8Z7P | pdb_00008z7p

Cryo-EM structure of SARS-CoV-2 S trimer in the early fusion intermediate conformation (E-FIC)

PDB DOI: https://doi.org/10.2210/pdb8Z7P/pdb
EM Map EMD-39822: EMDB EMDataResource

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

Deposited: 2024-04-20 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), National Key R&D Program of China, Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences, Non-profit Central Research Institute Fund of Chinese Academy of Medical SciencesMajor 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 S trimer in the early fusion intermediate conformation (E-FIC)

Liu, Z., Xing, L.

To be published.

Macromolecule Content

Total Structure Weight: 666.54 kDa
Atom Count: 41,499
Modelled Residue Count: 5,082
Deposited Residue Count: 5,757
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Angiotensin-converting enzyme 2	A [auth D], C [auth E], E [auth F]	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: 6	Glycosylation Focus chain A [auth D] Focus chain C [auth E] Focus chain E [auth F]	Go to GlyGen: Q9BYF1-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	B [auth A], D [auth B], F [auth C]	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 B [auth A] Focus chain D [auth B] Focus chain F [auth C]	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

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	AA [auth a], BA [auth b], CA [auth c], G, H, AA [auth a], BA [auth b], CA [auth c], G, H, I, J, K, L, M, O, P, Q, R, S, T, U, W, X, Y, Z	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain BA [auth b] Focus chain CA [auth c] Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain O Focus chain P Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain W Focus chain X Focus chain Y Focus chain Z Interactions & Density Focus chain AA [auth a] Focus chain BA [auth b] Focus chain CA [auth c] Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain O Focus chain P Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain W 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	DA [auth d], N, V	3		N-Glycosylation	Interactions Focus chain DA [auth d] Focus chain N Focus chain V Interactions & Density Focus chain DA [auth d] Focus chain N Focus chain V
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 BB [auth B] SDF format, chain DB [auth B] SDF format, chain EA [auth D] SDF format, chain EB [auth B] SDF format, chain FB [auth B] SDF format, chain GA [auth D] SDF format, chain GB [auth F] SDF format, chain HA [auth D] SDF format, chain HB [auth F] SDF format, chain IA [auth A] SDF format, chain IB [auth F] SDF format, chain JA [auth A] SDF format, chain JB [auth F] SDF format, chain KA [auth A] SDF format, chain KB [auth C] SDF format, chain LA [auth A] SDF format, chain MA [auth A] SDF format, chain MB [auth C] SDF format, chain NA [auth A] SDF format, chain NB [auth C] SDF format, chain OA [auth A] SDF format, chain OB [auth C] SDF format, chain PA [auth A] SDF format, chain QA [auth A] SDF format, chain QB [auth C] SDF format, chain RA [auth A] SDF format, chain SA [auth E] SDF format, chain TA [auth E] SDF format, chain TB [auth C] SDF format, chain UA [auth E] SDF format, chain VA [auth E] SDF format, chain WA [auth B] SDF format, chain ZA [auth B] SDF format, chain AB [auth B] SDF format, chain CB [auth B] SDF format, chain FA [auth D] SDF format, chain LB [auth C] SDF format, chain PB [auth C] SDF format, chain RB [auth C] SDF format, chain SB [auth C] SDF format, chain XA [auth B] SDF format, chain YA [auth B] MOL2 format, chain BB [auth B] MOL2 format, chain DB [auth B] MOL2 format, chain EA [auth D] MOL2 format, chain EB [auth B] MOL2 format, chain FB [auth B] MOL2 format, chain GA [auth D] MOL2 format, chain GB [auth F] MOL2 format, chain HA [auth D] MOL2 format, chain HB [auth F] MOL2 format, chain IA [auth A] MOL2 format, chain IB [auth F] MOL2 format, chain JA [auth A] MOL2 format, chain JB [auth F] MOL2 format, chain KA [auth A] MOL2 format, chain KB [auth C] MOL2 format, chain LA [auth A] MOL2 format, chain MA [auth A] MOL2 format, chain MB [auth C] MOL2 format, chain NA [auth A] MOL2 format, chain NB [auth C] MOL2 format, chain OA [auth A] MOL2 format, chain OB [auth C] MOL2 format, chain PA [auth A] MOL2 format, chain QA [auth A] MOL2 format, chain QB [auth C] MOL2 format, chain RA [auth A] MOL2 format, chain SA [auth E] MOL2 format, chain TA [auth E] MOL2 format, chain TB [auth C] MOL2 format, chain UA [auth E] MOL2 format, chain VA [auth E] MOL2 format, chain WA [auth B] MOL2 format, chain ZA [auth B] MOL2 format, chain AB [auth B] MOL2 format, chain CB [auth B] MOL2 format, chain FA [auth D] MOL2 format, chain LB [auth C] MOL2 format, chain PB [auth C] MOL2 format, chain RB [auth C] MOL2 format, chain SB [auth C] MOL2 format, chain XA [auth B] MOL2 format, chain YA [auth B] mmCIF format, chain BB [auth B] mmCIF format, chain DB [auth B] mmCIF format, chain EA [auth D] mmCIF format, chain EB [auth B] mmCIF format, chain FB [auth B] mmCIF format, chain GA [auth D] mmCIF format, chain GB [auth F] mmCIF format, chain HA [auth D] mmCIF format, chain HB [auth F] mmCIF format, chain IA [auth A] mmCIF format, chain IB [auth F] mmCIF format, chain JA [auth A] mmCIF format, chain JB [auth F] mmCIF format, chain KA [auth A] mmCIF format, chain KB [auth C] mmCIF format, chain LA [auth A] mmCIF format, chain MA [auth A] mmCIF format, chain MB [auth C] mmCIF format, chain NA [auth A] mmCIF format, chain NB [auth C] mmCIF format, chain OA [auth A] mmCIF format, chain OB [auth C] mmCIF format, chain PA [auth A] mmCIF format, chain QA [auth A] mmCIF format, chain QB [auth C] mmCIF format, chain RA [auth A] mmCIF format, chain SA [auth E] mmCIF format, chain TA [auth E] mmCIF format, chain TB [auth C] mmCIF format, chain UA [auth E] mmCIF format, chain VA [auth E] mmCIF format, chain WA [auth B] mmCIF format, chain ZA [auth B] mmCIF format, chain AB [auth B] mmCIF format, chain CB [auth B] mmCIF format, chain FA [auth D] mmCIF format, chain LB [auth C] mmCIF format, chain PB [auth C] mmCIF format, chain RB [auth C] mmCIF format, chain SB [auth C] mmCIF format, chain XA [auth B] mmCIF format, chain YA [auth B]	AB [auth B] BB [auth B] CB [auth B] DB [auth B] EA [auth D] AB [auth B], BB [auth B], CB [auth B], DB [auth B], EA [auth D], EB [auth B], FA [auth D], FB [auth B], GA [auth D], GB [auth F], HA [auth D], HB [auth F], IA [auth A], IB [auth F], JA [auth A], JB [auth F], KA [auth A], KB [auth C], LA [auth A], LB [auth C], MA [auth A], MB [auth C], NA [auth A], NB [auth C], OA [auth A], OB [auth C], PA [auth A], PB [auth C], QA [auth A], QB [auth C], RA [auth A], RB [auth C], SA [auth E], SB [auth C], TA [auth E], TB [auth C], UA [auth E], VA [auth E], WA [auth B], XA [auth B], YA [auth B], ZA [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth B] Focus chain BB [auth B] Focus chain CB [auth B] Focus chain DB [auth B] Focus chain EA [auth D] Focus chain EB [auth B] Focus chain FA [auth D] Focus chain FB [auth B] Focus chain GA [auth D] Focus chain GB [auth F] Focus chain HA [auth D] Focus chain HB [auth F] Focus chain IA [auth A] Focus chain IB [auth F] Focus chain JA [auth A] Focus chain JB [auth F] Focus chain KA [auth A] Focus chain KB [auth C] Focus chain LA [auth A] Focus chain LB [auth C] Focus chain MA [auth A] Focus chain MB [auth C] Focus chain NA [auth A] Focus chain NB [auth C] Focus chain OA [auth A] Focus chain OB [auth C] Focus chain PA [auth A] Focus chain PB [auth C] Focus chain QA [auth A] Focus chain QB [auth C] Focus chain RA [auth A] Focus chain RB [auth C] Focus chain SA [auth E] Focus chain SB [auth C] Focus chain TA [auth E] Focus chain TB [auth C] Focus chain UA [auth E] Focus chain VA [auth E] Focus chain WA [auth B] Focus chain XA [auth B] Focus chain YA [auth B] Focus chain ZA [auth B] Interactions & Density Focus chain AB [auth B] Focus chain BB [auth B] Focus chain CB [auth B] Focus chain DB [auth B] Focus chain EA [auth D] Focus chain EB [auth B] Focus chain FA [auth D] Focus chain FB [auth B] Focus chain GA [auth D] Focus chain GB [auth F] Focus chain HA [auth D] Focus chain HB [auth F] Focus chain IA [auth A] Focus chain IB [auth F] Focus chain JA [auth A] Focus chain JB [auth F] Focus chain KA [auth A] Focus chain KB [auth C] Focus chain LA [auth A] Focus chain LB [auth C] Focus chain MA [auth A] Focus chain MB [auth C] Focus chain NA [auth A] Focus chain NB [auth C] Focus chain OA [auth A] Focus chain OB [auth C] Focus chain PA [auth A] Focus chain PB [auth C] Focus chain QA [auth A] Focus chain QB [auth C] Focus chain RA [auth A] Focus chain RB [auth C] Focus chain SA [auth E] Focus chain SB [auth C] Focus chain TA [auth E] Focus chain TB [auth C] Focus chain UA [auth E] Focus chain VA [auth E] Focus chain WA [auth B] Focus chain XA [auth B] Focus chain YA [auth B] Focus chain ZA [auth B]

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
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
Non-profit Central Research Institute Fund of Chinese Academy of Medical SciencesMajor 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