7MDW | pdb_00007mdw

CryoEM structure of SARS-CoV-2 RBD in complex with nanobodies Nb21 and Nb105

PDB DOI: https://doi.org/10.2210/pdb7MDW/pdb
EM Map EMD-23782: EMDB EMDataResource

Classification: VIRAL PROTEIN/Immune System
Organism(s): Lama glama, Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG, Homo sapiens
Mutation(s): No

Deposited: 2021-04-06 Released: 2021-08-11
Deposition Author(s): Huang, W., Taylor, D.J.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.58 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 7MDW

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

Literature

Potent neutralizing nanobodies resist convergent circulating variants of SARS-CoV-2 by targeting diverse and conserved epitopes

Sun, D., Sang, Z., Kim, Y.J., Xiang, Y., Cohen, T., Belford, A.K., Huet, A., Conway, J.F., Sun, J., Taylor, D.J., Schneidman-Duhovny, D., Zhang, C., Huang, W., Shi, Y.

(2021) Nat Commun 12: 4676

DOI: https://doi.org/10.1038/s41467-021-24963-3

Macromolecule Content

Total Structure Weight: 48.39 kDa
Atom Count: 3,392
Modeled Residue Count: 435
Deposited Residue Count: 435
Unique protein chains: 3

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
nonobody Nb21	A	117	Lama glama	Mutation(s): 0

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	B [auth R]	194	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 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 B [auth R]	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
nanobody Nb105	C [auth B]	124	Lama glama	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 D [auth R] MOL2 format, chain D [auth R] mmCIF format, chain D [auth R]	D [auth R]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth R] Interactions & Density Focus chain D [auth R]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.58 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: 2021-08-11

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)		--

Revision History (Full details and data files)

Version 1.0: 2021-08-11
Type: Initial release
Version 1.1: 2024-11-20
Changes: Data collection, Structure summary
Version 1.2: 2025-05-28
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.