7V7H

Cryo-EM structure of SARS-CoV-2 S-Kappa variant (B.1.617.1), dimer of S trimer conformation 1

PDB DOI: https://doi.org/10.2210/pdb7V7H/pdb
EM Map EMD-31771: EMDB EMDataResource

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

Deposited: 2021-08-21 Released: 2021-10-06
Deposition Author(s): Yang, T.J., Yu, P.Y., Chang, Y.C., Hsu, S.T.D.
Funding Organization(s): Ministry of Science and Technology (MoST, Taiwan), Academia Sinica (Taiwan)

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 1.1 of the entry. See complete history.

Literature

Cryo-EM structure of SARS-CoV-2 S-Kappa variant (B.1.617.1), dimer of S trimer conformation 1

Yang, T.J., Yu, P.Y., Chang, Y.C., Hsu, S.T.D.

To be published.

Macromolecule Content

Total Structure Weight: 890.44 kDa
Atom Count: 50,949
Modelled Residue Count: 6,209
Deposited Residue Count: 7,698
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(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	1,283	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 12 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
Glycosylation
Glycosylation Sites: 16	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D Focus chain E Focus chain F	Go to GlyGen: P0DTC2-1
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], AB [auth 0], BA [auth b], BB [auth 1], CA [auth c], AA [auth a], AB [auth 0], BA [auth b], BB [auth 1], CA [auth c], CB [auth 2], DA [auth d], DB [auth 3], EA [auth e], EB [auth 4], FA [auth f], FB [auth 5], G, GA [auth g], H, HA [auth h], HB [auth 7], I, IB [auth 8], J, JA [auth j], JB [auth 9], KA [auth k], KB [auth AA], L, LA [auth l], LB [auth BA], M, MA [auth m], MB [auth CA], N, NA [auth n], NB [auth DA], O, OA [auth o], OB [auth EA], P, PA [auth p], PB [auth FA], Q, QA [auth q], QB [auth GA], R, RA [auth r], RB [auth HA], S, SA [auth s], T, TA [auth t], TB [auth JA], U, UB [auth KA], V, VA [auth v], VB [auth LA], WA [auth w], WB [auth MA], X, XA [auth x], XB [auth NA], Y, YA [auth y], YB [auth OA], Z, ZA [auth z], ZB [auth PA]	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain AB [auth 0] Focus chain BA [auth b] Focus chain BB [auth 1] Focus chain CA [auth c] Focus chain CB [auth 2] Focus chain DA [auth d] Focus chain DB [auth 3] Focus chain EA [auth e] Focus chain EB [auth 4] Focus chain FA [auth f] Focus chain FB [auth 5] Focus chain G Focus chain GA [auth g] Focus chain H Focus chain HA [auth h] Focus chain HB [auth 7] Focus chain I Focus chain IB [auth 8] Focus chain J Focus chain JA [auth j] Focus chain JB [auth 9] Focus chain KA [auth k] Focus chain KB [auth AA] Focus chain L Focus chain LA [auth l] Focus chain LB [auth BA] Focus chain M Focus chain MA [auth m] Focus chain MB [auth CA] Focus chain N Focus chain NA [auth n] Focus chain NB [auth DA] Focus chain O Focus chain OA [auth o] Focus chain OB [auth EA] Focus chain P Focus chain PA [auth p] Focus chain PB [auth FA] Focus chain Q Focus chain QA [auth q] Focus chain QB [auth GA] Focus chain R Focus chain RA [auth r] Focus chain RB [auth HA] Focus chain S Focus chain SA [auth s] Focus chain T Focus chain TA [auth t] Focus chain TB [auth JA] Focus chain U Focus chain UB [auth KA] Focus chain V Focus chain VA [auth v] Focus chain VB [auth LA] Focus chain WA [auth w] Focus chain WB [auth MA] Focus chain X Focus chain XA [auth x] Focus chain XB [auth NA] Focus chain Y Focus chain YA [auth y] Focus chain YB [auth OA] Focus chain Z Focus chain ZA [auth z] Focus chain ZB [auth PA] Interactions & Density Focus chain AA [auth a] Focus chain AB [auth 0] Focus chain BA [auth b] Focus chain BB [auth 1] Focus chain CA [auth c] Focus chain CB [auth 2] Focus chain DA [auth d] Focus chain DB [auth 3] Focus chain EA [auth e] Focus chain EB [auth 4] Focus chain FA [auth f] Focus chain FB [auth 5] Focus chain G Focus chain GA [auth g] Focus chain H Focus chain HA [auth h] Focus chain HB [auth 7] Focus chain I Focus chain IB [auth 8] Focus chain J Focus chain JA [auth j] Focus chain JB [auth 9] Focus chain KA [auth k] Focus chain KB [auth AA] Focus chain L Focus chain LA [auth l] Focus chain LB [auth BA] Focus chain M Focus chain MA [auth m] Focus chain MB [auth CA] Focus chain N Focus chain NA [auth n] Focus chain NB [auth DA] Focus chain O Focus chain OA [auth o] Focus chain OB [auth EA] Focus chain P Focus chain PA [auth p] Focus chain PB [auth FA] Focus chain Q Focus chain QA [auth q] Focus chain QB [auth GA] Focus chain R Focus chain RA [auth r] Focus chain RB [auth HA] Focus chain S Focus chain SA [auth s] Focus chain T Focus chain TA [auth t] Focus chain TB [auth JA] Focus chain U Focus chain UB [auth KA] Focus chain V Focus chain VA [auth v] Focus chain VB [auth LA] Focus chain WA [auth w] Focus chain WB [auth MA] Focus chain X Focus chain XA [auth x] Focus chain XB [auth NA] Focus chain Y Focus chain YA [auth y] Focus chain YB [auth OA] Focus chain Z Focus chain ZA [auth z] Focus chain ZB [auth PA]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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	GB [auth 6], IA [auth i], K, SB [auth IA], UA [auth u], GB [auth 6], IA [auth i], K, SB [auth IA], UA [auth u], W	3		N-Glycosylation	Interactions Focus chain GB [auth 6] Focus chain IA [auth i] Focus chain K Focus chain SB [auth IA] Focus chain UA [auth u] Focus chain W Interactions & Density Focus chain GB [auth 6] Focus chain IA [auth i] Focus chain K Focus chain SB [auth IA] Focus chain UA [auth u] Focus chain W
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain AC [auth A] SDF format, chain BC [auth A] SDF format, chain CC [auth A] SDF format, chain DC [auth A] SDF format, chain EC [auth B] SDF format, chain FC [auth B] SDF format, chain GC [auth B] SDF format, chain HC [auth B] SDF format, chain IC [auth C] SDF format, chain JC [auth C] SDF format, chain KC [auth C] SDF format, chain LC [auth C] SDF format, chain MC [auth D] SDF format, chain NC [auth D] SDF format, chain OC [auth D] SDF format, chain PC [auth D] SDF format, chain QC [auth E] SDF format, chain RC [auth E] SDF format, chain SC [auth E] SDF format, chain TC [auth E] SDF format, chain UC [auth F] SDF format, chain VC [auth F] SDF format, chain WC [auth F] SDF format, chain XC [auth F] MOL2 format, chain AC [auth A] MOL2 format, chain BC [auth A] MOL2 format, chain CC [auth A] MOL2 format, chain DC [auth A] MOL2 format, chain EC [auth B] MOL2 format, chain FC [auth B] MOL2 format, chain GC [auth B] MOL2 format, chain HC [auth B] MOL2 format, chain IC [auth C] MOL2 format, chain JC [auth C] MOL2 format, chain KC [auth C] MOL2 format, chain LC [auth C] MOL2 format, chain MC [auth D] MOL2 format, chain NC [auth D] MOL2 format, chain OC [auth D] MOL2 format, chain PC [auth D] MOL2 format, chain QC [auth E] MOL2 format, chain RC [auth E] MOL2 format, chain SC [auth E] MOL2 format, chain TC [auth E] MOL2 format, chain UC [auth F] MOL2 format, chain VC [auth F] MOL2 format, chain WC [auth F] MOL2 format, chain XC [auth F] mmCIF format, chain AC [auth A] mmCIF format, chain BC [auth A] mmCIF format, chain CC [auth A] mmCIF format, chain DC [auth A] mmCIF format, chain EC [auth B] mmCIF format, chain FC [auth B] mmCIF format, chain GC [auth B] mmCIF format, chain HC [auth B] mmCIF format, chain IC [auth C] mmCIF format, chain JC [auth C] mmCIF format, chain KC [auth C] mmCIF format, chain LC [auth C] mmCIF format, chain MC [auth D] mmCIF format, chain NC [auth D] mmCIF format, chain OC [auth D] mmCIF format, chain PC [auth D] mmCIF format, chain QC [auth E] mmCIF format, chain RC [auth E] mmCIF format, chain SC [auth E] mmCIF format, chain TC [auth E] mmCIF format, chain UC [auth F] mmCIF format, chain VC [auth F] mmCIF format, chain WC [auth F] mmCIF format, chain XC [auth F]	AC [auth A] BC [auth A] CC [auth A] DC [auth A] EC [auth B] AC [auth A], BC [auth A], CC [auth A], DC [auth A], EC [auth B], FC [auth B], GC [auth B], HC [auth B], IC [auth C], JC [auth C], KC [auth C], LC [auth C], MC [auth D], NC [auth D], OC [auth D], PC [auth D], QC [auth E], RC [auth E], SC [auth E], TC [auth E], UC [auth F], VC [auth F], WC [auth F], XC [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AC [auth A] Focus chain BC [auth A] Focus chain CC [auth A] Focus chain DC [auth A] Focus chain EC [auth B] Focus chain FC [auth B] Focus chain GC [auth B] Focus chain HC [auth B] Focus chain IC [auth C] Focus chain JC [auth C] Focus chain KC [auth C] Focus chain LC [auth C] Focus chain MC [auth D] Focus chain NC [auth D] Focus chain OC [auth D] Focus chain PC [auth D] Focus chain QC [auth E] Focus chain RC [auth E] Focus chain SC [auth E] Focus chain TC [auth E] Focus chain UC [auth F] Focus chain VC [auth F] Focus chain WC [auth F] Focus chain XC [auth F] Interactions & Density Focus chain AC [auth A] Focus chain BC [auth A] Focus chain CC [auth A] Focus chain DC [auth A] Focus chain EC [auth B] Focus chain FC [auth B] Focus chain GC [auth B] Focus chain HC [auth B] Focus chain IC [auth C] Focus chain JC [auth C] Focus chain KC [auth C] Focus chain LC [auth C] Focus chain MC [auth D] Focus chain NC [auth D] Focus chain OC [auth D] Focus chain PC [auth D] Focus chain QC [auth E] Focus chain RC [auth E] Focus chain SC [auth E] Focus chain TC [auth E] Focus chain UC [auth F] Focus chain VC [auth F] Focus chain WC [auth F] Focus chain XC [auth F]

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	cryoSPARC

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-10-06

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	109-3114-Y-001-001
Academia Sinica (Taiwan)	Taiwan	AS-CDA-109-L08
Academia Sinica (Taiwan)	Taiwan	AS-CFII-108-110
Academia Sinica (Taiwan)	Taiwan	AS-CFII108-111