E04
Components
  • 3-E04 Heavy chain
  • 3-E04 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: 3.8 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 V 1-138, the macaque homolog of human V 1-69, 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.
HIGHLIGHTS: Functional human-like public antibody lineages can be elicited to HA stem supersites in macaques. Macaque central stem bnAbs are predominantly derived from V 1-138, a V -gene homologous ...HIGHLIGHTS: Functional human-like public antibody lineages can be elicited to HA stem supersites in macaques. Macaque central stem bnAbs are predominantly derived from V 1-138, a V -gene homologous to human V 1-69. The human-like CDR L3 NWP anchor epitope-targeting lineage can be elicited in macaques.Central stem and anchor bnAbs from humans and macaques engage their respective epitopes with atomic level similarity.
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
H: 3-E04 Heavy chain
J: 3-E04 Heavy chain
K: 3-E04 Light chain
L: 3-E04 Light chain
M: 3-E04 Heavy chain
N: 3-E04 Light chain


Theoretical massNumber of molelcules
Total (without water)259,04812
Polymers259,04812
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-E04 Heavy chain


Mass: 13082.574 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-E04 Light chain


Mass: 11560.853 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 T009 3-E04 / 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: 2700 nm / Nominal defocus min: 1000 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
IDNameVersionCategoryDetails
1Topazparticle selection
2cryoSPARC4.3.1particle selectionTemplate picker
3SerialEM4.09image acquisition
5CTFFIND4.1CTF correction
8UCSF Chimera1.17.3model fitting
9Coot0.9.8model fitting
10ISOLDE1.6model fitting
12PHENIX1.2model refinement
13cryoSPARC4.3.1initial Euler assignment
14cryoSPARC4.3.1final Euler assignment
16cryoSPARC4.3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2054500
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 160012 / 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_d0.00315805
ELECTRON MICROSCOPYf_angle_d0.5121446
ELECTRON MICROSCOPYf_dihedral_angle_d4.4522108
ELECTRON MICROSCOPYf_chiral_restr0.0392322
ELECTRON MICROSCOPYf_plane_restr0.0032751

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