8F6X | pdb_00008f6x

cryo-EM structure of a structurally designed Human metapneumovirus F protein in complex with antibody MPE8

PDB DOI: https://doi.org/10.2210/pdb8F6X/pdb
EM Map EMD-28891: EMDB EMDataResource

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): human metapneumovirus, Escherichia phage T2, Homo sapiens
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2022-11-17 Released: 2023-08-02
Deposition Author(s): Zhou, T., Kwong, P.D., Morano, N.C., Ou, L.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.25 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 8F6X

This is version 1.2 of the entry. See complete history.

Literature

cryo-EM structure of a structurally designed Human metapneumovirus F protein in complex with antibody MPE8

Ou, L., Kwong, P.D.

To be published.

Macromolecule Content

Total Structure Weight: 267.37 kDa
Atom Count: 14,952
Modeled Residue Count: 1,980
Deposited Residue Count: 2,484
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Structurally designed HMPV F protein HMPV_v3B_D12_DS454,Fibritin	A, B, C	522	human metapneumovirus, Escherichia phage T2	Mutation(s): 7
UniProt
Find proteins for G3KCK8 (human metapneumovirus) Explore G3KCK8 Go to UniProtKB: G3KCK8
Find proteins for P10104 (Enterobacteria phage T4) Explore P10104 Go to UniProtKB: P10104
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	G3KCK8 P10104
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B Focus chain C
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MPE8 Single chain variable fragment	D, E, F	306	Homo sapiens	Mutation(s): 0

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 G [auth A] SDF format, chain I [auth C] SDF format, chain H [auth B] MOL2 format, chain G [auth A] MOL2 format, chain I [auth C] MOL2 format, chain H [auth B] mmCIF format, chain G [auth A] mmCIF format, chain I [auth C] mmCIF format, chain H [auth B]	G [auth A], H [auth B], I [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.25 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-08-02

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History (Full details and data files)

Version 1.0: 2023-08-02
Type: Initial release
Version 1.1: 2024-10-23
Changes: Data collection, Structure summary
Version 1.2: 2025-05-21
Changes: Data collection

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.