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- PDB-9md4: Neuraminidase complexed with mAb 5-16 -

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Basic information

Entry
Database: PDB / ID: 9md4
TitleNeuraminidase complexed with mAb 5-16
Components
  • Neuraminidase
  • mAb 5-16 Heavy chain
  • mAb 5-16 Light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Polyclonal antibody / Influenza / Neuraminidase / Cryo-EM / IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesInfluenza A virus
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsFerguson, J.A. / Raghavan, S.S.R. / Ward, A.B.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Sci Adv / Year: 2025
Title: Functional and epitope specific monoclonal antibody discovery directly from immune sera using cryo-EM.
Authors: James A Ferguson / Sai Sundar Rajan Raghavan / Garazi Peña Alzua / Disha Bhavsar / Jiachen Huang / Alesandra J Rodriguez / Jonathan L Torres / Maria Bottermann / Julianna Han / Florian ...Authors: James A Ferguson / Sai Sundar Rajan Raghavan / Garazi Peña Alzua / Disha Bhavsar / Jiachen Huang / Alesandra J Rodriguez / Jonathan L Torres / Maria Bottermann / Julianna Han / Florian Krammer / Facundo D Batista / Andrew B Ward /
Abstract: Antibodies are crucial therapeutics, comprising a substantial portion of approved drugs due to their safety and clinical efficacy. Traditional antibody discovery methods are labor-intensive, limiting ...Antibodies are crucial therapeutics, comprising a substantial portion of approved drugs due to their safety and clinical efficacy. Traditional antibody discovery methods are labor-intensive, limiting scalability and high-throughput analysis. Here, we improved upon our streamlined approach combining structural analysis and bioinformatics to infer heavy and light chain sequences from cryo-EM (cryo-electron microscopy) maps of serum-derived polyclonal antibodies (pAbs) bound to antigens. Using ModelAngelo, an automated structure-building tool, we accelerated pAb sequence determination and identified sequence matches in B cell repertoires via ModelAngelo-derived hidden Markov models (HMMs) associated with pAb structures. Benchmarking against results from a nonhuman primate HIV vaccine trial, our pipeline reduced analysis time from weeks to under a day with higher precision. Validation with murine immune sera from influenza vaccination revealed multiple protective antibodies. This workflow enhances antibody discovery, enabling faster, more accurate mapping of polyclonal responses with broad applications in vaccine development and therapeutic antibody discovery.
History
DepositionDec 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 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: Neuraminidase
H: mAb 5-16 Heavy chain
L: mAb 5-16 Light chain
B: Neuraminidase
E: mAb 5-16 Heavy chain
I: mAb 5-16 Light chain
C: Neuraminidase
F: mAb 5-16 Heavy chain
J: mAb 5-16 Light chain
D: Neuraminidase
G: mAb 5-16 Heavy chain
K: mAb 5-16 Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)317,11032
Polymers309,83912
Non-polymers7,27120
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Antibody , 2 types, 8 molecules HEFGLIJK

#2: Antibody
mAb 5-16 Heavy chain


Mass: 13838.407 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody
mAb 5-16 Light chain


Mass: 11774.132 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)

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Protein / Non-polymers , 2 types, 8 molecules ABCD

#1: Protein
Neuraminidase


Mass: 51847.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Production host: Homo sapiens (human)
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca

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Sugars , 2 types, 16 molecules

#4: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1114.016 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-1-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{}}}}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.: 12 / 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: Neuraminidase IND11 in complex with mAb 5-16 / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Influenza A virus
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 45 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21_5207 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 117508 / Symmetry type: POINT
RefinementHighest resolution: 2.7 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00320136
ELECTRON MICROSCOPYf_angle_d0.61827312
ELECTRON MICROSCOPYf_dihedral_angle_d13.6167572
ELECTRON MICROSCOPYf_chiral_restr0.0433060
ELECTRON MICROSCOPYf_plane_restr0.0053440

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