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- PDB-7tjq: SAN27-14 bound to a antigenic site V on prefusion-stabilized hMPV F -

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Basic information

Entry
Database: PDB / ID: 7tjq
TitleSAN27-14 bound to a antigenic site V on prefusion-stabilized hMPV F
Components
  • (SAN27-14 Fab ...) x 2
  • Fusion glycoprotein F0
  • MPE8 Fab heavy chain
  • MPE8 Fab light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / neutralizing antibodies / prefusion-specific antibodies / antigenic site V / hMPV F / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homologyPrecursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / fusion of virus membrane with host plasma membrane / host cell plasma membrane / virion membrane / plasma membrane / Fusion glycoprotein F0
Function and homology information
Biological speciesHomo sapiens (human)
Human metapneumovirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.13 Å
AuthorsHsieh, C.-L. / McLellan, J.S. / Rush, S.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Welch FoundationF-0003-19620604 United States
CitationJournal: Cell Rep / Year: 2022
Title: Characterization of prefusion-F-specific antibodies elicited by natural infection with human metapneumovirus.
Authors: Scott A Rush / Gurpreet Brar / Ching-Lin Hsieh / Emilie Chautard / Jennifer N Rainho-Tomko / Chris D Slade / Christine A Bricault / Ana Kume / James Kearns / Rachel Groppo / Sophia T Mundle ...Authors: Scott A Rush / Gurpreet Brar / Ching-Lin Hsieh / Emilie Chautard / Jennifer N Rainho-Tomko / Chris D Slade / Christine A Bricault / Ana Kume / James Kearns / Rachel Groppo / Sophia T Mundle / Linong Zhang / Danilo Casimiro / Tong-Ming Fu / Joshua M DiNapoli / Jason S McLellan /
Abstract: Human metapneumovirus (hMPV) is a major cause of acute respiratory infections in infants and older adults, for which no vaccines or therapeutics are available. The viral fusion (F) glycoprotein is ...Human metapneumovirus (hMPV) is a major cause of acute respiratory infections in infants and older adults, for which no vaccines or therapeutics are available. The viral fusion (F) glycoprotein is required for entry and is the primary target of neutralizing antibodies; however, little is known about the humoral immune response generated from natural infection. Here, using prefusion-stabilized F proteins to interrogate memory B cells from two older adults, we obtain over 700 paired non-IgM antibody sequences representing 563 clonotypes, indicative of a highly polyclonal response. Characterization of 136 monoclonal antibodies reveals broad recognition of the protein surface, with potently neutralizing antibodies targeting each antigenic site. Cryo-EM studies further reveal two non-canonical sites and the molecular basis for recognition of the apex of hMPV F by two prefusion-specific neutralizing antibodies. Collectively, these results provide insight into the humoral response to hMPV infection in older adults and will help guide vaccine development.
History
DepositionJan 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SAN27-14 Fab heavy chain
B: SAN27-14 Fab light chain
C: Fusion glycoprotein F0
D: SAN27-14 Fab heavy chain
E: SAN27-14 Fab light chain
F: Fusion glycoprotein F0
G: Fusion glycoprotein F0
H: SAN27-14 Fab heavy chain
I: MPE8 Fab heavy chain
J: MPE8 Fab heavy chain
K: MPE8 Fab light chain
L: SAN27-14 Fab light chain
M: MPE8 Fab light chain
N: MPE8 Fab heavy chain
O: MPE8 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)403,42221
Polymers400,87615
Non-polymers2,5466
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Antibody , 4 types, 12 molecules ADHBELIJNKMO

#1: Antibody SAN27-14 Fab heavy chain


Mass: 13867.521 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody SAN27-14 Fab light chain


Mass: 12546.019 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody MPE8 Fab heavy chain


Mass: 24201.002 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: Antibody MPE8 Fab light chain


Mass: 22556.883 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 9 molecules CFG

#3: Protein Fusion glycoprotein F0 / Fusion glycoprotein F1 / Fusion glycoprotein F2


Mass: 60453.852 Da / Num. of mol.: 3
Mutation: Q100R, S101R, L110C, T127C, A140C, N153C, A147C, A185P, L219K, V231I, G294E, N322C, T365C, E453Q, V463C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human metapneumovirus / Production host: Homo sapiens (human) / References: UniProt: H6X1Z0
#6: 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.: 6
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

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Details

Has ligand of interestN

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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 hMPV F with MPE8 Fab and SAN27-14 Fab / Type: COMPLEX / Entity ID: #1-#5 / Source: MULTIPLE SOURCES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
31Human metapneumovirus162145
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
Details: 2 mM Tris pH 7.5, 200 mM NaCl, 0.02% NaN3, 0.07% amphipol
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Collected on tilt, CF-1.2-1.3 grids with 0.5 mg/mL DSCavEs2 (2 mM Tris pH 7.5, 200 mM NaCl, 0.02% NaN3, 0.07% amphipol) and 2x fold molar excess MPE8 and 1.5x fold molar excess SAN27-14 ...Details: Collected on tilt, CF-1.2-1.3 grids with 0.5 mg/mL DSCavEs2 (2 mM Tris pH 7.5, 200 mM NaCl, 0.02% NaN3, 0.07% amphipol) and 2x fold molar excess MPE8 and 1.5x fold molar excess SAN27-14 spiked in ~10 minutes before freezing. 3 u of sample was deposited and the grid was plunge frozen using a Vitrobot Mark IV using 4 seconds blot time and -2 force at 100% humidity and 10 C
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 70 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 3492

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Processing

SoftwareName: PHENIX / Version: 1.20_4459: / Classification: refinement
EM softwareName: SerialEM / Category: image acquisition
CTF correctionType: NONE
3D reconstructionResolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 93710 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 36.81 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00421007
ELECTRON MICROSCOPYf_angle_d0.76628501
ELECTRON MICROSCOPYf_dihedral_angle_d13.3437573
ELECTRON MICROSCOPYf_chiral_restr0.0493270
ELECTRON MICROSCOPYf_plane_restr0.0083645

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