7SOB

SARS-CoV-2 S B.1.617.1 kappa variant + S309 + S2L20 Global Refinement

PDB DOI: 10.2210/pdb7SOB/pdb
EM Map EMD-25265: EMDB EMDataResource

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

Deposited: 2021-10-29 Released: 2021-11-17
Deposition Author(s): McCallum, M., Veesler, D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Molecular basis of immune evasion by the Delta and Kappa SARS-CoV-2 variants.

McCallum, M., Walls, A.C., Sprouse, K.R., Bowen, J.E., Rosen, L.E., Dang, H.V., De Marco, A., Franko, N., Tilles, S.W., Logue, J., Miranda, M.C., Ahlrichs, M., Carter, L., Snell, G., Pizzuto, M.S., Chu, H.Y., Van Voorhis, W.C., Corti, D., Veesler, D.

(2021) Science 374: 1621-1626

PubMed: 34751595 Search on PubMed
DOI: 10.1126/science.abl8506
Primary Citation of Related Structures:
7SO9, 7SOA, 7SOB, 7SOC, 7SOD, 7SOE, 7SOF

PubMed Abstract:

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, F [auth D], K	1277	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 16 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
Protein Feature View Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
S2L20 Fab light chain	B, G [auth E], L	107	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
S2L20 Fab heavy chain	C, H [auth F], M	121	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
S309 Fab heavy chain	D [auth G], I [auth H], N	128	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
S309 Fab light chain	E [auth I], J, O	100	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View Expand
Reference Sequence

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 AA [auth A] SDF format, chain AB [auth K] SDF format, chain BA [auth A] SDF format, chain BB [auth K] SDF format, chain CA [auth A] SDF format, chain CB [auth K] SDF format, chain DA [auth A] SDF format, chain DB [auth K] SDF format, chain EA [auth A] SDF format, chain EB [auth K] SDF format, chain FA [auth A] SDF format, chain FB [auth K] SDF format, chain GA [auth D] SDF format, chain GB [auth K] SDF format, chain HA [auth D] SDF format, chain HB [auth K] SDF format, chain IA [auth D] SDF format, chain IB [auth K] SDF format, chain JA [auth D] SDF format, chain JB [auth K] SDF format, chain KA [auth D] SDF format, chain KB [auth K] SDF format, chain LA [auth D] SDF format, chain LB [auth K] SDF format, chain MA [auth D] SDF format, chain MB [auth K] SDF format, chain NA [auth D] SDF format, chain NB [auth K] SDF format, chain OA [auth D] SDF format, chain P [auth A] SDF format, chain PA [auth D] SDF format, chain Q [auth A] SDF format, chain QA [auth D] SDF format, chain R [auth A] SDF format, chain RA [auth D] SDF format, chain S [auth A] SDF format, chain SA [auth D] SDF format, chain T [auth A] SDF format, chain TA [auth D] SDF format, chain U [auth A] SDF format, chain UA [auth D] SDF format, chain V [auth A] SDF format, chain VA [auth D] SDF format, chain W [auth A] SDF format, chain WA [auth D] SDF format, chain X [auth A] SDF format, chain XA [auth K] SDF format, chain Y [auth A] SDF format, chain YA [auth K] SDF format, chain Z [auth A] SDF format, chain ZA [auth K] MOL2 format, chain AA [auth A] MOL2 format, chain AB [auth K] MOL2 format, chain BA [auth A] MOL2 format, chain BB [auth K] MOL2 format, chain CA [auth A] MOL2 format, chain CB [auth K] MOL2 format, chain DA [auth A] MOL2 format, chain DB [auth K] MOL2 format, chain EA [auth A] MOL2 format, chain EB [auth K] MOL2 format, chain FA [auth A] MOL2 format, chain FB [auth K] MOL2 format, chain GA [auth D] MOL2 format, chain GB [auth K] MOL2 format, chain HA [auth D] MOL2 format, chain HB [auth K] MOL2 format, chain IA [auth D] MOL2 format, chain IB [auth K] MOL2 format, chain JA [auth D] MOL2 format, chain JB [auth K] MOL2 format, chain KA [auth D] MOL2 format, chain KB [auth K] MOL2 format, chain LA [auth D] MOL2 format, chain LB [auth K] MOL2 format, chain MA [auth D] MOL2 format, chain MB [auth K] MOL2 format, chain NA [auth D] MOL2 format, chain NB [auth K] MOL2 format, chain OA [auth D] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth D] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth D] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth D] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth D] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth D] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth D] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth D] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth K] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth K] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth K]	AA [auth A], AB [auth K], BA [auth A], BB [auth K], CA [auth A], AA [auth A], AB [auth K], BA [auth A], BB [auth K], CA [auth A], CB [auth K], DA [auth A], DB [auth K], EA [auth A], EB [auth K], FA [auth A], FB [auth K], GA [auth D], GB [auth K], HA [auth D], HB [auth K], IA [auth D], IB [auth K], JA [auth D], JB [auth K], KA [auth D], KB [auth K], LA [auth D], LB [auth K], MA [auth D], MB [auth K], NA [auth D], NB [auth K], OA [auth D], P [auth A], PA [auth D], Q [auth A], QA [auth D], R [auth A], RA [auth D], S [auth A], SA [auth D], T [auth A], TA [auth D], U [auth A], UA [auth D], V [auth A], VA [auth D], W [auth A], WA [auth D], X [auth A], XA [auth K], Y [auth A], YA [auth K], Z [auth A], ZA [auth K]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Ligand Interaction