8Z3W | pdb_00008z3w

Cryo-EM structure of SARS-CoV-2 D614G S with one ACE2 receptor binding (RB1) in prefusion conformation

PDB DOI: https://doi.org/10.2210/pdb8Z3W/pdb
EM Map EMD-39756: EMDB EMDataResource

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

Deposited: 2024-04-16 Released: 2025-02-05
Deposition Author(s): Liu, Z., Xing, L.
Funding Organization(s): Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC), Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences, National Key R&D Program of China, 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: 3.45 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 one ACE2 receptor binding (RB1) in prefusion conformation

Liu, Z., Xing, L.

To be published.

Macromolecule Content

Total Structure Weight: 515.92 kDa
Atom Count: 30,949
Modelled Residue Count: 3,803
Deposited Residue Count: 4,495
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], B, C [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: 16	Glycosylation Focus chain A [auth C] Focus chain B Focus chain C [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	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
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	E, F, G, H, I E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y	2		N-Glycosylation	Interactions Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L 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 Interactions & Density Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L 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
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 AA [auth C] SDF format, chain BA [auth C] SDF format, chain BB [auth A] SDF format, chain CA [auth C] SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain IA [auth B] SDF format, chain JA [auth B] SDF format, chain KA [auth B] SDF format, chain MA [auth B] SDF format, chain NA [auth B] SDF format, chain PA [auth B] SDF format, chain QA [auth B] SDF format, chain RA [auth B] SDF format, chain TA [auth A] SDF format, chain UA [auth A] SDF format, chain VA [auth A] SDF format, chain WA [auth A] SDF format, chain YA [auth A] SDF format, chain Z [auth C] SDF format, chain ZA [auth A] SDF format, chain AB [auth A] SDF format, chain DA [auth C] SDF format, chain LA [auth B] SDF format, chain OA [auth B] SDF format, chain SA [auth A] SDF format, chain XA [auth A] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain BB [auth A] MOL2 format, chain CA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain MA [auth B] MOL2 format, chain NA [auth B] MOL2 format, chain PA [auth B] MOL2 format, chain QA [auth B] MOL2 format, chain RA [auth B] MOL2 format, chain TA [auth A] MOL2 format, chain UA [auth A] MOL2 format, chain VA [auth A] MOL2 format, chain WA [auth A] MOL2 format, chain YA [auth A] MOL2 format, chain Z [auth C] MOL2 format, chain ZA [auth A] MOL2 format, chain AB [auth A] MOL2 format, chain DA [auth C] MOL2 format, chain LA [auth B] MOL2 format, chain OA [auth B] MOL2 format, chain SA [auth A] MOL2 format, chain XA [auth A] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain BB [auth A] mmCIF format, chain CA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain IA [auth B] mmCIF format, chain JA [auth B] mmCIF format, chain KA [auth B] mmCIF format, chain MA [auth B] mmCIF format, chain NA [auth B] mmCIF format, chain PA [auth B] mmCIF format, chain QA [auth B] mmCIF format, chain RA [auth B] mmCIF format, chain TA [auth A] mmCIF format, chain UA [auth A] mmCIF format, chain VA [auth A] mmCIF format, chain WA [auth A] mmCIF format, chain YA [auth A] mmCIF format, chain Z [auth C] mmCIF format, chain ZA [auth A] mmCIF format, chain AB [auth A] mmCIF format, chain DA [auth C] mmCIF format, chain LA [auth B] mmCIF format, chain OA [auth B] mmCIF format, chain SA [auth A] mmCIF format, chain XA [auth A]	AA [auth C] AB [auth A] BA [auth C] BB [auth A] CA [auth C] AA [auth C], AB [auth A], BA [auth C], BB [auth A], CA [auth C], DA [auth C], EA [auth C], FA [auth C], GA [auth C], HA [auth C], IA [auth B], JA [auth B], KA [auth B], LA [auth B], MA [auth B], NA [auth B], OA [auth B], PA [auth B], QA [auth B], RA [auth B], SA [auth A], TA [auth A], UA [auth A], VA [auth A], WA [auth A], XA [auth A], YA [auth A], Z [auth C], ZA [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth C] Focus chain AB [auth A] Focus chain BA [auth C] Focus chain BB [auth A] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] 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 A] Focus chain TA [auth A] Focus chain UA [auth A] Focus chain VA [auth A] Focus chain WA [auth A] Focus chain XA [auth A] Focus chain YA [auth A] Focus chain Z [auth C] Focus chain ZA [auth A] Interactions & Density Focus chain AA [auth C] Focus chain AB [auth A] Focus chain BA [auth C] Focus chain BB [auth A] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] 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 A] Focus chain TA [auth A] Focus chain UA [auth A] Focus chain VA [auth A] Focus chain WA [auth A] Focus chain XA [auth A] Focus chain YA [auth A] Focus chain Z [auth C] Focus chain ZA [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.45 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 Natural Science Foundation of China (NSFC)	China	82394463; 92169112; 82341036
Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences	China	2023-PT310-02
National Key R&D Program of China	China	2022YFC2604100; 2021YFC2300703; 2023YFC2307800
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