7F5G | pdb_00007f5g

The crystal structure of RBD-Nanobody complex, DL4 (SA4)

PDB DOI: https://doi.org/10.2210/pdb7F5G/pdb

Classification: VIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2, Vicugna pacos
Expression System: Spodoptera frugiperda, Escherichia coli
Mutation(s): No

Deposited: 2021-06-22 Released: 2022-05-25
Deposition Author(s): Li, T., Lai, Y., Zhou, Y., Tan, J., Li, D.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.217 (Depositor), 0.226 (DCC)
R-Value Work:
0.188 (Depositor)
R-Value Observed:
0.189 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

Literature

Isolation, characterization, and structure-based engineering of a neutralizing nanobody against SARS-CoV-2.

Li, T., Zhou, B., Li, Y., Huang, S., Luo, Z., Zhou, Y., Lai, Y., Gautam, A., Bourgeau, S., Wang, S., Bao, J., Tan, J., Lavillette, D., Li, D.

(2022) Int J Biol Macromol 209: 1379-1388

PubMed: 35460753 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.ijbiomac.2022.04.096
Primary Citation Related Structures:
7F5G

PubMed Abstract:
SARS-CoV-2 engages with human cells through the binding of its Spike receptor-binding domain (S-RBD) to the receptor ACE2. Molecular blocking of this engagement represents a proven strategy to treat COVID-19. Here, we report a single-chain antibody (nanobody, DL4) isolated from immunized alpaca with picomolar affinity to RBD. DL4 neutralizes SARS-CoV-2 pseudoviruses with an IC ₅₀ of 0.101 μg mL ^-1 (6.2 nM). A crystal structure of the DL4-RBD complex at 1.75-Å resolution unveils the interaction detail and reveals a direct competition mechanism for DL4's ACE2-blocking and hence neutralizing activity. The structural information allows us to rationally design a mutant with higher potency. Our work adds diversity of neutralizing nanobodies against SARS-CoV-2 and should encourage protein engineering to improve antibody affinities in general.

Organizational Affiliation

State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), 320 Yueyang Road, Shanghai 200030, China.

Macromolecule Content

Total Structure Weight: 83.33 kDa
Atom Count: 5,970
Modeled Residue Count: 631
Deposited Residue Count: 718
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, C	213	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 A Focus chain C	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody DL4	B, D	146	Vicugna pacos	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	E, F	4		N-Glycosylation	Interactions Focus chain E Focus chain F Interactions & Density Focus chain E Focus chain F
Glycosylation Resources
GlyTouCan: G63564LA GlyCosmos: G63564LA GlyGen: G63564LA

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain EA [auth D] SDF format, chain G [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain T [auth A] SDF format, chain U [auth B] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain CA [auth D] SDF format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth B] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain CA [auth D] MOL2 format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth B] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain CA [auth D] mmCIF format, chain AA [auth D]	AA [auth D] BA [auth D] CA [auth D] EA [auth D] G [auth A] AA [auth D], BA [auth D], CA [auth D], EA [auth D], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], T [auth A], U [auth B], W [auth C], X [auth C], Y [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain EA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain T [auth A] Focus chain U [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain EA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain T [auth A] Focus chain U [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain FA [auth D] SDF format, chain M [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain S [auth A] SDF format, chain V [auth B] SDF format, chain Z [auth C] SDF format, chain R [auth A] SDF format, chain N [auth A] MOL2 format, chain DA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain S [auth A] MOL2 format, chain V [auth B] MOL2 format, chain Z [auth C] MOL2 format, chain R [auth A] MOL2 format, chain N [auth A] mmCIF format, chain DA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain S [auth A] mmCIF format, chain V [auth B] mmCIF format, chain Z [auth C] mmCIF format, chain R [auth A] mmCIF format, chain N [auth A]	DA [auth D] FA [auth D] M [auth A] N [auth A] O [auth A] DA [auth D], FA [auth D], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], V [auth B], Z [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain DA [auth D] Focus chain FA [auth D] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain V [auth B] Focus chain Z [auth C] Interactions & Density Focus chain DA [auth D] Focus chain FA [auth D] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain V [auth B] Focus chain Z [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.217 (Depositor), 0.226 (DCC)
R-Value Work: 0.188 (Depositor)
R-Value Observed: 0.189 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.818	α = 90
b = 95.04	β = 90
c = 118.915	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-05-25

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31870726

Revision History (Full details and data files)

Version 1.0: 2022-05-25
Type: Initial release
Version 2.0: 2022-06-01
Changes: Atomic model, Data collection, Derived calculations
Version 2.1: 2023-11-29
Changes: Data collection, Refinement description
Version 2.2: 2024-11-20
Changes: Structure summary