9OS5 | pdb_00009os5

Human antibody Fab MPV498 bound to hMPV B2 post-fusion F

PDB DOI: https://doi.org/10.2210/pdb9OS5/pdb
EM Map EMD-70793: EMDB EMDataResource

Classification: IMMUNE SYSTEM, ANTIVIRAL PROTEIN
Organism(s): human metapneumovirus, Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2025-05-23 Released: 2025-09-03
Deposition Author(s): Ghazi Esfahani, B., Mousa, J., Khalil, A.M.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.61 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Human metapneumovirus-specific antibodies isolated from infected children target diverse epitopes and have prophylactic efficacy in mice

Khalil, A.M., Ghazi Esfahani, B., Mousa, J.

To be published.

Macromolecule Content

Total Structure Weight: 378.71 kDa
Atom Count: 14,897
Modeled Residue Count: 1,936
Deposited Residue Count: 3,462
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fusion glycoprotein F0	A, B, C, D, E A, B, C, D, E, F	465	human metapneumovirus	Mutation(s): 0
UniProt
Find proteins for Q6W8S4 (human metapneumovirus) Explore Q6W8S4 Go to UniProtKB: Q6W8S4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6W8S4
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D Focus chain E Focus chain F
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MPV498 Fab heavy chain	G, I [auth H], K [auth I]	124	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
MPV498 Fab light chain	H [auth J], J [auth K], L	100	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth D] SDF format, chain R [auth D] SDF format, chain S [auth E] SDF format, chain T [auth F] SDF format, chain U [auth F] MOL2 format, chain M [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] MOL2 format, chain S [auth E] MOL2 format, chain T [auth F] MOL2 format, chain U [auth F] mmCIF format, chain M [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth D] mmCIF format, chain S [auth E] mmCIF format, chain T [auth F] mmCIF format, chain U [auth F]	M [auth A] N [auth B] O [auth B] P [auth C] Q [auth D] M [auth A], N [auth B], O [auth B], P [auth C], Q [auth D], R [auth D], S [auth E], T [auth F], U [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth E] Focus chain T [auth F] Focus chain U [auth F] Interactions & Density Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth E] Focus chain T [auth F] Focus chain U [auth F]