9V2P | pdb_00009v2p

Complex structure of GX2012 spike RBD bound to human DPP4

PDB DOI: https://doi.org/10.2210/pdb9V2P/pdb
EM Map EMD-64736: EMDB EMDataResource

Classification: VIRAL PROTEIN/HYDROLASE
Organism(s): Homo sapiens, BtTp-BetaCoV/GX2012
Expression System: Homo sapiens, Trichoplusia ni
Mutation(s): No

Deposited: 2025-05-20 Released: 2025-12-24
Deposition Author(s): Wang, X., Lin, Z.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9V2P

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

Literature

Complex structure of GX2012 spike RBD bound to human DPP4

Wang, X., Lin, Z.

To be published.

Macromolecule Content

Total Structure Weight: 197.26 kDa
Atom Count: 13,891
Modeled Residue Count: 1,663
Deposited Residue Count: 1,663
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl peptidase 4 soluble form	A, B	727	Homo sapiens	Mutation(s): 0 Gene Names: DPP4, ADCP2, CD26 EC: 3.4.14.5
UniProt & NIH Common Fund Data Resources
Find proteins for P27487 (Homo sapiens) Explore P27487 Go to UniProtKB: P27487
PHAROS: P27487 GTEx: ENSG00000197635
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P27487
Glycosylation
Glycosylation Sites: 6	Glycosylation Focus chain A Focus chain B	Go to GlyGen: P27487-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	C [auth G]	209	BtTp-BetaCoV/GX2012	Mutation(s): 0
UniProt
Find proteins for A0A0U1WJZ6 (BtTp-BetaCoV/GX2012) Explore A0A0U1WJZ6 Go to UniProtKB: A0A0U1WJZ6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0U1WJZ6
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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	D [auth C], E [auth D], F [auth E], G [auth F], H, D [auth C], E [auth D], F [auth E], G [auth F], H, I, J, K, L, M, N	2		N-Glycosylation	Interactions Focus chain D [auth C] Focus chain E [auth D] Focus chain F [auth E] Focus chain G [auth F] Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain N Interactions & Density Focus chain D [auth C] Focus chain E [auth D] Focus chain F [auth E] Focus chain G [auth F] Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain N
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	O	3		N-Glycosylation	Interactions Focus chain O Interactions & Density Focus chain O
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

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

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	Coot

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-12-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-12-24
Type: Initial release

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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.