8XZ9 | pdb_00008xz9

BA.2.86 Spike in complex with bovine ACE2 (bound 2 ACE2)

PDB DOI: https://doi.org/10.2210/pdb8XZ9/pdb
EM Map EMD-38790: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Bos taurus, Severe acute respiratory syndrome coronavirus 2
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2024-01-21 Released: 2024-11-13
Deposition Author(s): Yue, C., Liu, P.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.37 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 8XZ9

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

Literature

BA.2.86 Spike in complex with bovine ACE2

Yue, C., Liu, P.

To be published.

Macromolecule Content

Total Structure Weight: 517.86 kDa
Atom Count: 35,083
Modeled Residue Count: 4,380
Deposited Residue Count: 4,552
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Processed angiotensin-converting enzyme 2	A, E	596	Bos taurus	Mutation(s): 0 Gene Names: ACE2 EC: 3.4.17 (UniProt), 3.4.17.23 (UniProt)
UniProt
Find proteins for Q58DD0 (Bos taurus) Explore Q58DD0 Go to UniProtKB: Q58DD0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q58DD0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	B, C, D	1,120	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 25 Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2 Go to UniProtKB: P0DTC2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTC2
Glycosylation
Glycosylation Sites: 6	Glycosylation Focus chain B Focus chain C Focus chain D	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, G [auth H], H [auth I], I [auth J], J [auth K], F, G [auth H], H [auth I], I [auth J], J [auth K], L [auth M], M [auth N], N [auth O], O [auth P], P [auth Q], Q [auth R], R [auth G]	2		N-Glycosylation	Interactions Focus chain F Focus chain G [auth H] Focus chain H [auth I] Focus chain I [auth J] Focus chain J [auth K] Focus chain L [auth M] Focus chain M [auth N] Focus chain N [auth O] Focus chain O [auth P] Focus chain P [auth Q] Focus chain Q [auth R] Focus chain R [auth G] Interactions & Density Focus chain F Focus chain G [auth H] Focus chain H [auth I] Focus chain I [auth J] Focus chain J [auth K] Focus chain L [auth M] Focus chain M [auth N] Focus chain N [auth O] Focus chain O [auth P] Focus chain P [auth Q] Focus chain Q [auth R] Focus chain R [auth G]
Glycosylation Resources
GlyTouCan: G90333CG GlyCosmos: G90333CG GlyGen: G90333CG

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

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.37 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-11-13

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-11-13
Type: Initial release
Version 1.1: 2024-11-20
Changes: Data collection, Source and taxonomy
Version 1.2: 2024-11-27
Changes: Data collection

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.