7AKD | pdb_00007akd

Structure of the SARS-CoV-2 spike glycoprotein in complex with the 47D11 neutralizing antibody Fab fragment

PDB DOI: https://doi.org/10.2210/pdb7AKD/pdb
EM Map EMD-11812: EMDB EMDataResource

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

Deposited: 2020-09-30 Released: 2021-05-19
Deposition Author(s): Fedry, J., Hurdiss, D.L., Wang, C., Li, W., Obal, G., Drulyte, I., Howes, S.C., van Kuppeveld, F.J.M., Foerster, F., Bosch, B.J.
Funding Organization(s): European Research Council (ERC), H2020 Marie Curie Actions of the European Commission, European Molecular Biology Organization (EMBO)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.00 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

Structural insights into the cross-neutralization of SARS-CoV and SARS-CoV-2 by the human monoclonal antibody 47D11.

Fedry, J., Hurdiss, D.L., Wang, C., Li, W., Obal, G., Drulyte, I., Du, W., Howes, S.C., van Kuppeveld, F.J.M., Forster, F., Bosch, B.J.

(2021) Sci Adv 7

PubMed: 33958322 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/sciadv.abf5632
Primary Citation Related Structures:
7AKD, 7AKJ

PubMed Abstract:
The emergence of SARS-CoV-2 antibody escape mutations highlights the urgent need for broadly neutralizing therapeutics. We previously identified a human monoclonal antibody, 47D11, capable of cross-neutralizing SARS-CoV-2 and SARS-CoV and protecting against the associated respiratory disease in an animal model. Here, we report cryo-EM structures of both trimeric spike ectodomains in complex with the 47D11 Fab. 47D11 binds to the closed receptor-binding domain, distal to the ACE2 binding site. The CDRL3 stabilizes the N343 glycan in an upright conformation, exposing a mutationally constrained hydrophobic pocket, into which the CDRH3 loop inserts two aromatic residues. 47D11 stabilizes a partially open conformation of the SARS-CoV-2 spike, suggesting that it could be used effectively in combination with other antibodies targeting the exposed receptor-binding motif. Together, these results reveal a cross-protective epitope on the SARS-CoV-2 spike and provide a structural roadmap for the development of 47D11 as a prophylactic or postexposure therapy for COVID-19.

Organizational Affiliation

Cryo-Electron Microscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands.

Macromolecule Content

Total Structure Weight: 490.25 kDa
Atom Count: 27,358
Modeled Residue Count: 3,404
Deposited Residue Count: 4,312
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,286	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: 6	Glycosylation Focus chain A Focus chain B 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
47D11 neutralizing antibody heavy chain	D, F [auth H]	121	Homo sapiens	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
47D11 neutralizing antibody light chain	E, G [auth L]	106	Homo sapiens	Mutation(s): 0

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	H [auth F], K [auth J], L [auth K], M, P, H [auth F], K [auth J], L [auth K], M, P, Q, R, V, W, X	2		N-Glycosylation	Interactions Focus chain H [auth F] Focus chain K [auth J] Focus chain L [auth K] Focus chain M Focus chain P Focus chain Q Focus chain R Focus chain V Focus chain W Focus chain X Interactions & Density Focus chain H [auth F] Focus chain K [auth J] Focus chain L [auth K] Focus chain M Focus chain P Focus chain Q Focus chain R Focus chain V Focus chain W Focus chain X
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 5
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	I [auth G], J [auth I], N	3		N-Glycosylation	Interactions Focus chain I [auth G] Focus chain J [auth I] Focus chain N Interactions & Density Focus chain I [auth G] Focus chain J [auth I] Focus chain N
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(3-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	O	5	N/A	N-Glycosylation	Interactions Focus chain O Interactions & Density Focus chain O

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	S	4		N-Glycosylation	Interactions Focus chain S Interactions & Density Focus chain S
Glycosylation Resources
GlyTouCan: G32152BH GlyCosmos: G32152BH GlyGen: G32152BH

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	T	6		N-Glycosylation	Interactions Focus chain T Interactions & Density Focus chain T
Glycosylation Resources
GlyTouCan: G29616NS GlyCosmos: G29616NS GlyGen: G29616NS

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose	U	2		N/A	Interactions Focus chain U Interactions & Density Focus chain U
Glycosylation Resources
GlyTouCan: G77384RA GlyCosmos: G77384RA GlyGen: G77384RA

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG 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 WA [auth C] SDF format, chain VA [auth C] SDF format, chain UA [auth B] SDF format, chain TA [auth B] SDF format, chain SA [auth B] SDF format, chain RA [auth B] SDF format, chain QA [auth B] SDF format, chain PA [auth B] SDF format, chain OA [auth B] SDF format, chain MA [auth B] SDF format, chain LA [auth B] SDF format, chain KA [auth B] SDF format, chain JA [auth B] SDF format, chain IA [auth B] SDF format, chain GA [auth A] SDF format, chain FA [auth A] SDF format, chain EA [auth A] SDF format, chain DA [auth A] 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 WA [auth C] MOL2 format, chain VA [auth C] MOL2 format, chain UA [auth B] MOL2 format, chain TA [auth B] MOL2 format, chain SA [auth B] MOL2 format, chain RA [auth B] MOL2 format, chain QA [auth B] MOL2 format, chain PA [auth B] MOL2 format, chain OA [auth B] MOL2 format, chain MA [auth B] MOL2 format, chain LA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain GA [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain DA [auth A] 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 WA [auth C] mmCIF format, chain VA [auth C] mmCIF format, chain UA [auth B] mmCIF format, chain TA [auth B] mmCIF format, chain SA [auth B] mmCIF format, chain RA [auth B] mmCIF format, chain QA [auth B] mmCIF format, chain PA [auth B] mmCIF format, chain OA [auth B] mmCIF format, chain MA [auth B] mmCIF format, chain LA [auth B] mmCIF format, chain KA [auth B] mmCIF format, chain JA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain GA [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain DA [auth A] 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], DA [auth A], EA [auth A], FA [auth A], GA [auth A], IA [auth B], JA [auth B], KA [auth B], LA [auth B], MA [auth B], OA [auth B], PA [auth B], QA [auth B], RA [auth B], SA [auth B], TA [auth B], UA [auth B], VA [auth C], WA [auth C], 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 DA [auth A] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain UA [auth B] Focus chain VA [auth C] Focus chain WA [auth C] 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 DA [auth A] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain UA [auth B] Focus chain VA [auth C] Focus chain WA [auth C] 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]
MAN Query on MAN Download:Ideal Coordinates CCD File SDF format, chain EB [auth H] SDF format, chain DB [auth D] MOL2 format, chain EB [auth H] MOL2 format, chain DB [auth D] mmCIF format, chain EB [auth H] mmCIF format, chain DB [auth D]	DB [auth D], EB [auth H]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain DB [auth D] Focus chain EB [auth H] Interactions & Density Focus chain DB [auth D] Focus chain EB [auth H]
FUC Query on FUC Download:Ideal Coordinates CCD File SDF format, chain NA [auth B] SDF format, chain HA [auth A] SDF format, chain CB [auth C] MOL2 format, chain NA [auth B] MOL2 format, chain HA [auth A] MOL2 format, chain CB [auth C] mmCIF format, chain NA [auth B] mmCIF format, chain HA [auth A] mmCIF format, chain CB [auth C]	CB [auth C], HA [auth A], NA [auth B]	alpha-L-fucopyranose C₆ H₁₂ O₅ SHZGCJCMOBCMKK-SXUWKVJYSA-N		Interactions Focus chain CB [auth C] Focus chain HA [auth A] Focus chain NA [auth B] Interactions & Density Focus chain CB [auth C] Focus chain HA [auth A] Focus chain NA [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-05-19

Deposition Author(s):

van Kuppeveld, F.J.M.

Foerster, F.

Bosch, B.J.

Funding Organization	Location	Grant Number
European Research Council (ERC)	Netherlands	724425-BENDER
H2020 Marie Curie Actions of the European Commission	Netherlands	792575
H2020 Marie Curie Actions of the European Commission	Netherlands	842333
European Molecular Biology Organization (EMBO)	Netherlands	ALTF-948-2017
European Molecular Biology Organization (EMBO)	Netherlands	ALTF-1172-2018

Revision History (Full details and data files)

Version 1.0: 2021-05-19
Type: Initial release
Version 1.1: 2021-06-16
Changes: Database references
Version 1.2: 2024-11-06
Changes: Data collection, Database references, Structure summary