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- PDB-9j5l: Complex structure of influenza hemagglutinin HA stem with CR9114 ... -

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Basic information

Entry
Database: PDB / ID: 9j5l
TitleComplex structure of influenza hemagglutinin HA stem with CR9114 Fab and FISW84 Fab
Components
  • (Designed influenza hemagglutinin stem #219 ...) x 2
  • CR9114 heavy chain
  • CR9114 light chain
  • FISW84 heavy chain
  • FISW84 light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / antigen / complex / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciessynthetic construct (others)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsRu, Y.X. / Liu, D.J. / Deng, L. / Li, Y.W.
Funding support1items
OrganizationGrant numberCountry
Other governmentK22227503
CitationJournal: To Be Published
Title: Structure-based design of a broadly protective influenza hemagglutinin stem immunogen
Authors: Ru, Y.X. / Liu, D.J. / Deng, L. / Li, Y.W.
History
DepositionAug 12, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 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
2: Designed influenza hemagglutinin stem #219 HA2
B: CR9114 light chain
C: CR9114 heavy chain
D: FISW84 light chain
E: FISW84 heavy chain
J: Designed influenza hemagglutinin stem #219 HA2
1: Designed influenza hemagglutinin stem #219 HA1
H: Designed influenza hemagglutinin stem #219 HA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,97911
Polymers202,3158
Non-polymers6643
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Designed influenza hemagglutinin stem #219 ... , 2 types, 4 molecules 2J1H

#1: Protein Designed influenza hemagglutinin stem #219 HA2


Mass: 22529.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Spodoptera frugiperda (fall armyworm)
#6: Protein Designed influenza hemagglutinin stem #219 HA1


Mass: 6535.295 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Spodoptera frugiperda (fall armyworm)

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Antibody , 4 types, 4 molecules BCDE

#2: Antibody CR9114 light chain


Mass: 22840.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#3: Antibody CR9114 heavy chain


Mass: 49157.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#4: Antibody FISW84 light chain


Mass: 23380.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#5: Antibody FISW84 heavy chain


Mass: 48808.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)

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Sugars , 1 types, 3 molecules

#7: 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 / Feature type: SUBJECT OF INVESTIGATION
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 interestY
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 influenza hemagglutinin HA stem with CR9114 Fab and FISW84 Fab
Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen 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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 242713 / Symmetry type: POINT
RefinementHighest resolution: 2.97 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0055136
ELECTRON MICROSCOPYf_angle_d0.7596957
ELECTRON MICROSCOPYf_dihedral_angle_d14.2621822
ELECTRON MICROSCOPYf_chiral_restr0.077774
ELECTRON MICROSCOPYf_plane_restr0.011892

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