8G70

SARS-CoV-2 spike/nanobody mixture complex

PDB DOI: https://doi.org/10.2210/pdb8G70/pdb
EM Map EMD-29792: EMDB EMDataResource

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Severe acute respiratory syndrome coronavirus 2, Vicugna pacos
Expression System: Homo sapiens, Escherichia coli
Mutation(s): No

Deposited: 2023-02-16 Released: 2024-02-21
Deposition Author(s): Ye, G., Bu, F., Liu, B., Li, F.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.40 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

SARS-CoV-2 spike/nanobody mixture complex

Ye, G., Bu, F., Pan, R., Wen, W., Mendoza, A., Spiller, B., Du, L., Perlman, S., Liu, B., Li, F.

To be published.

Macromolecule Content

Total Structure Weight: 563.7 kDa
Atom Count: 34,437
Modelled Residue Count: 4,307
Deposited Residue Count: 4,962
Unique protein chains: 5

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 [auth D]	1,234	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 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: 19	Glycosylation Focus chain A Focus chain B Focus chain C [auth D]	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanosota-5	D [auth E], E [auth H], F [auth I]	137	Vicugna pacos	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanosota-6	G, H [auth F], I [auth K]	141	Vicugna pacos	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanosota-4	J [auth N]	150	Vicugna pacos	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: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanosota-3	K [auth O], L [auth M]	138	Vicugna pacos	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	M [auth P], N [auth C], O [auth J], P [auth L], Q, M [auth P], N [auth C], O [auth J], P [auth L], Q, R, S, T, U, V, W, X	2		N-Glycosylation	Interactions Focus chain M [auth P] Focus chain N [auth C] Focus chain O [auth J] Focus chain P [auth L] Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W Focus chain X Interactions & Density Focus chain M [auth P] Focus chain N [auth C] Focus chain O [auth J] Focus chain P [auth L] Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W Focus chain X
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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 AA [auth A] SDF format, chain AB [auth B] SDF format, chain BA [auth A] SDF format, chain BB [auth B] SDF format, chain CA [auth A] SDF format, chain CB [auth D] SDF format, chain DA [auth A] SDF format, chain DB [auth D] SDF format, chain EA [auth A] SDF format, chain EB [auth D] SDF format, chain FA [auth A] SDF format, chain FB [auth D] SDF format, chain GA [auth A] SDF format, chain GB [auth D] SDF format, chain HA [auth A] SDF format, chain HB [auth D] SDF format, chain IA [auth A] SDF format, chain IB [auth D] SDF format, chain JA [auth A] SDF format, chain JB [auth D] SDF format, chain KA [auth A] SDF format, chain KB [auth D] SDF format, chain LA [auth A] SDF format, chain LB [auth D] SDF format, chain MA [auth B] SDF format, chain MB [auth D] SDF format, chain NA [auth B] SDF format, chain NB [auth D] SDF format, chain OA [auth B] SDF format, chain OB [auth D] SDF format, chain PA [auth B] SDF format, chain PB [auth D] SDF format, chain QA [auth B] SDF format, chain QB [auth D] SDF format, chain RA [auth B] SDF format, chain SA [auth B] SDF format, chain TA [auth B] SDF format, chain UA [auth B] SDF format, chain VA [auth B] SDF format, chain WA [auth B] SDF format, chain XA [auth B] SDF format, chain Y [auth A] SDF format, chain YA [auth B] SDF format, chain Z [auth A] SDF format, chain ZA [auth B] MOL2 format, chain AA [auth A] MOL2 format, chain AB [auth B] MOL2 format, chain BA [auth A] MOL2 format, chain BB [auth B] MOL2 format, chain CA [auth A] MOL2 format, chain CB [auth D] MOL2 format, chain DA [auth A] MOL2 format, chain DB [auth D] MOL2 format, chain EA [auth A] MOL2 format, chain EB [auth D] MOL2 format, chain FA [auth A] MOL2 format, chain FB [auth D] MOL2 format, chain GA [auth A] MOL2 format, chain GB [auth D] MOL2 format, chain HA [auth A] MOL2 format, chain HB [auth D] MOL2 format, chain IA [auth A] MOL2 format, chain IB [auth D] MOL2 format, chain JA [auth A] MOL2 format, chain JB [auth D] MOL2 format, chain KA [auth A] MOL2 format, chain KB [auth D] MOL2 format, chain LA [auth A] MOL2 format, chain LB [auth D] MOL2 format, chain MA [auth B] MOL2 format, chain MB [auth D] MOL2 format, chain NA [auth B] MOL2 format, chain NB [auth D] MOL2 format, chain OA [auth B] MOL2 format, chain OB [auth D] MOL2 format, chain PA [auth B] MOL2 format, chain PB [auth D] MOL2 format, chain QA [auth B] MOL2 format, chain QB [auth D] MOL2 format, chain RA [auth B] MOL2 format, chain SA [auth B] MOL2 format, chain TA [auth B] MOL2 format, chain UA [auth B] MOL2 format, chain VA [auth B] MOL2 format, chain WA [auth B] MOL2 format, chain XA [auth B] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth B] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth B] mmCIF format, chain AA [auth A] mmCIF format, chain AB [auth B] mmCIF format, chain BA [auth A] mmCIF format, chain BB [auth B] mmCIF format, chain CA [auth A] mmCIF format, chain CB [auth D] mmCIF format, chain DA [auth A] mmCIF format, chain DB [auth D] mmCIF format, chain EA [auth A] mmCIF format, chain EB [auth D] mmCIF format, chain FA [auth A] mmCIF format, chain FB [auth D] mmCIF format, chain GA [auth A] mmCIF format, chain GB [auth D] mmCIF format, chain HA [auth A] mmCIF format, chain HB [auth D] mmCIF format, chain IA [auth A] mmCIF format, chain IB [auth D] mmCIF format, chain JA [auth A] mmCIF format, chain JB [auth D] mmCIF format, chain KA [auth A] mmCIF format, chain KB [auth D] mmCIF format, chain LA [auth A] mmCIF format, chain LB [auth D] mmCIF format, chain MA [auth B] mmCIF format, chain MB [auth D] mmCIF format, chain NA [auth B] mmCIF format, chain NB [auth D] mmCIF format, chain OA [auth B] mmCIF format, chain OB [auth D] mmCIF format, chain PA [auth B] mmCIF format, chain PB [auth D] mmCIF format, chain QA [auth B] mmCIF format, chain QB [auth D] mmCIF format, chain RA [auth B] mmCIF format, chain SA [auth B] mmCIF format, chain TA [auth B] mmCIF format, chain UA [auth B] mmCIF format, chain VA [auth B] mmCIF format, chain WA [auth B] mmCIF format, chain XA [auth B] mmCIF format, chain Y [auth A] mmCIF format, chain YA [auth B] mmCIF format, chain Z [auth A] mmCIF format, chain ZA [auth B]	AA [auth A] AB [auth B] BA [auth A] BB [auth B] CA [auth A] AA [auth A], AB [auth B], BA [auth A], BB [auth B], 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], IB [auth D], JA [auth A], JB [auth D], KA [auth A], KB [auth D], LA [auth A], LB [auth D], MA [auth B], MB [auth D], NA [auth B], NB [auth D], OA [auth B], OB [auth D], PA [auth B], PB [auth D], QA [auth B], QB [auth D], RA [auth B], SA [auth B], TA [auth B], UA [auth B], VA [auth B], WA [auth B], XA [auth B], Y [auth A], YA [auth B], Z [auth A], ZA [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth A] Focus chain AB [auth B] Focus chain BA [auth A] Focus chain BB [auth B] 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 IB [auth D] Focus chain JA [auth A] Focus chain JB [auth D] Focus chain KA [auth A] Focus chain KB [auth D] Focus chain LA [auth A] Focus chain LB [auth D] Focus chain MA [auth B] Focus chain MB [auth D] Focus chain NA [auth B] Focus chain NB [auth D] Focus chain OA [auth B] Focus chain OB [auth D] Focus chain PA [auth B] Focus chain PB [auth D] Focus chain QA [auth B] Focus chain QB [auth D] 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 B] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain Z [auth A] Focus chain ZA [auth B] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth B] Focus chain BA [auth A] Focus chain BB [auth B] 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 IB [auth D] Focus chain JA [auth A] Focus chain JB [auth D] Focus chain KA [auth A] Focus chain KB [auth D] Focus chain LA [auth A] Focus chain LB [auth D] Focus chain MA [auth B] Focus chain MB [auth D] Focus chain NA [auth B] Focus chain NB [auth D] Focus chain OA [auth B] Focus chain OB [auth D] Focus chain PA [auth B] Focus chain PB [auth D] Focus chain QA [auth B] Focus chain QB [auth D] 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 B] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain Z [auth A] Focus chain ZA [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-02-21

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI089728
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI110700