7TF2

Cryo-EM structure of SARS-CoV-2 Kappa (B.1.617.1) Q484I spike protein

PDB DOI: https://doi.org/10.2210/pdb7TF2/pdb
EM Map EMD-25859: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2022-01-06 Released: 2022-03-30
Deposition Author(s): Zhu, X., Saville, J.W., Mannar, D., Srivastava, S.S., Berezuk, A.M., Demers, J.P., Zhou, S., Tuttle, K.S., Subramaniam, S.
Funding Organization(s): Canada Excellence Research Chair Award, Other government

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.62 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.

Macromolecule Content

Total Structure Weight: 880.7 kDa
Atom Count: 50,292
Modelled Residue Count: 6,228
Deposited Residue Count: 7,728
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C, D, E A, B, C, D, E, F	1,288	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 15 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTC2
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
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], G, GA [auth g], H, HA [auth h], I, IA [auth i], J, JA [auth j], K, KA [auth k], L, LA [auth l], M, MA [auth m], N, NA [auth n], O, OA [auth o], P, PA [auth p], Q, R, S, T, U, V, W, X, Y, Z	2	N/A	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 G Focus chain GA [auth g] Focus chain H Focus chain HA [auth h] Focus chain I Focus chain IA [auth i] Focus chain J Focus chain JA [auth j] Focus chain K Focus chain KA [auth k] Focus chain L Focus chain LA [auth l] Focus chain M Focus chain MA [auth m] Focus chain N Focus chain NA [auth n] Focus chain O Focus chain OA [auth o] Focus chain P Focus chain PA [auth p] Focus chain Q Focus chain R 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 G Focus chain GA [auth g] Focus chain H Focus chain HA [auth h] Focus chain I Focus chain IA [auth i] Focus chain J Focus chain JA [auth j] Focus chain K Focus chain KA [auth k] Focus chain L Focus chain LA [auth l] Focus chain M Focus chain MA [auth m] Focus chain N Focus chain NA [auth n] Focus chain O Focus chain OA [auth o] Focus chain P Focus chain PA [auth p] Focus chain Q Focus chain R 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 AB [auth B] SDF format, chain AC [auth E] SDF format, chain BB [auth B] SDF format, chain BC [auth E] SDF format, chain CB [auth B] SDF format, chain CC [auth E] SDF format, chain DB [auth B] SDF format, chain DC [auth E] SDF format, chain EB [auth B] SDF format, chain EC [auth F] SDF format, chain FB [auth B] SDF format, chain FC [auth F] SDF format, chain GB [auth C] SDF format, chain GC [auth F] SDF format, chain HB [auth C] SDF format, chain HC [auth F] SDF format, chain IB [auth C] SDF format, chain IC [auth F] SDF format, chain JB [auth C] SDF format, chain JC [auth F] SDF format, chain KB [auth C] SDF format, chain KC [auth F] SDF format, chain LB [auth C] SDF format, chain LC [auth F] SDF format, chain MB [auth C] SDF format, chain NB [auth C] SDF format, chain OB [auth D] SDF format, chain PB [auth D] SDF format, chain QA [auth A] SDF format, chain QB [auth D] SDF format, chain RA [auth A] SDF format, chain RB [auth D] SDF format, chain SA [auth A] SDF format, chain SB [auth D] SDF format, chain TA [auth A] SDF format, chain TB [auth D] SDF format, chain UA [auth A] SDF format, chain UB [auth D] SDF format, chain VA [auth A] SDF format, chain VB [auth D] SDF format, chain WA [auth A] SDF format, chain WB [auth E] SDF format, chain XA [auth A] SDF format, chain XB [auth E] SDF format, chain YA [auth B] SDF format, chain YB [auth E] SDF format, chain ZA [auth B] SDF format, chain ZB [auth E] MOL2 format, chain AB [auth B] MOL2 format, chain AC [auth E] MOL2 format, chain BB [auth B] MOL2 format, chain BC [auth E] MOL2 format, chain CB [auth B] MOL2 format, chain CC [auth E] MOL2 format, chain DB [auth B] MOL2 format, chain DC [auth E] MOL2 format, chain EB [auth B] MOL2 format, chain EC [auth F] MOL2 format, chain FB [auth B] MOL2 format, chain FC [auth F] MOL2 format, chain GB [auth C] MOL2 format, chain GC [auth F] MOL2 format, chain HB [auth C] MOL2 format, chain HC [auth F] MOL2 format, chain IB [auth C] MOL2 format, chain IC [auth F] MOL2 format, chain JB [auth C] MOL2 format, chain JC [auth F] MOL2 format, chain KB [auth C] MOL2 format, chain KC [auth F] MOL2 format, chain LB [auth C] MOL2 format, chain LC [auth F] MOL2 format, chain MB [auth C] MOL2 format, chain NB [auth C] MOL2 format, chain OB [auth D] MOL2 format, chain PB [auth D] MOL2 format, chain QA [auth A] MOL2 format, chain QB [auth D] MOL2 format, chain RA [auth A] MOL2 format, chain RB [auth D] MOL2 format, chain SA [auth A] MOL2 format, chain SB [auth D] MOL2 format, chain TA [auth A] MOL2 format, chain TB [auth D] MOL2 format, chain UA [auth A] MOL2 format, chain UB [auth D] MOL2 format, chain VA [auth A] MOL2 format, chain VB [auth D] MOL2 format, chain WA [auth A] MOL2 format, chain WB [auth E] MOL2 format, chain XA [auth A] MOL2 format, chain XB [auth E] MOL2 format, chain YA [auth B] MOL2 format, chain YB [auth E] MOL2 format, chain ZA [auth B] MOL2 format, chain ZB [auth E]	AB [auth B] AC [auth E] BB [auth B] BC [auth E] CB [auth B] AB [auth B], AC [auth E], BB [auth B], BC [auth E], CB [auth B], CC [auth E], DB [auth B], DC [auth E], EB [auth B], EC [auth F], FB [auth B], FC [auth F], GB [auth C], GC [auth F], HB [auth C], HC [auth F], IB [auth C], IC [auth F], JB [auth C], JC [auth F], KB [auth C], KC [auth F], LB [auth C], LC [auth F], MB [auth C], NB [auth C], OB [auth D], PB [auth D], QA [auth A], QB [auth D], RA [auth A], RB [auth D], SA [auth A], SB [auth D], TA [auth A], TB [auth D], UA [auth A], UB [auth D], VA [auth A], VB [auth D], WA [auth A], WB [auth E], XA [auth A], XB [auth E], YA [auth B], YB [auth E], ZA [auth B], ZB [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth B] Focus chain AC [auth E] Focus chain BB [auth B] Focus chain BC [auth E] Focus chain CB [auth B] Focus chain CC [auth E] Focus chain DB [auth B] Focus chain DC [auth E] Focus chain EB [auth B] Focus chain EC [auth F] Focus chain FB [auth B] Focus chain FC [auth F] Focus chain GB [auth C] Focus chain GC [auth F] Focus chain HB [auth C] Focus chain HC [auth F] Focus chain IB [auth C] Focus chain IC [auth F] Focus chain JB [auth C] Focus chain JC [auth F] Focus chain KB [auth C] Focus chain KC [auth F] Focus chain LB [auth C] Focus chain LC [auth F] Focus chain MB [auth C] Focus chain NB [auth C] Focus chain OB [auth D] Focus chain PB [auth D] Focus chain QA [auth A] Focus chain QB [auth D] Focus chain RA [auth A] Focus chain RB [auth D] Focus chain SA [auth A] Focus chain SB [auth D] Focus chain TA [auth A] Focus chain TB [auth D] Focus chain UA [auth A] Focus chain UB [auth D] Focus chain VA [auth A] Focus chain VB [auth D] Focus chain WA [auth A] Focus chain WB [auth E] Focus chain XA [auth A] Focus chain XB [auth E] Focus chain YA [auth B] Focus chain YB [auth E] Focus chain ZA [auth B] Focus chain ZB [auth E] Interactions & Density Focus chain AB [auth B] Focus chain AC [auth E] Focus chain BB [auth B] Focus chain BC [auth E] Focus chain CB [auth B] Focus chain CC [auth E] Focus chain DB [auth B] Focus chain DC [auth E] Focus chain EB [auth B] Focus chain EC [auth F] Focus chain FB [auth B] Focus chain FC [auth F] Focus chain GB [auth C] Focus chain GC [auth F] Focus chain HB [auth C] Focus chain HC [auth F] Focus chain IB [auth C] Focus chain IC [auth F] Focus chain JB [auth C] Focus chain JC [auth F] Focus chain KB [auth C] Focus chain KC [auth F] Focus chain LB [auth C] Focus chain LC [auth F] Focus chain MB [auth C] Focus chain NB [auth C] Focus chain OB [auth D] Focus chain PB [auth D] Focus chain QA [auth A] Focus chain QB [auth D] Focus chain RA [auth A] Focus chain RB [auth D] Focus chain SA [auth A] Focus chain SB [auth D] Focus chain TA [auth A] Focus chain TB [auth D] Focus chain UA [auth A] Focus chain UB [auth D] Focus chain VA [auth A] Focus chain VB [auth D] Focus chain WA [auth A] Focus chain WB [auth E] Focus chain XA [auth A] Focus chain XB [auth E] Focus chain YA [auth B] Focus chain YB [auth E] Focus chain ZA [auth B] Focus chain ZB [auth E]