7B0A | pdb_00007b0a

Puumala virus-like particle glycoprotein spike and lattice contacts model.

PDB DOI: https://doi.org/10.2210/pdb7B0A/pdb
EM Map EMD-11966: EMDB EMDataResource

Classification: VIRUS LIKE PARTICLE
Organism(s): Orthohantavirus puumalaense
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2020-11-19 Released: 2020-12-16
Deposition Author(s): Rissanen, I., Stass, R., Huiskonen, J.T., Bowden, T.A.
Funding Organization(s): European Research Council (ERC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 13.9 Å
Aggregation State: PARTICLE
Reconstruction Method: SUBTOMOGRAM AVERAGING

wwPDB Validation 3D Report Full Report

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

Literature

Molecular rationale for antibody-mediated targeting of the hantavirus fusion glycoprotein.

Rissanen, I., Stass, R., Krumm, S.A., Seow, J., Hulswit, R.J., Paesen, G.C., Hepojoki, J., Vapalahti, O., Lundkvist, A., Reynard, O., Volchkov, V., Doores, K.J., Huiskonen, J.T., Bowden, T.A.

(2020) Elife 9

PubMed: 33349334 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.7554/eLife.58242
Primary Citation Related Structures:
6Z06, 7B09, 7B0A

PubMed Abstract:
The intricate lattice of Gn and Gc glycoprotein spike complexes on the hantavirus envelope facilitates host-cell entry and is the primary target of the neutralizing antibody-mediated immune response. Through study of a neutralizing monoclonal antibody termed mAb P-4G2, which neutralizes the zoonotic pathogen Puumala virus (PUUV), we provide a molecular-level basis for antibody-mediated targeting of the hantaviral glycoprotein lattice. Crystallographic analysis demonstrates that P-4G2 binds to a multi-domain site on PUUV Gc and may preclude fusogenic rearrangements of the glycoprotein that are required for host-cell entry. Furthermore, cryo-electron microscopy of PUUV-like particles in the presence of P-4G2 reveals a lattice-independent configuration of the Gc, demonstrating that P-4G2 perturbs the (Gn-Gc) ₄ lattice. This work provides a structure-based blueprint for rationalizing antibody-mediated targeting of hantaviruses.

Organizational Affiliation

Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.

Macromolecule Content

Total Structure Weight: 182.57 kDa
Atom Count: 11,624
Modeled Residue Count: 1,506
Deposited Residue Count: 1,654
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope polyprotein	A, C [auth D]	460	Orthohantavirus puumalaense	Mutation(s): 0 Gene Names: gpc
UniProt
Find proteins for Q9WJ31 (Orthohantavirus puumalaense) Explore Q9WJ31 Go to UniProtKB: Q9WJ31
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9WJ31
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain C [auth D]
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope polyprotein	B, D [auth G]	367	Orthohantavirus puumalaense	Mutation(s): 0 Gene Names: gpc
UniProt
Find proteins for Q9WJ31 (Orthohantavirus puumalaense) Explore Q9WJ31 Go to UniProtKB: Q9WJ31
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9WJ31
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain B Focus chain D [auth G]
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth C], G [auth E]	2		N-Glycosylation	Interactions Focus chain E [auth C] Focus chain G [auth E] Interactions & Density Focus chain E [auth C] Focus chain G [auth E]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F [auth H], H [auth M]	4		N-Glycosylation	Interactions Focus chain F [auth H] Focus chain H [auth M] Interactions & Density Focus chain F [auth H] Focus chain H [auth M]
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

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

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 13.9 Å
Aggregation State: PARTICLE
Reconstruction Method: SUBTOMOGRAM AVERAGING

EM Software:

Task	Software Package	Version
RECONSTRUCTION	Dynamo

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-12-16

Deposition Author(s):

Funding Organization	Location	Grant Number
European Research Council (ERC)	United Kingdom	649053

Revision History (Full details and data files)

Version 1.0: 2020-12-16
Type: Initial release
Version 1.1: 2021-01-13
Changes: Database references
Version 1.2: 2024-11-13
Changes: Data collection, Database references, Structure summary