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- PDB-9nj6: Computationally optimized broadly reactive influenza B hemaggluti... -

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Basic information

Entry
Database: PDB / ID: 9nj6
TitleComputationally optimized broadly reactive influenza B hemagglutinin BC2 bound by antibody #3978
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 speciesInfluenza B virus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.36 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 26, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)321,29518
Polymers317,6479
Non-polymers3,6489
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 "A"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_1ens_2chain "J"
d_2ens_2chain "H"
d_3ens_2chain "Q"
d_1ens_3chain "L"
d_2ens_3chain "K"
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_1PHEPHECYSCYSAA41 - 32141 - 321
d_12ens_1NAGNAGNAGNAGDJ1
d_13ens_1NAGNAGNAGNAGDJ2
d_14ens_1NAGNAGNAGNAGAP601
d_15ens_1NAGNAGNAGNAGEK1
d_16ens_1NAGNAGNAGNAGEK2
d_17ens_1FUCFUCFUCFUCEK3
d_21ens_1PHEPHECYSCYSBD41 - 32141 - 321
d_22ens_1NAGNAGNAGNAGFL1
d_23ens_1NAGNAGNAGNAGFL2
d_24ens_1NAGNAGNAGNAGBQ601
d_25ens_1NAGNAGNAGNAGGM1
d_26ens_1NAGNAGNAGNAGGM2
d_27ens_1FUCFUCFUCFUCGM3
d_31ens_1PHEPHECYSCYSCG41 - 32141 - 321
d_32ens_1NAGNAGNAGNAGIN1
d_33ens_1NAGNAGNAGNAGIN2
d_34ens_1NAGNAGNAGNAGCR601
d_35ens_1NAGNAGNAGNAGMO1
d_36ens_1NAGNAGNAGNAGMO2
d_37ens_1FUCFUCFUCFUCMO3
d_11ens_2VALVALVALVALJE2 - 1112 - 130
d_21ens_2VALVALVALVALHB2 - 1112 - 130
d_31ens_2VALVALVALVALQH2 - 1112 - 130
d_11ens_3SERSERVALVALLC2 - 1062 - 110
d_21ens_3SERSERVALVALKF2 - 1062 - 110
d_31ens_3SERSERVALVALPI2 - 1062 - 110

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.50020532457, 0.865906716332, -0.000438043155433), (-0.865906795988, -0.500205378252, -1.51572122753E-5), (-0.000232236274164, 0.000371722826939, 0.999999903944)104.699174342, 390.277278303, -0.0221320769259
2given(-0.499870953715, -0.866099781162, 0.000445761401415), (0.866099884293, -0.499870964991, 9.37401121071E-5), (0.000141634891299, 0.000432931857428, 0.999999896255)390.178077208, 104.518697175, -0.0826001609525
3given(-0.500205208528, -0.865906863263, -0.000231334407929), (0.865906784039, -0.500205261801, 0.000370705503703), (-0.000436711127988, -1.48852094247E-5, 0.999999904531)390.314659653, 104.55920426, 0.0736342076238
4given(-0.499925253491, 0.866068521119, 0.000240101322882), (-0.866068544328, -0.499925186183, -0.000291109653893), (-0.000132088208886, -0.000353477270715, 0.999999928803)104.512894256, 390.30411537, 0.0913844137364
5given(-0.500204137107, 0.865907402462, -0.000437700471687), (-0.865907481332, -0.500204191756, -1.79790251058E-5), (-0.000234507781599, 0.000370014930277, 0.999999904048)104.698839655, 390.277713374, -0.0215409508968
6given(-0.499870709635, -0.86609991994, 0.00044981083709), (0.86610002473, -0.499870721792, 9.30450409996E-5), (0.000144260965245, 0.0004360916678, 0.999999894506)390.177309668, 104.518740102, -0.0833306230632

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Components

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Protein , 1 types, 3 molecules ABC

#1: 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

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Antibody , 2 types, 6 molecules HJQLKP

#2: Antibody Fab A Heavy Chain


Mass: 25610.729 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: Antibody Fab A Light Chain


Mass: 22896.277 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)

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Sugars , 3 types, 9 molecules

#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: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#6: 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.: 3 / 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

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Details

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 an antibody / 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: 2.36 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 185640 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model building

3D fitting-ID: 1 / Accession code: 9NJ3 / Initial refinement model-ID: 1 / PDB-ID: 9NJ3

9nj3

/ Source name: PDB / Type: experimental model

IDPdb chain-IDChain-ID
1AA
2HH
3LL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 62.09 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.001411976
ELECTRON MICROSCOPYf_angle_d0.436616224
ELECTRON MICROSCOPYf_chiral_restr0.04131800
ELECTRON MICROSCOPYf_plane_restr0.00372076
ELECTRON MICROSCOPYf_dihedral_angle_d8.72264626
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAELECTRON MICROSCOPYNCS constraints6.1142014222E-12
ens_1d_3AAELECTRON MICROSCOPYNCS constraints1.22531352557E-11
ens_2d_2EJELECTRON MICROSCOPYNCS constraints9.75558678178E-11
ens_2d_3EJELECTRON MICROSCOPYNCS constraints7.84982508083E-12
ens_3d_2CLELECTRON MICROSCOPYNCS constraints4.95923448009E-11
ens_3d_3CLELECTRON MICROSCOPYNCS constraints7.81984572558E-12

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