7SBW

Structure of OC43 spike in complex with polyclonal Fab5 (Donor 1051)

PDB DOI: https://doi.org/10.2210/pdb7SBW/pdb
EM Map EMD-24990: EMDB EMDataResource

Classification: VIRAL PROTEIN/Immune System
Organism(s): Homo sapiens, Human coronavirus OC43
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2021-09-26 Released: 2022-05-04
Deposition Author(s): Bangaru, S., Antanasijevic, A., Ward, A.
Funding Organization(s): Bill & Melinda Gates Foundation, National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.20 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 mapping of antibody landscapes to human betacoronavirus spike proteins.

Bangaru, S., Antanasijevic, A., Kose, N., Sewall, L.M., Jackson, A.M., Suryadevara, N., Zhan, X., Torres, J.L., Copps, J., de la Pena, A.T., Crowe Jr., J.E., Ward, A.B.

(2022) Sci Adv 8: eabn2911-eabn2911

PubMed: 35507649 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1126/sciadv.abn2911
Primary Citation of Related Structures:
7SB3, 7SB4, 7SB5, 7SBV, 7SBW, 7SBX, 7SBY

PubMed Abstract:
Preexisting immunity against seasonal coronaviruses (CoVs) represents an important variable in predicting antibody responses and disease severity to severe acute respiratory syndrome CoV-2 (SARS-CoV-2) infections. We used electron microscopy-based polyclonal epitope mapping (EMPEM) to characterize the antibody specificities against β-CoV spike proteins in prepandemic (PP) sera or SARS-CoV-2 convalescent (SC) sera. We observed that most PP sera had antibodies specific to seasonal human CoVs (HCoVs) OC43 and HKU1 spike proteins while the SC sera showed reactivity across all human β-CoVs. Detailed molecular mapping of spike-antibody complexes revealed epitopes that were differentially targeted by preexisting antibodies and SC serum antibodies. Our studies provide an antigenic landscape to β-HCoV spikes in the general population serving as a basis for cross-reactive epitope analyses in SARS-CoV-2-infected individuals.

Organizational Affiliation

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

Macromolecule Content

Total Structure Weight: 492.01 kDa
Atom Count: 30,061
Modelled Residue Count: 3,790
Deposited Residue Count: 4,339
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Human polyclonal Fab model with polyalanine backbone - Heavy chain	A [auth H], B [auth L]	119	Homo sapiens	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein	C [auth J], D [auth A], E [auth B]	1,367	Human coronavirus OC43	Mutation(s): 0
UniProt
Find proteins for A0A0B4N7I3 (Human coronavirus OC43) Explore A0A0B4N7I3 Go to UniProtKB: A0A0B4N7I3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0B4N7I3
Glycosylation
Glycosylation Sites: 14	Glycosylation Focus chain C [auth J] Focus chain D [auth A] Focus chain E [auth B]
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	CA [auth c], F [auth C], G [auth D], HA [auth h], J [auth G], CA [auth c], F [auth C], G [auth D], HA [auth h], J [auth G], M, Q, R, T, V, Y	3		N-Glycosylation	Interactions Focus chain CA [auth c] Focus chain F [auth C] Focus chain G [auth D] Focus chain HA [auth h] Focus chain J [auth G] Focus chain M Focus chain Q Focus chain R Focus chain T Focus chain V Focus chain Y Interactions & Density Focus chain CA [auth c] Focus chain F [auth C] Focus chain G [auth D] Focus chain HA [auth h] Focus chain J [auth G] Focus chain M Focus chain Q Focus chain R Focus chain T Focus chain V Focus chain Y
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a], BA [auth b], DA [auth d], EA [auth e], FA [auth f], AA [auth a], BA [auth b], DA [auth d], EA [auth e], FA [auth f], GA [auth g], H [auth E], I [auth F], IA [auth i], JA [auth j], K [auth I], L [auth K], N, O, P, S, U, W, X, Z	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain BA [auth b] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain H [auth E] Focus chain I [auth F] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain K [auth I] Focus chain L [auth K] Focus chain N Focus chain O Focus chain P Focus chain S Focus chain U Focus chain W Focus chain X Focus chain Z Interactions & Density Focus chain AA [auth a] Focus chain BA [auth b] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain H [auth E] Focus chain I [auth F] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain K [auth I] Focus chain L [auth K] Focus chain N Focus chain O Focus chain P Focus chain S Focus chain U Focus chain W Focus chain X Focus chain Z
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8Z9 Query on 8Z9 Download Ideal Coordinates CCD File SDF format, chain SA [auth A] SDF format, chain XA [auth B] SDF format, chain YA [auth B] MOL2 format, chain SA [auth A] MOL2 format, chain XA [auth B] MOL2 format, chain YA [auth B] mmCIF format, chain SA [auth A] mmCIF format, chain XA [auth B] mmCIF format, chain YA [auth B]	SA [auth A], XA [auth B], YA [auth B]	Sapienic acid C₁₆ H₃₀ O₂ NNNVXFKZMRGJPM-KHPPLWFESA-N		Interactions Focus chain SA [auth A] Focus chain XA [auth B] Focus chain YA [auth B] Interactions & Density Focus chain SA [auth A] Focus chain XA [auth B] Focus chain YA [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain KA [auth J] SDF format, chain LA [auth J] SDF format, chain MA [auth J] SDF format, chain NA [auth J] SDF format, chain OA [auth A] SDF format, chain PA [auth A] SDF format, chain QA [auth A] SDF format, chain RA [auth A] SDF format, chain TA [auth B] SDF format, chain UA [auth B] SDF format, chain VA [auth B] SDF format, chain WA [auth B] MOL2 format, chain KA [auth J] MOL2 format, chain LA [auth J] MOL2 format, chain MA [auth J] MOL2 format, chain NA [auth J] MOL2 format, chain OA [auth A] MOL2 format, chain PA [auth A] MOL2 format, chain QA [auth A] MOL2 format, chain RA [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain UA [auth B] MOL2 format, chain VA [auth B] MOL2 format, chain WA [auth B] mmCIF format, chain KA [auth J] mmCIF format, chain LA [auth J] mmCIF format, chain MA [auth J] mmCIF format, chain NA [auth J] mmCIF format, chain OA [auth A] mmCIF format, chain PA [auth A] mmCIF format, chain QA [auth A] mmCIF format, chain RA [auth A] mmCIF format, chain TA [auth B] mmCIF format, chain UA [auth B] mmCIF format, chain VA [auth B] mmCIF format, chain WA [auth B]	KA [auth J] LA [auth J] MA [auth J] NA [auth J] OA [auth A] KA [auth J], LA [auth J], MA [auth J], NA [auth J], OA [auth A], PA [auth A], QA [auth A], RA [auth A], TA [auth B], UA [auth B], VA [auth B], WA [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain KA [auth J] Focus chain LA [auth J] Focus chain MA [auth J] Focus chain NA [auth J] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain QA [auth A] Focus chain RA [auth A] Focus chain TA [auth B] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain WA [auth B] Interactions & Density Focus chain KA [auth J] Focus chain LA [auth J] Focus chain MA [auth J] Focus chain NA [auth J] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain QA [auth A] Focus chain RA [auth A] Focus chain TA [auth B] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain WA [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2022-05-04

Deposition Author(s):

Bangaru, S.

Antanasijevic, A.

Ward, A.

Funding Organization	Location	Grant Number
Bill & Melinda Gates Foundation	United States	OPP1170236
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	P01 AI110657

Revision History (Full details and data files)

Version 1.0: 2022-05-04
Type: Initial release
Version 1.1: 2022-05-18
Changes: Database references
Version 1.2: 2024-11-20
Changes: Data collection, Structure summary

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Deposit Data

Help and Resources

7SBW

Structure of OC43 spike in complex with polyclonal Fab5 (Donor 1051)

Structural mapping of antibody landscapes to human betacoronavirus spike proteins.

Entity ID: 1

Sequence Annotations

Expand

Entity ID: 2

UniProt

Entity Groups

Glycosylation