8Z4X | pdb_00008z4x

Cryo-EM structure of SARS-CoV-2 D614G S with two ACE2 receptors binding (RB2) in prefusion conformation

PDB DOI: https://doi.org/10.2210/pdb8Z4X/pdb
EM Map EMD-39771: EMDB EMDataResource

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

Deposited: 2024-04-17 Released: 2025-02-05
Deposition Author(s): Liu, Z., Xing, L.
Funding Organization(s): Ministry of Science and Technology (MoST, China), National Science Foundation (NSF, China), National Key R&D Program of China, Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences, Major Project of Guangzhou National Laboratory, R&D Program of Guangzhou Laboratory, Shanghai Municipal Science and Technology Major Project

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 1.0 of the entry. See complete history.

Literature

Cryo-EM structure of SARS-CoV-2 D614G S with two ACE2 receptors binding (RB2) in prefusion conformation

Liu, Z., Xing, L.

To be published.

Macromolecule Content

Total Structure Weight: 591.01 kDa
Atom Count: 36,081
Modelled Residue Count: 4,418
Deposited Residue Count: 5,126
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A [auth C], D [auth B], E [auth A]	1,288	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1 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: 17	Glycosylation Focus chain A [auth C] Focus chain D [auth B] Focus chain E [auth A]	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Angiotensin-converting enzyme 2	B [auth E], C [auth D]	631	Homo sapiens	Mutation(s): 0 Gene Names: ACE2, UNQ868/PRO1885 EC: 3.4.17.23 (PDB Primary Data), 3.4.17 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYF1 (Homo sapiens) Explore Q9BYF1 Go to UniProtKB: Q9BYF1
PHAROS: Q9BYF1 GTEx: ENSG00000130234
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9BYF1
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain B [auth E] Focus chain C [auth D]	Go to GlyGen: Q9BYF1-1
Sequence Annotations Expand
Reference Sequence LOADING

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	BA [auth b], F, G, H, I, BA [auth b], F, G, H, I, L, M, N, O, P, Q, S, T, U, V, X, Y, Z	2		N-Glycosylation	Interactions Focus chain BA [auth b] Focus chain F Focus chain G Focus chain H Focus chain I Focus chain L Focus chain M Focus chain N Focus chain O Focus chain P Focus chain Q Focus chain S Focus chain T Focus chain U Focus chain V Focus chain X Focus chain Y Focus chain Z Interactions & Density Focus chain BA [auth b] Focus chain F Focus chain G Focus chain H Focus chain I Focus chain L Focus chain M Focus chain N Focus chain O Focus chain P Focus chain Q Focus chain S Focus chain T Focus chain U Focus chain V Focus chain X Focus chain Y Focus chain Z
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
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	AA [auth a], J, K, R, W	3		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain J Focus chain K Focus chain R Focus chain W Interactions & Density Focus chain AA [auth a] Focus chain J Focus chain K Focus chain R 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 Query on NAG Download Ideal Coordinates CCD File SDF format, chain AB [auth A] SDF format, chain BB [auth A] SDF format, chain CA [auth C] SDF format, chain CB [auth A] SDF format, chain DA [auth C] SDF format, chain DB [auth A] SDF format, chain EA [auth C] SDF format, chain EB [auth A] SDF format, chain FA [auth C] SDF format, chain FB [auth A] SDF format, chain GA [auth C] SDF format, chain GB [auth A] SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain JA [auth C] SDF format, chain KA [auth C] SDF format, chain LA [auth E] SDF format, chain MA [auth E] SDF format, chain NA [auth D] SDF format, chain OA [auth B] SDF format, chain PA [auth B] SDF format, chain QA [auth B] 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 A] SDF format, chain YA [auth A] SDF format, chain ZA [auth A] MOL2 format, chain AB [auth A] MOL2 format, chain BB [auth A] MOL2 format, chain CA [auth C] MOL2 format, chain CB [auth A] MOL2 format, chain DA [auth C] MOL2 format, chain DB [auth A] MOL2 format, chain EA [auth C] MOL2 format, chain EB [auth A] MOL2 format, chain FA [auth C] MOL2 format, chain FB [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain GB [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain LA [auth E] MOL2 format, chain MA [auth E] MOL2 format, chain NA [auth D] MOL2 format, chain OA [auth B] MOL2 format, chain PA [auth B] MOL2 format, chain QA [auth B] 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 A] MOL2 format, chain YA [auth A] MOL2 format, chain ZA [auth A] mmCIF format, chain AB [auth A] mmCIF format, chain BB [auth A] mmCIF format, chain CA [auth C] mmCIF format, chain CB [auth A] mmCIF format, chain DA [auth C] mmCIF format, chain DB [auth A] mmCIF format, chain EA [auth C] mmCIF format, chain EB [auth A] mmCIF format, chain FA [auth C] mmCIF format, chain FB [auth A] mmCIF format, chain GA [auth C] mmCIF format, chain GB [auth A] mmCIF format, chain HA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain JA [auth C] mmCIF format, chain KA [auth C] mmCIF format, chain LA [auth E] mmCIF format, chain MA [auth E] mmCIF format, chain NA [auth D] mmCIF format, chain OA [auth B] mmCIF format, chain PA [auth B] mmCIF format, chain QA [auth B] 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 A] mmCIF format, chain YA [auth A] mmCIF format, chain ZA [auth A]	AB [auth A] BB [auth A] CA [auth C] CB [auth A] DA [auth C] AB [auth A], BB [auth A], CA [auth C], CB [auth A], DA [auth C], DB [auth A], EA [auth C], EB [auth A], FA [auth C], FB [auth A], GA [auth C], GB [auth A], HA [auth C], IA [auth C], JA [auth C], KA [auth C], LA [auth E], MA [auth E], NA [auth D], 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 A], YA [auth A], ZA [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth A] Focus chain BB [auth A] Focus chain CA [auth C] Focus chain CB [auth A] Focus chain DA [auth C] Focus chain DB [auth A] Focus chain EA [auth C] Focus chain EB [auth A] Focus chain FA [auth C] Focus chain FB [auth A] Focus chain GA [auth C] Focus chain GB [auth A] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth E] Focus chain MA [auth E] Focus chain NA [auth D] 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 A] Focus chain YA [auth A] Focus chain ZA [auth A] Interactions & Density Focus chain AB [auth A] Focus chain BB [auth A] Focus chain CA [auth C] Focus chain CB [auth A] Focus chain DA [auth C] Focus chain DB [auth A] Focus chain EA [auth C] Focus chain EB [auth A] Focus chain FA [auth C] Focus chain FB [auth A] Focus chain GA [auth C] Focus chain GB [auth A] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth E] Focus chain MA [auth E] Focus chain NA [auth D] 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 A] Focus chain YA [auth A] Focus chain ZA [auth A]

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: 2025-02-05

Deposition Author(s):

Liu, Z.

Xing, L.

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2021YFC2302500
National Science Foundation (NSF, China)	China	82394463; 92169112; 82341036
National Key R&D Program of China	China	2022YFC2604100; 2021YFC2300703; 2023YFC2307800
Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences	China	2023-PT310-02
Major Project of Guangzhou National Laboratory	China	GZNL2023A01008; GZNL2024A01008
R&D Program of Guangzhou Laboratory	China	SRPG22-003
Shanghai Municipal Science and Technology Major Project	China	ZD2021CY001