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- PDB-9nja: Computationally optimized broadly reactive influenza B hemaggluti... -

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Basic information

Entry
Database: PDB / ID: 9nja
TitleComputationally optimized broadly reactive influenza B hemagglutinin BC2 bound by antibody #46
Components
  • Fab A Heavy Chain
  • Fab A Light Chain
  • Hemagglutinin
KeywordsVIRAL PROTEIN/Immune System / influenza / antibody / cell entry / hemagglutination / VIRAL PROTEIN / VIRAL PROTEIN-Immune System complex
Function / homology
Function and homology information


viral budding from plasma membrane / host cell surface receptor binding / endocytosis involved in viral entry into host cell / 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 B / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Influenza B virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsDzimianski, J.V. / Kunkel, I. / Balasco Serrao, V.H. / DuBois, R.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93019C00052 United States
CitationJournal: To Be Published
Title: Computationally optimized broadly reactive influenza B hemagglutinin BC2 bound by antibodies #46 and #3978
Authors: Dzimianski, J.V. / Kunkel, I. / Balasco Serrao, V.H. / DuBois, R.M.
History
DepositionFeb 27, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Additional map / Part number: 3 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Fab A Light Chain
H: Fab A Heavy Chain
A: Hemagglutinin
K: Fab A Light Chain
J: Fab A Heavy Chain
B: Hemagglutinin
P: Fab A Light Chain
Q: Fab A Heavy Chain
C: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)318,88418
Polymers316,2849
Non-polymers2,6009
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "B"
d_2ens_1chain "A"
d_3ens_1chain "C"
d_1ens_2chain "Q"
d_2ens_2chain "J"
d_3ens_2chain "H"
d_1ens_3chain "K"
d_2ens_3chain "L"
d_3ens_3chain "P"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1PROPROPROPROBF36 - 32236 - 322
d_12ens_1NAGNAGNAGNAGEK1
d_13ens_1NAGNAGNAGNAGEK2
d_14ens_1NAGNAGNAGNAGBO601
d_15ens_1NAGNAGNAGNAGBP602
d_21ens_1PROPROPROPROAC36 - 32236 - 322
d_22ens_1NAGNAGNAGNAGDJ1
d_23ens_1NAGNAGNAGNAGDJ2
d_24ens_1NAGNAGNAGNAGAM601
d_25ens_1NAGNAGNAGNAGAN602
d_31ens_1PROPROPROPROCI36 - 32236 - 322
d_32ens_1NAGNAGNAGNAGFL1
d_33ens_1NAGNAGNAGNAGFL2
d_34ens_1NAGNAGNAGNAGCQ601
d_35ens_1NAGNAGNAGNAGCR602
d_11ens_2VALVALVALVALQH2 - 1112 - 124
d_21ens_2VALVALVALVALJE2 - 1112 - 124
d_31ens_2VALVALVALVALHB2 - 1112 - 124
d_11ens_3GLUGLUVALVALKD9 - 1119 - 111
d_21ens_3GLUGLUVALVALLA9 - 1119 - 111
d_31ens_3GLUGLUVALVALPG9 - 1119 - 111

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.500152763904, -0.865937186867, -3.40562266895E-5), (0.865937186574, -0.500152764816, 2.74777779931E-5), (-4.08273457147E-5, -1.57474665157E-5, 0.999999999043)390.271818855, 104.601251428, 0.00957941352624
2given(-0.500008250797, 0.866020640086, 8.97595395425E-6), (-0.866020639776, -0.500008250862, 2.34878001375E-5), (2.48289707457E-5, 3.97073247574E-6, 0.999999999684)104.567233159, 390.251413851, -0.00554500610664
3given(-0.50000794287, -0.8660208175, 2.68972615752E-5), (0.866020817858, -0.50000794296, 3.74544223028E-6), (1.02052134893E-5, 2.51663393322E-5, 0.999999999631)390.24989434, 104.571521082, -0.00507727661397
4given(-0.499838053735, 0.866118881827, -5.07975151331E-5), (-0.866118883155, -0.499838051646, 4.86760091699E-5), (1.67686796414E-5, 6.83268087612E-5, 0.999999997525)104.534583434, 390.231320908, -0.0130618853308
5given(-0.500150637041, -0.865938415416, -3.12158236249E-5), (0.865938415057, -0.500150637846, 2.81039084123E-5), (-3.99488680144E-5, -1.29747931387E-5, 0.999999999118)390.271174585, 104.600682011, 0.00905794255908
6given(-0.500010966269, 0.866019072288, 6.61237241446E-6), (-0.866019071908, -0.500010966255, 2.67682557571E-5), (2.64880787378E-5, 7.65798080499E-6, 0.99999999962)104.568258446, 390.250996143, -0.00629443801918

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Components

#1: Antibody Fab A Light Chain


Mass: 23206.629 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Fab A Heavy Chain


Mass: 24845.973 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein Hemagglutinin


Mass: 57375.242 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza B virus / Gene: HA / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P17504
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN
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: Complex of a viral protein with two antibodies / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Cricetulus griseus (Chinese hamster)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2800 nm / Nominal defocus min: 500 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 35025

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.5.3particle selection
2SerialEM4.1.21image acquisition
4cryoSPARC4.5.3CTF correction
7UCSF ChimeraXmodel fitting
8Cootmodel fitting
10cryoSPARC4.5.3initial Euler assignment
11cryoSPARC4.5.3final Euler assignment
12cryoSPARC4.5.3classification
13cryoSPARC4.5.33D reconstruction
14PHENIX1.21.2_5419model refinement
15ISOLDEmodel refinement
16Cootmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1165223
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 209227 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model building

3D fitting-ID: 1 / Accession code: 9NJ3

IDPDB-IDPdb chain-IDChain-IDInitial refinement model-IDSource nameType
19NJ3

9nj3

AA1PDBexperimental model
2H2AlphaFoldin silico model
3L2AlphaFoldin silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 69.34 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002211946
ELECTRON MICROSCOPYf_angle_d0.452916197
ELECTRON MICROSCOPYf_chiral_restr0.04331821
ELECTRON MICROSCOPYf_plane_restr0.00422088
ELECTRON MICROSCOPYf_dihedral_angle_d9.50314557
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2FBELECTRON MICROSCOPYNCS constraints1.63741827793E-11
ens_1d_3FBELECTRON MICROSCOPYNCS constraints3.49500069082E-13
ens_2d_2HQELECTRON MICROSCOPYNCS constraints1.26059578785E-12
ens_2d_3HQELECTRON MICROSCOPYNCS constraints3.33496760512E-11
ens_3d_2DKELECTRON MICROSCOPYNCS constraints2.93392996105E-13
ens_3d_3DKELECTRON MICROSCOPYNCS constraints3.75670424386E-13

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