1LD4

Placement of the Structural Proteins in Sindbis Virus

• PDB DOI:  https://doi.org/10.2210/pdb1LD4/pdb

• Classification: VIRUS
• Organism(s): Sindbis virus, Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2002-04-08 Released: 2002-11-04 
• Deposition Author(s): Zhang, W., Mukhopadhyay, S., Pletnev, S.V., Baker, T.S., Kuhn, R.J., Rossmann, M.G.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 11.4 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Placement of the Structural Proteins in Sindbis virus

Zhang, W., Mukhopadhyay, S., Pletnev, S.V., Baker, T.S., Kuhn, R.J., Rossmann, M.G.

(2002) J Virol 76: 11645-11658

• PubMed: 12388725 
• DOI: https://doi.org/10.1128/jvi.76.22.11645-11658.2002
• Primary Citation of Related Structures:  
  1LD4


• PubMed Abstract: 
  

The structure of the lipid-enveloped Sindbis virus has been determined by fitting atomic resolution crystallographic structures of component proteins into an 11-A resolution cryoelectron microscopy map. The virus has T=4 quasisymmetry elements that are accurately maintained between the external glycoproteins, the transmembrane helical region, and the internal nucleocapsid core. The crystal structure of the E1 glycoprotein was fitted into the cryoelectron microscopy density, in part by using the known carbohydrate positions as restraints. A difference map showed that the E2 glycoprotein was shaped similarly to E1, suggesting a possible common evolutionary origin for these two glycoproteins. The structure shows that the E2 glycoprotein would have to move away from the center of the trimeric spike in order to expose enough viral membrane surface to permit fusion with the cellular membrane during the initial stages of host infection. The well-resolved E1-E2 transmembrane regions form alpha-helical coiled coils that were consistent with T=4 symmetry. The known structure of the capsid protein was fitted into the density corresponding to the nucleocapsid, revising the structure published earlier.

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Organizational Affiliation: 

Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907-1392, USA.

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (3D View)
Global Stoichiometry: Hetero 960-mer - A480B240C240 

Biological assembly 1 assigned by authors and generated by (software)

Macromolecule Content

• Total Structure Weight: 361.06 kDa 
• Atom Count: 15,680 
• Modelled Residue Count: 2,304 
• Deposited Residue Count: 3,268 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coat protein C	A, B, C, D	264	Sindbis virus	Mutation(s): 0  EC: 3.4.21 (PDB Primary Data), 3.4.21.90 (UniProt)
UniProt
Find proteins for P03316 (Sindbis virus) Explore P03316  Go to UniProtKB:  P03316

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GENERAL CONTROL PROTEIN GCN4	E, F, G, H, I, J, K, L	57	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P03069 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P03069  Go to UniProtKB:  P03069

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein E1	M, N, O, P	439	Sindbis virus	Mutation(s): 0  EC: 3.4.21.90
UniProt
Find proteins for P03316 (Sindbis virus) Explore P03316  Go to UniProtKB:  P03316

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UNX	AA [auth M], BA [auth M], CA [auth N], DA [auth N], EA [auth N], FA [auth N], GA [auth N], HA [auth N], IA [auth O], JA [auth O], KA [auth O], LA [auth O], MA [auth O], NA [auth O], OA [auth O], PA [auth O], Q [auth F], QA [auth P], R [auth F], RA [auth P], S [auth H], SA [auth P], T [auth J], TA [auth P], U [auth L], UA [auth P], V [auth M], VA [auth P], W [auth M], X [auth M], Y [auth M], Z [auth M]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 11.4 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	EM3DR

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-11-04 
Deposition Author(s): Zhang, W., Mukhopadhyay, S., Pletnev, S.V., Baker, T.S., Kuhn, R.J., Rossmann, M.G.

Revision History  

• Version 1.0: 2002-11-04
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-07-18
  Changes: Data collection
• Version 1.4: 2019-11-06
  Changes: Data collection, Other