6ZP5

SARS-CoV-2 spike in prefusion state (flexibility analysis, 1-up closed conformation)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history. 


Literature

Continuous flexibility analysis of SARS-CoV-2 spike prefusion structures.

Melero, R., Sorzano, C.O.S., Foster, B., Vilas, J.L., Martinez, M., Marabini, R., Ramirez-Aportela, E., Sanchez-Garcia, R., Herreros, D., Del Cano, L., Losana, P., Fonseca-Reyna, Y.C., Conesa, P., Wrapp, D., Chacon, P., McLellan, J.S., Tagare, H.D., Carazo, J.M.

(2020) IUCrJ 7: 1059-1069

  • DOI: https://doi.org/10.1107/S2052252520012725
  • Primary Citation of Related Structures:  
    6ZOW, 6ZP5, 6ZP7

  • PubMed Abstract: 

    • Using a new consensus-based image-processing approach together with principal component analysis, the flexibility and conformational dynamics of the SARS-CoV-2 spike in the prefusion state have been analysed. These studies revealed concerted motions involving the receptor-binding domain (RBD), N-terminal domain, and subdomains 1 and 2 around the previously characterized 1-RBD-up state, which have been modeled as elastic deformations ...

    Using a new consensus-based image-processing approach together with principal component analysis, the flexibility and conformational dynamics of the SARS-CoV-2 spike in the prefusion state have been analysed. These studies revealed concerted motions involving the receptor-binding domain (RBD), N-terminal domain, and subdomains 1 and 2 around the previously characterized 1-RBD-up state, which have been modeled as elastic deformations. It is shown that in this data set there are not well defined, stable spike conformations, but virtually a continuum of states. An ensemble map was obtained with minimum bias, from which the extremes of the change along the direction of maximal variance were modeled by flexible fitting. The results provide a warning of the potential image-processing classification instability of these complicated data sets, which has a direct impact on the interpretability of the results.

    Related Citations: 
    • Continuous flexibility analysis of SARS-CoV-2 Spike prefusion structures.
      Melero, R., Sorzano, C.O.S., Foster, B., Vilas, J.L., Martinez, M., Marabini, R., Ramirez-Aportela, E., Sanchez-Garcia, R., Herreros, D., Del Cano, L., Losana, P., Fonseca-Reyna, Y.C., Conesa, P., Wrapp, D., Chacon, P., McLellan, J.S., Tagare, H.D., Carazo, J.M.
      (2020) Biorxiv --: --
    Organizational Affiliation: 

    Centro Nacional de Biotecnologia-CSIC, Calle Darwin 3, 28049 Cantoblanco, Madrid, Spain.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Spike glycoprotein
A, B, C
1,288Severe acute respiratory syndrome coronavirus 2Mutation(s): 5 
Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC2
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
CA [auth c],
D,
DA [auth d],
G,
H,
CA [auth c],
D,
DA [auth d],
G,
H,
I,
J,
K,
L,
M,
P,
S,
T,
V,
X,
Z
2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, F, R, U
4N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D 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],
BA [auth b],
N,
O,
W,
AA [auth a],
BA [auth b],
N,
O,
W,
Y
3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
Q
3N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G62916OK
GlyCosmos:  G62916OK
GlyGen:  G62916OK
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
AB [auth C]
EA [auth A]
FA [auth A]
GA [auth A]
HA [auth A]
AB [auth C],
EA [auth A],
FA [auth A],
GA [auth A],
HA [auth A],
IA [auth A],
JA [auth A],
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 C],
XA [auth C],
YA [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
MAN
Query on MAN
Download Ideal Coordinates CCD File 
KA [auth A],
ZA [auth C]		alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N		 Ligand Interaction
DMS
Query on DMS
Download Ideal Coordinates CCD File 
LA [auth A],
MA [auth A],
NA [auth A]		DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Spanish National Research CouncilSpainPIE/COVID-19 202020E079
Spanish Ministry of Science, Innovation, and UniversitiesSpainSEV 2017-0712
European Research Council (ERC)SpainERC - 2018 - SyG, Proposal: 810057
National Institutes of Health/National Library of Medicine (NIH/NLM)United StatesGM125769
National Institutes of Health/National Library of Medicine (NIH/NLM)United StatesR01-AI127521

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-29
    Type: Initial release
  • Version 2.0: 2021-02-03
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2022-12-21
    Changes: Database references, Refinement description