7RW2 | pdb_00007rw2

Cryo-EM structure of NTD-directed neutralizing antibody 5-7 in complex with prefusion SARS-CoV-2 spike glycoprotein

PDB DOI: https://doi.org/10.2210/pdb7RW2/pdb
Entry: 7RW2 supersedes: 7N01
EM Map EMD-24708: EMDB EMDataResource

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2021-08-19 Released: 2021-09-01
Deposition Author(s): Cerutti, G., Shapiro, L.
Funding Organization(s): Jack Ma Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Neutralizing antibody 5-7 defines a distinct site of vulnerability in SARS-CoV-2 spike N-terminal domain.

Cerutti, G., Guo, Y., Wang, P., Nair, M.S., Wang, M., Huang, Y., Yu, J., Liu, L., Katsamba, P.S., Bahna, F., Reddem, E.R., Kwong, P.D., Ho, D.D., Sheng, Z., Shapiro, L.

(2021) Cell Rep 37: 109928-109928

PubMed: 34706271 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.celrep.2021.109928
Primary Citation Related Structures:
7RW2

PubMed Abstract:
Antibodies that potently neutralize SARS-CoV-2 target mainly the receptor-binding domain or the N-terminal domain (NTD). Over a dozen potently neutralizing NTD-directed antibodies have been studied structurally, and all target a single antigenic supersite in NTD (site 1). Here, we report the cryo-EM structure of a potent NTD-directed neutralizing antibody 5-7, which recognizes a site distinct from other potently neutralizing antibodies, inserting a binding loop into an exposed hydrophobic pocket between the two sheets of the NTD β sandwich. Interestingly, this pocket was previously identified as the binding site for hydrophobic molecules, including heme metabolites, but we observe that their presence does not substantially impede 5-7 recognition. Mirroring its distinctive binding, antibody 5-7 retains neutralization potency with many variants of concern (VOCs). Overall, we reveal that a hydrophobic pocket in NTD proposed for immune evasion can be used by the immune system for recognition.

Organizational Affiliation

Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA.

Macromolecule Content

Total Structure Weight: 591.08 kDa
Atom Count: 31,614
Modeled Residue Count: 3,951
Deposited Residue Count: 5,250
Unique protein chains: 3

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,288	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: 18	Glycosylation Focus chain A Focus chain B Focus chain C	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
5-7 heavy chain	D [auth H], F [auth G], H [auth I]	248	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
5-7 light chain	E [auth L], G [auth J], I [auth K]	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: 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	J [auth D], K [auth E], L [auth F], M, N, J [auth D], K [auth E], L [auth F], M, N, O	2		N-Glycosylation	Interactions Focus chain J [auth D] Focus chain K [auth E] Focus chain L [auth F] Focus chain M Focus chain N Focus chain O Interactions & Density Focus chain J [auth D] Focus chain K [auth E] Focus chain L [auth F] Focus chain M Focus chain N Focus chain O
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download:Ideal Coordinates CCD File SDF format, chain ZA [auth C] SDF format, chain Z [auth A] SDF format, chain YA [auth C] SDF format, chain Y [auth A] SDF format, chain XA [auth C] SDF format, chain X [auth A] SDF format, chain WA [auth C] SDF format, chain W [auth A] SDF format, chain VA [auth C] SDF format, chain V [auth A] SDF format, chain UA [auth B] SDF format, chain U [auth A] SDF format, chain TA [auth B] SDF format, chain T [auth A] SDF format, chain SA [auth B] SDF format, chain S [auth A] SDF format, chain RA [auth B] SDF format, chain R [auth A] SDF format, chain QA [auth B] SDF format, chain Q [auth A] SDF format, chain PA [auth B] SDF format, chain P [auth A] SDF format, chain OA [auth B] SDF format, chain NA [auth B] SDF format, chain MA [auth B] SDF format, chain LA [auth B] SDF format, chain KB [auth C] SDF format, chain KA [auth B] SDF format, chain JB [auth C] SDF format, chain JA [auth B] SDF format, chain IB [auth C] SDF format, chain IA [auth B] SDF format, chain HB [auth C] SDF format, chain HA [auth B] SDF format, chain GB [auth C] SDF format, chain GA [auth B] SDF format, chain FB [auth C] SDF format, chain FA [auth B] SDF format, chain EB [auth C] SDF format, chain EA [auth A] SDF format, chain DB [auth C] SDF format, chain DA [auth A] SDF format, chain CB [auth C] SDF format, chain CA [auth A] SDF format, chain BB [auth C] SDF format, chain BA [auth A] SDF format, chain AB [auth C] SDF format, chain AA [auth A] MOL2 format, chain ZA [auth C] MOL2 format, chain Z [auth A] MOL2 format, chain YA [auth C] MOL2 format, chain Y [auth A] MOL2 format, chain XA [auth C] MOL2 format, chain X [auth A] MOL2 format, chain WA [auth C] MOL2 format, chain W [auth A] MOL2 format, chain VA [auth C] MOL2 format, chain V [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain NA [auth B] MOL2 format, chain MA [auth B] MOL2 format, chain LA [auth B] MOL2 format, chain KB [auth C] MOL2 format, chain KA [auth B] MOL2 format, chain JB [auth C] MOL2 format, chain JA [auth B] MOL2 format, chain IB [auth C] MOL2 format, chain IA [auth B] MOL2 format, chain HB [auth C] MOL2 format, chain HA [auth B] MOL2 format, chain GB [auth C] MOL2 format, chain GA [auth B] MOL2 format, chain FB [auth C] MOL2 format, chain FA [auth B] MOL2 format, chain EB [auth C] MOL2 format, chain EA [auth A] MOL2 format, chain DB [auth C] MOL2 format, chain DA [auth A] MOL2 format, chain CB [auth C] MOL2 format, chain CA [auth A] MOL2 format, chain BB [auth C] MOL2 format, chain BA [auth A] MOL2 format, chain AB [auth C] MOL2 format, chain AA [auth A] mmCIF format, chain ZA [auth C] mmCIF format, chain Z [auth A] mmCIF format, chain YA [auth C] mmCIF format, chain Y [auth A] mmCIF format, chain XA [auth C] mmCIF format, chain X [auth A] mmCIF format, chain WA [auth C] mmCIF format, chain W [auth A] mmCIF format, chain VA [auth C] mmCIF format, chain V [auth A] mmCIF format, chain UA [auth B] mmCIF format, chain U [auth A] mmCIF format, chain TA [auth B] mmCIF format, chain T [auth A] mmCIF format, chain SA [auth B] mmCIF format, chain S [auth A] mmCIF format, chain RA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain QA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain PA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain OA [auth B] mmCIF format, chain NA [auth B] mmCIF format, chain MA [auth B] mmCIF format, chain LA [auth B] mmCIF format, chain KB [auth C] mmCIF format, chain KA [auth B] mmCIF format, chain JB [auth C] mmCIF format, chain JA [auth B] mmCIF format, chain IB [auth C] mmCIF format, chain IA [auth B] mmCIF format, chain HB [auth C] mmCIF format, chain HA [auth B] mmCIF format, chain GB [auth C] mmCIF format, chain GA [auth B] mmCIF format, chain FB [auth C] mmCIF format, chain FA [auth B] mmCIF format, chain EB [auth C] mmCIF format, chain EA [auth A] mmCIF format, chain DB [auth C] mmCIF format, chain DA [auth A] mmCIF format, chain CB [auth C] mmCIF format, chain CA [auth A] mmCIF format, chain BB [auth C] mmCIF format, chain BA [auth A] mmCIF format, chain AB [auth C] mmCIF format, chain AA [auth A]	AA [auth A] AB [auth C] BA [auth A] BB [auth C] CA [auth A] AA [auth A], AB [auth C], BA [auth A], BB [auth C], CA [auth A], CB [auth C], DA [auth A], DB [auth C], EA [auth A], EB [auth C], FA [auth B], FB [auth C], GA [auth B], GB [auth C], HA [auth B], HB [auth C], IA [auth B], IB [auth C], JA [auth B], JB [auth C], KA [auth B], KB [auth C], LA [auth B], MA [auth B], NA [auth B], OA [auth B], P [auth A], PA [auth B], Q [auth A], QA [auth B], R [auth A], RA [auth B], S [auth A], SA [auth B], T [auth A], TA [auth B], U [auth A], UA [auth B], V [auth A], VA [auth C], W [auth A], WA [auth C], X [auth A], XA [auth C], Y [auth A], YA [auth C], Z [auth A], ZA [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth A] Focus chain AB [auth C] Focus chain BA [auth A] Focus chain BB [auth C] Focus chain CA [auth A] Focus chain CB [auth C] Focus chain DA [auth A] Focus chain DB [auth C] Focus chain EA [auth A] Focus chain EB [auth C] Focus chain FA [auth B] Focus chain FB [auth C] Focus chain GA [auth B] Focus chain GB [auth C] Focus chain HA [auth B] Focus chain HB [auth C] Focus chain IA [auth B] Focus chain IB [auth C] Focus chain JA [auth B] Focus chain JB [auth C] Focus chain KA [auth B] Focus chain KB [auth C] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth C] Focus chain W [auth A] Focus chain WA [auth C] Focus chain X [auth A] Focus chain XA [auth C] Focus chain Y [auth A] Focus chain YA [auth C] Focus chain Z [auth A] Focus chain ZA [auth C] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth C] Focus chain BA [auth A] Focus chain BB [auth C] Focus chain CA [auth A] Focus chain CB [auth C] Focus chain DA [auth A] Focus chain DB [auth C] Focus chain EA [auth A] Focus chain EB [auth C] Focus chain FA [auth B] Focus chain FB [auth C] Focus chain GA [auth B] Focus chain GB [auth C] Focus chain HA [auth B] Focus chain HB [auth C] Focus chain IA [auth B] Focus chain IB [auth C] Focus chain JA [auth B] Focus chain JB [auth C] Focus chain KA [auth B] Focus chain KB [auth C] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth C] Focus chain W [auth A] Focus chain WA [auth C] Focus chain X [auth A] Focus chain XA [auth C] Focus chain Y [auth A] Focus chain YA [auth C] Focus chain Z [auth A] Focus chain ZA [auth C]