9XI9 | pdb_00009xi9

SARS-CoV-2 Omicron LP.8.1 spike trimer (S-6P) in complex with 3 ZL58 Fabs and 3 ZL525 Fabs, focused refinement of RBD and Fab region

PDB DOI: https://doi.org/10.2210/pdb9XI9/pdb
EM Map EMD-66901: EMDB EMDataResource

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

Deposited: 2025-11-02 Released: 2026-08-12
Deposition Author(s): Niu, C., Liu, B., Gao, X., Li, Z., He, J., Xiong, X.
Funding Organization(s): Other government, National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.93 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

AI identifies Elite Antibodies that Tolerate Escape Mutations from a Population Antibody Class Exerting Continued Selection Over SARS-CoV-2

Niu, C., Huang, X., Yan, Q., Liu, B., Gao, X., Song, Y., Wang, J., Wang, L., Li, Z., Zheng, H., He, P., Huang, X., Yuan, H., Zou, B., Yang, Y., Wu, F., Yao, Y., Chen, X., Chen, L., He, J., Yao, J., Zhao, J., Xiong, X.

To be published.

Macromolecule Content

Total Structure Weight: 116.52 kDa
Atom Count: 8,086
Modeled Residue Count: 1,061
Deposited Residue Count: 1,075
Unique protein chains: 5

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of ZL525 Fab	A	228	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of ZL525 Fab	B	217	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of ZL58 Fab	C [auth H]	221	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	D [auth C]	195	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 28 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: 1	Glycosylation Focus chain D [auth C]	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of ZL58 Fab	E [auth L]	214	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 6
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	F [auth D]	3		N-Glycosylation	Interactions Focus chain F [auth D] Interactions & Density Focus chain F [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.93 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.19.1_4122
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-08-12

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government		2021YFA1300903
National Natural Science Foundation of China (NSFC)	China	82341085
Other government		EKPG21-06
Other government		SRPG22-002
Other government		2021A1515011289
Other government		2023B1212060050
Other government		2023B1212120009
Other government		GIBHBRP24-02