8ZHJ

SARS-CoV-2 spike trimer (6P) in complex with three H18 Fabs, head-to-head aggregate (C1 symmetry)

PDB DOI: https://doi.org/10.2210/pdb8ZHJ/pdb
EM Map EMD-60105: EMDB EMDataResource

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Severe acute respiratory syndrome coronavirus 2, Enterobacteria phage T6, synthetic construct, Homo sapiens
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2024-05-11 Released: 2024-08-21
Deposition Author(s): Yan, Q., Gao, X., Liu, B., Hou, R., He, P., Li, Z., Chen, Q., Wang, J., He, J., Chen, L., Zhao, J., Xiong, X.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 8.45 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

Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein helping to drive the genesis of Omicron variants

Yan, Q., Gao, X., Liu, B., Hou, R., He, P., Ma, Y., Zhang, Y., Zhang, Y., Li, Z., Chen, Q., Wang, J., Huang, X., Liang, H., Zheng, H., Yao, Y., Chen, X., Niu, X., He, J., Chen, L., Zhao, J., Xiong, X.

To be published.

Macromolecule Content

Total Structure Weight: 1,182.13 kDa
Atom Count: 70,950
Modelled Residue Count: 8,980
Deposited Residue Count: 10,584
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein,Fibritin,Expression Tag	A B C J [auth G] K [auth H] A, B, C, J [auth G], K [auth H], L [auth I]	1,278	Severe acute respiratory syndrome coronavirus 2, Enterobacteria phage T6, synthetic construct This entity is chimeric	Mutation(s): 2 Gene Names: S, 2, wac, EcT6_00157
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2 Go to UniProtKB: P0DTC2
Find proteins for A0A346FJN8 (Enterobacteria phage T6) Explore A0A346FJN8 Go to UniProtKB: A0A346FJN8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P0DTC2A0A346FJN8
Glycosylation
Glycosylation Sites: 15	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain J [auth G] Focus chain K [auth H] Focus chain L [auth I]	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of H18 Fab	D F H [auth K] M [auth L] O D, F, H [auth K], M [auth L], O, Q	243	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
Heavy chain of H18 Fab	E G [auth J] I [auth M] N P E, G [auth J], I [auth M], N, P, R	243	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
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a], BA [auth b], CA [auth c], DA [auth d], EA [auth e], AA [auth a], BA [auth b], CA [auth c], DA [auth d], EA [auth e], FA [auth f], GA [auth g], HA [auth h], IA [auth i], JA [auth j], KA [auth k], LA [auth l], MA [auth m], NA [auth n], OA [auth o], PA [auth p], S, T, U, V, W, X, Y, Z	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain BA [auth b] Focus chain CA [auth c] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain KA [auth k] Focus chain LA [auth l] Focus chain MA [auth m] Focus chain NA [auth n] Focus chain OA [auth o] Focus chain PA [auth p] Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W Focus chain X Focus chain Y Focus chain Z Interactions & Density Focus chain AA [auth a] Focus chain BA [auth b] Focus chain CA [auth c] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain KA [auth k] Focus chain LA [auth l] Focus chain MA [auth m] Focus chain NA [auth n] Focus chain OA [auth o] Focus chain PA [auth p] Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W Focus chain X Focus chain Y Focus chain Z
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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 AD [auth I] SDF format, chain CB [auth B] SDF format, chain CD [auth I] SDF format, chain DB [auth B] SDF format, chain EC [auth G] SDF format, chain HC [auth G] SDF format, chain IC [auth H] SDF format, chain JC [auth H] SDF format, chain KB [auth B] SDF format, chain KC [auth H] SDF format, chain QA [auth A] SDF format, chain RB [auth C] SDF format, chain RC [auth H] SDF format, chain SA [auth A] SDF format, chain SB [auth C] SDF format, chain TC [auth I] SDF format, chain WA [auth A] SDF format, chain XB [auth G] SDF format, chain ZA [auth A] SDF format, chain ZB [auth G] SDF format, chain AB [auth A] SDF format, chain AC [auth G] SDF format, chain BB [auth B] SDF format, chain BC [auth G] SDF format, chain BD [auth I] SDF format, chain CC [auth G] SDF format, chain DC [auth G] SDF format, chain DD [auth I] SDF format, chain EB [auth B] SDF format, chain FB [auth B] SDF format, chain FC [auth G] SDF format, chain GB [auth B] SDF format, chain GC [auth G] SDF format, chain HB [auth B] SDF format, chain IB [auth B] SDF format, chain JB [auth B] SDF format, chain LB [auth B] SDF format, chain LC [auth H] SDF format, chain MB [auth C] SDF format, chain MC [auth H] SDF format, chain NB [auth C] SDF format, chain NC [auth H] SDF format, chain OB [auth C] SDF format, chain OC [auth H] SDF format, chain PB [auth C] SDF format, chain PC [auth H] SDF format, chain QB [auth C] SDF format, chain QC [auth H] SDF format, chain RA [auth A] SDF format, chain SC [auth H] 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 UC [auth I] SDF format, chain VA [auth A] SDF format, chain VB [auth C] SDF format, chain VC [auth I] SDF format, chain WB [auth C] SDF format, chain WC [auth I] SDF format, chain XA [auth A] SDF format, chain XC [auth I] SDF format, chain YA [auth A] SDF format, chain YB [auth G] SDF format, chain YC [auth I] SDF format, chain ZC [auth I] MOL2 format, chain AD [auth I] MOL2 format, chain CB [auth B] MOL2 format, chain CD [auth I] MOL2 format, chain DB [auth B] MOL2 format, chain EC [auth G] MOL2 format, chain HC [auth G] MOL2 format, chain IC [auth H] MOL2 format, chain JC [auth H] MOL2 format, chain KB [auth B] MOL2 format, chain KC [auth H] MOL2 format, chain QA [auth A] MOL2 format, chain RB [auth C] MOL2 format, chain RC [auth H] MOL2 format, chain SA [auth A] MOL2 format, chain SB [auth C] MOL2 format, chain TC [auth I] MOL2 format, chain WA [auth A] MOL2 format, chain XB [auth G] MOL2 format, chain ZA [auth A] MOL2 format, chain ZB [auth G] MOL2 format, chain AB [auth A] MOL2 format, chain AC [auth G] MOL2 format, chain BB [auth B] MOL2 format, chain BC [auth G] MOL2 format, chain BD [auth I] MOL2 format, chain CC [auth G] MOL2 format, chain DC [auth G] MOL2 format, chain DD [auth I] MOL2 format, chain EB [auth B] MOL2 format, chain FB [auth B] MOL2 format, chain FC [auth G] MOL2 format, chain GB [auth B] MOL2 format, chain GC [auth G] MOL2 format, chain HB [auth B] MOL2 format, chain IB [auth B] MOL2 format, chain JB [auth B] MOL2 format, chain LB [auth B] MOL2 format, chain LC [auth H] MOL2 format, chain MB [auth C] MOL2 format, chain MC [auth H] MOL2 format, chain NB [auth C] MOL2 format, chain NC [auth H] MOL2 format, chain OB [auth C] MOL2 format, chain OC [auth H] MOL2 format, chain PB [auth C] MOL2 format, chain PC [auth H] MOL2 format, chain QB [auth C] MOL2 format, chain QC [auth H] MOL2 format, chain RA [auth A] MOL2 format, chain SC [auth H] 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 UC [auth I] MOL2 format, chain VA [auth A] MOL2 format, chain VB [auth C] MOL2 format, chain VC [auth I] MOL2 format, chain WB [auth C] MOL2 format, chain WC [auth I] MOL2 format, chain XA [auth A] MOL2 format, chain XC [auth I] MOL2 format, chain YA [auth A] MOL2 format, chain YB [auth G] MOL2 format, chain YC [auth I] MOL2 format, chain ZC [auth I]	AB [auth A] AC [auth G] AD [auth I] BB [auth B] BC [auth G] AB [auth A], AC [auth G], AD [auth I], BB [auth B], BC [auth G], BD [auth I], CB [auth B], CC [auth G], CD [auth I], DB [auth B], DC [auth G], DD [auth I], EB [auth B], EC [auth G], FB [auth B], FC [auth G], GB [auth B], GC [auth G], HB [auth B], HC [auth G], IB [auth B], IC [auth H], JB [auth B], JC [auth H], KB [auth B], KC [auth H], LB [auth B], LC [auth H], MB [auth C], MC [auth H], NB [auth C], NC [auth H], OB [auth C], OC [auth H], PB [auth C], PC [auth H], QA [auth A], QB [auth C], QC [auth H], RA [auth A], RB [auth C], RC [auth H], SA [auth A], SB [auth C], SC [auth H], TA [auth A], TB [auth C], TC [auth I], UA [auth A], UB [auth C], UC [auth I], VA [auth A], VB [auth C], VC [auth I], WA [auth A], WB [auth C], WC [auth I], XA [auth A], XB [auth G], XC [auth I], YA [auth A], YB [auth G], YC [auth I], ZA [auth A], ZB [auth G], ZC [auth I]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth A] Focus chain AC [auth G] Focus chain AD [auth I] Focus chain BB [auth B] Focus chain BC [auth G] Focus chain BD [auth I] Focus chain CB [auth B] Focus chain CC [auth G] Focus chain CD [auth I] Focus chain DB [auth B] Focus chain DC [auth G] Focus chain DD [auth I] Focus chain EB [auth B] Focus chain EC [auth G] Focus chain FB [auth B] Focus chain FC [auth G] Focus chain GB [auth B] Focus chain GC [auth G] Focus chain HB [auth B] Focus chain HC [auth G] Focus chain IB [auth B] Focus chain IC [auth H] Focus chain JB [auth B] Focus chain JC [auth H] Focus chain KB [auth B] Focus chain KC [auth H] Focus chain LB [auth B] Focus chain LC [auth H] Focus chain MB [auth C] Focus chain MC [auth H] Focus chain NB [auth C] Focus chain NC [auth H] Focus chain OB [auth C] Focus chain OC [auth H] Focus chain PB [auth C] Focus chain PC [auth H] Focus chain QA [auth A] Focus chain QB [auth C] Focus chain QC [auth H] Focus chain RA [auth A] Focus chain RB [auth C] Focus chain RC [auth H] Focus chain SA [auth A] Focus chain SB [auth C] Focus chain SC [auth H] Focus chain TA [auth A] Focus chain TB [auth C] Focus chain TC [auth I] Focus chain UA [auth A] Focus chain UB [auth C] Focus chain UC [auth I] Focus chain VA [auth A] Focus chain VB [auth C] Focus chain VC [auth I] Focus chain WA [auth A] Focus chain WB [auth C] Focus chain WC [auth I] Focus chain XA [auth A] Focus chain XB [auth G] Focus chain XC [auth I] Focus chain YA [auth A] Focus chain YB [auth G] Focus chain YC [auth I] Focus chain ZA [auth A] Focus chain ZB [auth G] Focus chain ZC [auth I] Interactions & Density Focus chain AB [auth A] Focus chain AC [auth G] Focus chain AD [auth I] Focus chain BB [auth B] Focus chain BC [auth G] Focus chain BD [auth I] Focus chain CB [auth B] Focus chain CC [auth G] Focus chain CD [auth I] Focus chain DB [auth B] Focus chain DC [auth G] Focus chain DD [auth I] Focus chain EB [auth B] Focus chain EC [auth G] Focus chain FB [auth B] Focus chain FC [auth G] Focus chain GB [auth B] Focus chain GC [auth G] Focus chain HB [auth B] Focus chain HC [auth G] Focus chain IB [auth B] Focus chain IC [auth H] Focus chain JB [auth B] Focus chain JC [auth H] Focus chain KB [auth B] Focus chain KC [auth H] Focus chain LB [auth B] Focus chain LC [auth H] Focus chain MB [auth C] Focus chain MC [auth H] Focus chain NB [auth C] Focus chain NC [auth H] Focus chain OB [auth C] Focus chain OC [auth H] Focus chain PB [auth C] Focus chain PC [auth H] Focus chain QA [auth A] Focus chain QB [auth C] Focus chain QC [auth H] Focus chain RA [auth A] Focus chain RB [auth C] Focus chain RC [auth H] Focus chain SA [auth A] Focus chain SB [auth C] Focus chain SC [auth H] Focus chain TA [auth A] Focus chain TB [auth C] Focus chain TC [auth I] Focus chain UA [auth A] Focus chain UB [auth C] Focus chain UC [auth I] Focus chain VA [auth A] Focus chain VB [auth C] Focus chain VC [auth I] Focus chain WA [auth A] Focus chain WB [auth C] Focus chain WC [auth I] Focus chain XA [auth A] Focus chain XB [auth G] Focus chain XC [auth I] Focus chain YA [auth A] Focus chain YB [auth G] Focus chain YC [auth I] Focus chain ZA [auth A] Focus chain ZB [auth G] Focus chain ZC [auth I]