7Y0N | pdb_00007y0n

SARS-CoV-2 WT Spike in complex with R15 Fab and P14 Nanobody

PDB DOI: https://doi.org/10.2210/pdb7Y0N/pdb
EM Map EMD-33550: EMDB EMDataResource

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

Deposited: 2022-06-05 Released: 2023-09-13
Deposition Author(s): Wang, L.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

SARS-CoV-2 WT Spike in complex with R15 Fab and P14 Nanobody

Wang, L.

To be published.

Macromolecule Content

Total Structure Weight: 508.22 kDa
Atom Count: 31,989
Modeled Residue Count: 4,047
Deposited Residue Count: 4,482
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, D	1,147	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2 Go to UniProtKB: P0DTC2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTC2
Glycosylation
Glycosylation Sites: 16	Glycosylation Focus chain A Focus chain B Focus chain D	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of R15-F7	C, E, F	116	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
P14 Nanobody	G, H, I	123	Vicugna pacos	Mutation(s): 0

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of R15-F7	J, K, L	108	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a], M, N, O, P, AA [auth a], M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain M Focus chain N Focus chain O Focus chain 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 M Focus chain N Focus chain O Focus chain 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 ZA [auth D] SDF format, chain YA [auth D] SDF format, chain XA [auth D] SDF format, chain WA [auth B] SDF format, chain VA [auth B] SDF format, chain UA [auth B] SDF format, chain TA [auth B] SDF format, chain SA [auth B] SDF format, chain RA [auth B] SDF format, chain QA [auth B] SDF format, chain PA [auth B] SDF format, chain OA [auth B] SDF format, chain NA [auth B] SDF format, chain MA [auth B] SDF format, chain LA [auth A] SDF format, chain KA [auth A] SDF format, chain JA [auth A] SDF format, chain IA [auth A] SDF format, chain HB [auth D] SDF format, chain HA [auth A] SDF format, chain GB [auth D] SDF format, chain GA [auth A] SDF format, chain FB [auth D] SDF format, chain FA [auth A] SDF format, chain EB [auth D] SDF format, chain EA [auth A] SDF format, chain DB [auth D] SDF format, chain DA [auth A] SDF format, chain CB [auth D] SDF format, chain CA [auth A] SDF format, chain BB [auth D] SDF format, chain BA [auth A] SDF format, chain AB [auth D] MOL2 format, chain ZA [auth D] MOL2 format, chain YA [auth D] MOL2 format, chain XA [auth D] MOL2 format, chain WA [auth B] MOL2 format, chain VA [auth B] MOL2 format, chain UA [auth B] MOL2 format, chain TA [auth B] MOL2 format, chain SA [auth B] MOL2 format, chain RA [auth B] MOL2 format, chain QA [auth B] MOL2 format, chain PA [auth B] MOL2 format, chain OA [auth B] MOL2 format, chain NA [auth B] MOL2 format, chain MA [auth B] MOL2 format, chain LA [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain HB [auth D] MOL2 format, chain HA [auth A] MOL2 format, chain GB [auth D] MOL2 format, chain GA [auth A] MOL2 format, chain FB [auth D] MOL2 format, chain FA [auth A] MOL2 format, chain EB [auth D] MOL2 format, chain EA [auth A] MOL2 format, chain DB [auth D] MOL2 format, chain DA [auth A] MOL2 format, chain CB [auth D] MOL2 format, chain CA [auth A] MOL2 format, chain BB [auth D] MOL2 format, chain BA [auth A] MOL2 format, chain AB [auth D] mmCIF format, chain ZA [auth D] mmCIF format, chain YA [auth D] mmCIF format, chain XA [auth D] mmCIF format, chain WA [auth B] mmCIF format, chain VA [auth B] mmCIF format, chain UA [auth B] mmCIF format, chain TA [auth B] mmCIF format, chain SA [auth B] mmCIF format, chain RA [auth B] mmCIF format, chain QA [auth B] mmCIF format, chain PA [auth B] mmCIF format, chain OA [auth B] mmCIF format, chain NA [auth B] mmCIF format, chain MA [auth B] mmCIF format, chain LA [auth A] mmCIF format, chain KA [auth A] mmCIF format, chain JA [auth A] mmCIF format, chain IA [auth A] mmCIF format, chain HB [auth D] mmCIF format, chain HA [auth A] mmCIF format, chain GB [auth D] mmCIF format, chain GA [auth A] mmCIF format, chain FB [auth D] mmCIF format, chain FA [auth A] mmCIF format, chain EB [auth D] mmCIF format, chain EA [auth A] mmCIF format, chain DB [auth D] mmCIF format, chain DA [auth A] mmCIF format, chain CB [auth D] mmCIF format, chain CA [auth A] mmCIF format, chain BB [auth D] mmCIF format, chain BA [auth A] mmCIF format, chain AB [auth D]	AB [auth D] BA [auth A] BB [auth D] CA [auth A] CB [auth D] AB [auth D], BA [auth A], BB [auth D], CA [auth A], CB [auth D], DA [auth A], DB [auth D], EA [auth A], EB [auth D], FA [auth A], FB [auth D], GA [auth A], GB [auth D], HA [auth A], HB [auth D], IA [auth A], JA [auth A], KA [auth A], LA [auth A], MA [auth B], NA [auth B], OA [auth B], PA [auth B], QA [auth B], RA [auth B], SA [auth B], TA [auth B], UA [auth B], VA [auth B], WA [auth B], XA [auth D], YA [auth D], ZA [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth D] Focus chain BA [auth A] Focus chain BB [auth D] Focus chain CA [auth A] Focus chain CB [auth D] Focus chain DA [auth A] Focus chain DB [auth D] Focus chain EA [auth A] Focus chain EB [auth D] Focus chain FA [auth A] Focus chain FB [auth D] Focus chain GA [auth A] Focus chain GB [auth D] Focus chain HA [auth A] Focus chain HB [auth D] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain WA [auth B] Focus chain XA [auth D] Focus chain YA [auth D] Focus chain ZA [auth D] Interactions & Density Focus chain AB [auth D] Focus chain BA [auth A] Focus chain BB [auth D] Focus chain CA [auth A] Focus chain CB [auth D] Focus chain DA [auth A] Focus chain DB [auth D] Focus chain EA [auth A] Focus chain EB [auth D] Focus chain FA [auth A] Focus chain FB [auth D] Focus chain GA [auth A] Focus chain GB [auth D] Focus chain HA [auth A] Focus chain HB [auth D] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain WA [auth B] Focus chain XA [auth D] Focus chain YA [auth D] Focus chain ZA [auth D]