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- PDB-12ie: Cryo-EM structure of B/Lee/1940 hemagglutinin trimer in complex w... -

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Basic information

Entry
Database: PDB / ID: 12ie
TitleCryo-EM structure of B/Lee/1940 hemagglutinin trimer in complex with three KL-BHA-4C2 Fab fragments
Components
  • Hemagglutinin
  • KL-BHA-4C2 heavy chain
  • KL-BHA-4C2 light chain
KeywordsImmune System/Viral Protein / hemagglutinin / Fab / viral glycoprotein / Immune System-Viral Protein complex
Function / homology:
Function and homology information
Biological speciesMus musculus (house mouse)
Influenza B virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.61 Å
AuthorsCivljak, A. / Bonnettaz, B. / Bajic, G.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI117287 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI109946 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI097092 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201400008C United States
Other private United States
CitationJournal: To Be Published
Title: Cryo-EM structure of B/Lee/1940 hemagglutinin trimer in complex with three KL-BHA-4C2 Fab fragments
Authors: Civljak, A. / Bonnettaz, B. / Bajic, G.
History
DepositionApr 7, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: KL-BHA-4C2 heavy chain
A: Hemagglutinin
L: KL-BHA-4C2 light chain
N: KL-BHA-4C2 light chain
E: KL-BHA-4C2 light chain
C: Hemagglutinin
B: Hemagglutinin
D: KL-BHA-4C2 heavy chain
M: KL-BHA-4C2 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,59015
Polymers246,5579
Non-polymers3,0336
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 (eV)
d_1ens_1chain "C"
d_2ens_1chain "B"
d_3ens_1chain "A"
d_1ens_2chain "D"
d_2ens_2chain "H"
d_3ens_2chain "M"
d_1ens_3chain "N"
d_2ens_3chain "L"
d_3ens_3chain "E"

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_1SERSERASPASPCF12 - 45812 - 458
d_12ens_1NAGNAGNAGNAGIL1
d_13ens_1NAGNAGNAGNAGIL2
d_14ens_1BMABMABMABMAIL3
d_15ens_1NAGNAGNAGNAGJM1
d_16ens_1NAGNAGNAGNAGJM2
d_21ens_1SERSERASPASPBG12 - 45812 - 458
d_22ens_1NAGNAGNAGNAGKN1
d_23ens_1NAGNAGNAGNAGKN2
d_24ens_1BMABMABMABMAKN3
d_25ens_1NAGNAGNAGNAGOO1
d_26ens_1NAGNAGNAGNAGOO2
d_31ens_1SERSERASPASPAB12 - 45812 - 458
d_32ens_1NAGNAGNAGNAGFJ1
d_33ens_1NAGNAGNAGNAGFJ2
d_34ens_1BMABMABMABMAFJ3
d_35ens_1NAGNAGNAGNAGGK1
d_36ens_1NAGNAGNAGNAGGK2
d_11ens_2GLNGLNSERSERDH1 - 1201 - 120
d_21ens_2GLNGLNSERSERHA1 - 1201 - 120
d_31ens_2GLNGLNSERSERMI1 - 1201 - 120
d_11ens_3ASPASPLYSLYSND1 - 1111 - 111
d_21ens_3ASPASPLYSLYSLC1 - 1111 - 111
d_31ens_3ASPASPLYSLYSEE1 - 1111 - 111

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.500825358703, 0.865548349783, -0.00011944962442), (-0.865548316959, -0.500825287661, 0.000377159026014), (0.000266625980061, 0.00029228022587, 0.999999921741)137.309519328, 511.238535171, -0.124900601236
2given(-0.500644853512, -0.865652772681, 8.83251139208E-5), (0.865652772772, -0.500644838047, 0.000152084613216), (-8.74329547581E-5, 0.000152599258676, 0.999999984534)511.292927052, 137.184210064, -0.00664451732632
3given(-0.499859583129, 0.866106208986, -0.000657197890797), (-0.866103352294, -0.499859678785, -0.00229884080394), (-0.00231954702036, -0.000579896309599, 0.999997141707)137.091932208, 511.740914775, 0.644030965671
4given(-0.500734993027, -0.865600630352, -0.000124469756006), (0.865599928104, -0.500734760766, 0.00120988690623), (-0.00110960520218, 0.000498091699703, 0.99999926034)511.37246438, 136.974654256, 0.178601964757
5given(-0.497804263467, -0.867289206901, -0.00058895422578), (0.867282326303, -0.497802828601, 0.00370274496314), (-0.00350453382195, 0.00133245263816, 0.999992971382)511.172093771, 135.285465746, 0.521598905963
6given(-0.501908006774, 0.864916744625, -0.00271617446543), (-0.864918695901, -0.501911452947, -0.000736805316797), (-0.00200055432843, 0.00197946158854, 0.999996039749)138.364380973, 511.61472852, -0.0195605663644

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Components

#1: Protein KL-BHA-4C2 heavy chain


Mass: 13255.941 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#2: Protein Hemagglutinin


Mass: 56640.168 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza B virus (B/Lee/1940) / Strain: B/Lee/1940 / Gene: HA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q0PLR5
#3: Antibody KL-BHA-4C2 light chain


Mass: 12289.717 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#5: 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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
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: Cryo-EM structure of B/Lee/1940 hemagglutinin trimer in complex with three KL-BHA-4C2 Fab fragments
Type: COMPLEX
Details: B/Lee/1940 hemagglutinin expressed using Sf9 insect cells
Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Mus musculus (house mouse)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 58.92 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1Topazparticle selection
2PHENIX1.21.2_5419model refinement
5cryoSPARCCTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 80242 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 46.44 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003514937
ELECTRON MICROSCOPYf_angle_d0.704320277
ELECTRON MICROSCOPYf_chiral_restr0.04972340
ELECTRON MICROSCOPYf_plane_restr0.00672592
ELECTRON MICROSCOPYf_dihedral_angle_d5.87962316
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2FCELECTRON MICROSCOPYNCS constraints8.58244040306E-13
ens_1d_3FCELECTRON MICROSCOPYNCS constraints1.98120688767E-10
ens_2d_2HDELECTRON MICROSCOPYNCS constraints9.02721152232E-11
ens_2d_3HDELECTRON MICROSCOPYNCS constraints4.07772971273E-13
ens_3d_2DNELECTRON MICROSCOPYNCS constraints1.40650218384E-10
ens_3d_3DNELECTRON MICROSCOPYNCS constraints2.59451123384E-13

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