9OFO | pdb_00009ofo

HCoV-229E S2P bound by three DH1533 Fabs

PDB DOI: https://doi.org/10.2210/pdb9OFO/pdb
EM Map EMD-70440: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Human coronavirus 229E, Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2025-04-30 Released: 2025-12-03
Deposition Author(s): Wrapp, D.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.82 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

A potently neutralizing human antibody induces movement of the HCoV-229E receptor binding domain

Liccione, M.F., Scobey, T., Froggatt, H.M., Pajon, C., Yount, B.L., Yin, Q., Spence, T.N., Walter, E.B., Saunders, K.O., Edwards, R.J., Baric, R.S., Haynes, B.F., Cain, D.W., Sheahan, T.P., Wrapp, D.

To be published.

Macromolecule Content

Total Structure Weight: 543.05 kDa
Atom Count: 30,270
Modeled Residue Count: 3,726
Deposited Residue Count: 4,761
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Surface glycoprotein	A, B, C	1,134	Human coronavirus 229E	Mutation(s): 0
UniProt
Find proteins for A0A1B3TN99 (Human coronavirus 229E) Explore A0A1B3TN99 Go to UniProtKB: A0A1B3TN99
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1B3TN99
Glycosylation
Glycosylation Sites: 25	Glycosylation Focus chain A Focus chain B Focus chain C
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DH1533 FAB heavy chain	D [auth H], F [auth M], H [auth O]	239	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DH1533 FAB light chain	E [auth L], G [auth N], I [auth P]	214	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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)-2-acetamido-2-deoxy-beta-D-glucopyranose	DA [auth d], J [auth D], T	5		N-Glycosylation	Interactions Focus chain DA [auth d] Focus chain J [auth D] Focus chain T Interactions & Density Focus chain DA [auth d] Focus chain J [auth D] Focus chain T

Entity ID: 5
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	AA [auth a], EA [auth e], GA [auth g], HA [auth h], K [auth E], AA [auth a], EA [auth e], GA [auth g], HA [auth h], K [auth E], KA [auth k], M [auth G], N [auth I], Q, U, W, X	3		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain EA [auth e] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain K [auth E] Focus chain KA [auth k] Focus chain M [auth G] Focus chain N [auth I] Focus chain Q Focus chain U Focus chain W Focus chain X Interactions & Density Focus chain AA [auth a] Focus chain EA [auth e] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain K [auth E] Focus chain KA [auth k] Focus chain M [auth G] Focus chain N [auth I] Focus chain Q Focus chain U Focus chain W Focus chain X

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	BA [auth b], CA [auth c], FA [auth f], IA [auth i], JA [auth j], BA [auth b], CA [auth c], FA [auth f], IA [auth i], JA [auth j], L [auth F], LA [auth l], MA [auth m], O [auth J], P [auth K], R, S, V, Y, Z	2		N-Glycosylation	Interactions Focus chain BA [auth b] Focus chain CA [auth c] Focus chain FA [auth f] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain L [auth F] Focus chain LA [auth l] Focus chain MA [auth m] Focus chain O [auth J] Focus chain P [auth K] Focus chain R Focus chain S Focus chain V Focus chain Y Focus chain Z Interactions & Density Focus chain BA [auth b] Focus chain CA [auth c] Focus chain FA [auth f] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain L [auth F] Focus chain LA [auth l] Focus chain MA [auth m] Focus chain O [auth J] Focus chain P [auth K] Focus chain R Focus chain S Focus chain V Focus chain Y Focus chain Z

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 AB [auth A] SDF format, chain AC [auth C] SDF format, chain BB [auth A] SDF format, chain BC [auth C] SDF format, chain CB [auth B] SDF format, chain CC [auth C] SDF format, chain DB [auth B] SDF format, chain DC [auth C] SDF format, chain EB [auth B] SDF format, chain EC [auth C] SDF format, chain FB [auth B] SDF format, chain FC [auth C] SDF format, chain GB [auth B] SDF format, chain HB [auth B] SDF format, chain IB [auth B] SDF format, chain JB [auth B] SDF format, chain KB [auth B] SDF format, chain LB [auth B] SDF format, chain MB [auth B] SDF format, chain NA [auth A] SDF format, chain NB [auth B] SDF format, chain OA [auth A] SDF format, chain OB [auth B] SDF format, chain PA [auth A] SDF format, chain PB [auth B] SDF format, chain QA [auth A] SDF format, chain QB [auth B] SDF format, chain RA [auth A] SDF format, chain RB [auth C] SDF format, chain SA [auth A] SDF format, chain SB [auth C] SDF format, chain TA [auth A] SDF format, chain TB [auth C] SDF format, chain UA [auth A] SDF format, chain UB [auth C] SDF format, chain VA [auth A] SDF format, chain VB [auth C] SDF format, chain WA [auth A] SDF format, chain WB [auth C] SDF format, chain XA [auth A] SDF format, chain XB [auth C] SDF format, chain YA [auth A] SDF format, chain YB [auth C] SDF format, chain ZA [auth A] SDF format, chain ZB [auth C] MOL2 format, chain AB [auth A] MOL2 format, chain AC [auth C] MOL2 format, chain BB [auth A] MOL2 format, chain BC [auth C] MOL2 format, chain CB [auth B] MOL2 format, chain CC [auth C] MOL2 format, chain DB [auth B] MOL2 format, chain DC [auth C] MOL2 format, chain EB [auth B] MOL2 format, chain EC [auth C] MOL2 format, chain FB [auth B] MOL2 format, chain FC [auth C] MOL2 format, chain GB [auth B] MOL2 format, chain HB [auth B] MOL2 format, chain IB [auth B] MOL2 format, chain JB [auth B] MOL2 format, chain KB [auth B] MOL2 format, chain LB [auth B] MOL2 format, chain MB [auth B] MOL2 format, chain NA [auth A] MOL2 format, chain NB [auth B] MOL2 format, chain OA [auth A] MOL2 format, chain OB [auth B] MOL2 format, chain PA [auth A] MOL2 format, chain PB [auth B] MOL2 format, chain QA [auth A] MOL2 format, chain QB [auth B] MOL2 format, chain RA [auth A] MOL2 format, chain RB [auth C] MOL2 format, chain SA [auth A] MOL2 format, chain SB [auth C] MOL2 format, chain TA [auth A] MOL2 format, chain TB [auth C] MOL2 format, chain UA [auth A] MOL2 format, chain UB [auth C] MOL2 format, chain VA [auth A] MOL2 format, chain VB [auth C] MOL2 format, chain WA [auth A] MOL2 format, chain WB [auth C] MOL2 format, chain XA [auth A] MOL2 format, chain XB [auth C] MOL2 format, chain YA [auth A] MOL2 format, chain YB [auth C] MOL2 format, chain ZA [auth A] MOL2 format, chain ZB [auth C] mmCIF format, chain AB [auth A] mmCIF format, chain AC [auth C] mmCIF format, chain BB [auth A] mmCIF format, chain BC [auth C] mmCIF format, chain CB [auth B] mmCIF format, chain CC [auth C] mmCIF format, chain DB [auth B] mmCIF format, chain DC [auth C] mmCIF format, chain EB [auth B] mmCIF format, chain EC [auth C] mmCIF format, chain FB [auth B] mmCIF format, chain FC [auth C] mmCIF format, chain GB [auth B] mmCIF format, chain HB [auth B] mmCIF format, chain IB [auth B] mmCIF format, chain JB [auth B] mmCIF format, chain KB [auth B] mmCIF format, chain LB [auth B] mmCIF format, chain MB [auth B] mmCIF format, chain NA [auth A] mmCIF format, chain NB [auth B] mmCIF format, chain OA [auth A] mmCIF format, chain OB [auth B] mmCIF format, chain PA [auth A] mmCIF format, chain PB [auth B] mmCIF format, chain QA [auth A] mmCIF format, chain QB [auth B] mmCIF format, chain RA [auth A] mmCIF format, chain RB [auth C] mmCIF format, chain SA [auth A] mmCIF format, chain SB [auth C] mmCIF format, chain TA [auth A] mmCIF format, chain TB [auth C] mmCIF format, chain UA [auth A] mmCIF format, chain UB [auth C] mmCIF format, chain VA [auth A] mmCIF format, chain VB [auth C] mmCIF format, chain WA [auth A] mmCIF format, chain WB [auth C] mmCIF format, chain XA [auth A] mmCIF format, chain XB [auth C] mmCIF format, chain YA [auth A] mmCIF format, chain YB [auth C] mmCIF format, chain ZA [auth A] mmCIF format, chain ZB [auth C]	AB [auth A] AC [auth C] BB [auth A] BC [auth C] CB [auth B] AB [auth A], AC [auth C], BB [auth A], BC [auth C], CB [auth B], CC [auth C], DB [auth B], DC [auth C], EB [auth B], EC [auth C], FB [auth B], FC [auth C], GB [auth B], HB [auth B], IB [auth B], JB [auth B], KB [auth B], LB [auth B], MB [auth B], NA [auth A], NB [auth B], OA [auth A], OB [auth B], PA [auth A], PB [auth B], QA [auth A], QB [auth B], RA [auth A], RB [auth C], SA [auth A], SB [auth C], TA [auth A], TB [auth C], UA [auth A], UB [auth C], VA [auth A], VB [auth C], WA [auth A], WB [auth C], XA [auth A], XB [auth C], YA [auth A], YB [auth C], ZA [auth A], ZB [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth A] Focus chain AC [auth C] Focus chain BB [auth A] Focus chain BC [auth C] Focus chain CB [auth B] Focus chain CC [auth C] Focus chain DB [auth B] Focus chain DC [auth C] Focus chain EB [auth B] Focus chain EC [auth C] Focus chain FB [auth B] Focus chain FC [auth C] Focus chain GB [auth B] Focus chain HB [auth B] Focus chain IB [auth B] Focus chain JB [auth B] Focus chain KB [auth B] Focus chain LB [auth B] Focus chain MB [auth B] Focus chain NA [auth A] Focus chain NB [auth B] Focus chain OA [auth A] Focus chain OB [auth B] Focus chain PA [auth A] Focus chain PB [auth B] Focus chain QA [auth A] Focus chain QB [auth B] Focus chain RA [auth A] Focus chain RB [auth C] Focus chain SA [auth A] Focus chain SB [auth C] Focus chain TA [auth A] Focus chain TB [auth C] Focus chain UA [auth A] Focus chain UB [auth C] Focus chain VA [auth A] Focus chain VB [auth C] Focus chain WA [auth A] Focus chain WB [auth C] Focus chain XA [auth A] Focus chain XB [auth C] Focus chain YA [auth A] Focus chain YB [auth C] Focus chain ZA [auth A] Focus chain ZB [auth C] Interactions & Density Focus chain AB [auth A] Focus chain AC [auth C] Focus chain BB [auth A] Focus chain BC [auth C] Focus chain CB [auth B] Focus chain CC [auth C] Focus chain DB [auth B] Focus chain DC [auth C] Focus chain EB [auth B] Focus chain EC [auth C] Focus chain FB [auth B] Focus chain FC [auth C] Focus chain GB [auth B] Focus chain HB [auth B] Focus chain IB [auth B] Focus chain JB [auth B] Focus chain KB [auth B] Focus chain LB [auth B] Focus chain MB [auth B] Focus chain NA [auth A] Focus chain NB [auth B] Focus chain OA [auth A] Focus chain OB [auth B] Focus chain PA [auth A] Focus chain PB [auth B] Focus chain QA [auth A] Focus chain QB [auth B] Focus chain RA [auth A] Focus chain RB [auth C] Focus chain SA [auth A] Focus chain SB [auth C] Focus chain TA [auth A] Focus chain TB [auth C] Focus chain UA [auth A] Focus chain UB [auth C] Focus chain VA [auth A] Focus chain VB [auth C] Focus chain WA [auth A] Focus chain WB [auth C] Focus chain XA [auth A] Focus chain XB [auth C] Focus chain YA [auth A] Focus chain YB [auth C] Focus chain ZA [auth A] Focus chain ZB [auth C]