9OFQ | pdb_00009ofq

HCoV-229E S2P bound by one DH1533 Fab

PDB DOI: https://doi.org/10.2210/pdb9OFQ/pdb
EM Map EMD-70442: 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: 2.88 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: 453.5 kDa
Atom Count: 25,152
Modeled Residue Count: 2,987
Deposited Residue Count: 3,855
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 [auth C], B [auth A], E [auth B]	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: 21	Glycosylation Focus chain A [auth C] Focus chain B [auth A] Focus chain E [auth B]
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DH1533 FAB heavy chain	C [auth H]	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	D [auth L]	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	BB [auth 1], DB [auth 3], F [auth D], KA [auth k], OA [auth o], BB [auth 1], DB [auth 3], F [auth D], KA [auth k], OA [auth o], T, V	5		N-Glycosylation	Interactions Focus chain BB [auth 1] Focus chain DB [auth 3] Focus chain F [auth D] Focus chain KA [auth k] Focus chain OA [auth o] Focus chain T Focus chain V Interactions & Density Focus chain BB [auth 1] Focus chain DB [auth 3] Focus chain F [auth D] Focus chain KA [auth k] Focus chain OA [auth o] Focus chain T Focus chain V

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	BA [auth b], CA [auth c], G [auth E], H [auth F], MA [auth m], BA [auth b], CA [auth c], G [auth E], H [auth F], MA [auth m], RA [auth r], VA [auth v], W	3		N-Glycosylation	Interactions Focus chain BA [auth b] Focus chain CA [auth c] Focus chain G [auth E] Focus chain H [auth F] Focus chain MA [auth m] Focus chain RA [auth r] Focus chain VA [auth v] Focus chain W Interactions & Density Focus chain BA [auth b] Focus chain CA [auth c] Focus chain G [auth E] Focus chain H [auth F] Focus chain MA [auth m] Focus chain RA [auth r] Focus chain VA [auth v] Focus chain W

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	AA [auth a], DA [auth d], EA [auth e], EB [auth 4], FA [auth f], AA [auth a], DA [auth d], EA [auth e], EB [auth 4], FA [auth f], GA [auth g], HA [auth h], I [auth G], IA [auth i], J [auth I], K [auth J], L [auth K], M, N, NA [auth n], O, P, PA [auth p], Q, QA [auth q], R, SA [auth s], UA [auth u], WA [auth w], XA [auth x], YA [auth y], Z, ZA [auth z]	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain EB [auth 4] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain I [auth G] Focus chain IA [auth i] Focus chain J [auth I] Focus chain K [auth J] Focus chain L [auth K] Focus chain M Focus chain N Focus chain NA [auth n] Focus chain O Focus chain P Focus chain PA [auth p] Focus chain Q Focus chain QA [auth q] Focus chain R Focus chain SA [auth s] Focus chain UA [auth u] Focus chain WA [auth w] Focus chain XA [auth x] Focus chain YA [auth y] Focus chain Z Focus chain ZA [auth z] Interactions & Density Focus chain AA [auth a] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain EB [auth 4] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain I [auth G] Focus chain IA [auth i] Focus chain J [auth I] Focus chain K [auth J] Focus chain L [auth K] Focus chain M Focus chain N Focus chain NA [auth n] Focus chain O Focus chain P Focus chain PA [auth p] Focus chain Q Focus chain QA [auth q] Focus chain R Focus chain SA [auth s] Focus chain UA [auth u] Focus chain WA [auth w] Focus chain XA [auth x] Focus chain YA [auth y] Focus chain Z Focus chain ZA [auth z]

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	AB [auth 0], CB [auth 2], LA [auth l], S, U	4		N-Glycosylation	Interactions Focus chain AB [auth 0] Focus chain CB [auth 2] Focus chain LA [auth l] Focus chain S Focus chain U Interactions & Density Focus chain AB [auth 0] Focus chain CB [auth 2] Focus chain LA [auth l] Focus chain S Focus chain U

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	X	6		N-Glycosylation	Interactions Focus chain X Interactions & Density Focus chain X

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	JA [auth j], TA [auth t], Y	4		N-Glycosylation	Interactions Focus chain JA [auth j] Focus chain TA [auth t] Focus chain Y Interactions & Density Focus chain JA [auth j] Focus chain TA [auth t] Focus chain Y

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 FB [auth C] SDF format, chain GB [auth C] SDF format, chain HB [auth C] SDF format, chain IB [auth C] SDF format, chain JB [auth C] SDF format, chain KB [auth A] SDF format, chain LB [auth A] SDF format, chain MB [auth A] SDF format, chain NB [auth A] SDF format, chain OB [auth A] SDF format, chain PB [auth A] SDF format, chain QB [auth A] SDF format, chain RB [auth A] SDF format, chain SB [auth B] SDF format, chain TB [auth B] SDF format, chain UB [auth B] SDF format, chain VB [auth B] SDF format, chain WB [auth B] MOL2 format, chain FB [auth C] MOL2 format, chain GB [auth C] MOL2 format, chain HB [auth C] MOL2 format, chain IB [auth C] MOL2 format, chain JB [auth C] MOL2 format, chain KB [auth A] MOL2 format, chain LB [auth A] MOL2 format, chain MB [auth A] MOL2 format, chain NB [auth A] MOL2 format, chain OB [auth A] MOL2 format, chain PB [auth A] MOL2 format, chain QB [auth A] MOL2 format, chain RB [auth A] MOL2 format, chain SB [auth B] MOL2 format, chain TB [auth B] MOL2 format, chain UB [auth B] MOL2 format, chain VB [auth B] MOL2 format, chain WB [auth B] mmCIF format, chain FB [auth C] mmCIF format, chain GB [auth C] mmCIF format, chain HB [auth C] mmCIF format, chain IB [auth C] mmCIF format, chain JB [auth C] mmCIF format, chain KB [auth A] mmCIF format, chain LB [auth A] mmCIF format, chain MB [auth A] mmCIF format, chain NB [auth A] mmCIF format, chain OB [auth A] mmCIF format, chain PB [auth A] mmCIF format, chain QB [auth A] mmCIF format, chain RB [auth A] mmCIF format, chain SB [auth B] mmCIF format, chain TB [auth B] mmCIF format, chain UB [auth B] mmCIF format, chain VB [auth B] mmCIF format, chain WB [auth B]	FB [auth C] GB [auth C] HB [auth C] IB [auth C] JB [auth C] FB [auth C], GB [auth C], HB [auth C], IB [auth C], JB [auth C], KB [auth A], LB [auth A], MB [auth A], NB [auth A], OB [auth A], PB [auth A], QB [auth A], RB [auth A], SB [auth B], TB [auth B], UB [auth B], VB [auth B], WB [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain FB [auth C] Focus chain GB [auth C] Focus chain HB [auth C] Focus chain IB [auth C] Focus chain JB [auth C] Focus chain KB [auth A] Focus chain LB [auth A] Focus chain MB [auth A] Focus chain NB [auth A] Focus chain OB [auth A] Focus chain PB [auth A] Focus chain QB [auth A] Focus chain RB [auth A] Focus chain SB [auth B] Focus chain TB [auth B] Focus chain UB [auth B] Focus chain VB [auth B] Focus chain WB [auth B] Interactions & Density Focus chain FB [auth C] Focus chain GB [auth C] Focus chain HB [auth C] Focus chain IB [auth C] Focus chain JB [auth C] Focus chain KB [auth A] Focus chain LB [auth A] Focus chain MB [auth A] Focus chain NB [auth A] Focus chain OB [auth A] Focus chain PB [auth A] Focus chain QB [auth A] Focus chain RB [auth A] Focus chain SB [auth B] Focus chain TB [auth B] Focus chain UB [auth B] Focus chain VB [auth B] Focus chain WB [auth B]