4Y4Y | pdb_00004y4y

Classification: VIRUS
Organism(s): Staphylococcus aureus subsp. aureus NCTC 8325, Sesbania mosaic virus
Expression System: Escherichia coli
Mutation(s): No

Experimental Data Snapshot

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

(2015) Virology 489: 34-43

PubMed Abstract:
The capsid protein (CP) of Sesbania mosaic virus (SeMV, a T=3 plant virus) consists of a disordered N-terminal R-domain and an ordered S-domain. Removal of the R-domain results in the formation of T=1 particles. In the current study, the R-domain was replaced with unrelated polypeptides of similar lengths: the B-domain of Staphylococcus aureus SpA, and SeMV encoded polypeptides P8 and P10. The chimeric proteins contained T=3 or larger virus-like particles (VLPs) and could not be crystallized. The presence of metal ions during purification resulted in a large number of heterogeneous nucleoprotein complexes. N∆65-B (R domain replaced with B domain) could also be purified in a dimeric form. Its crystal structure revealed T=1 particles devoid of metal ions and the B-domain was disordered. However, the B-domain was functional in N∆65-B VLPs, suggesting possible biotechnological applications. These studies illustrate the importance of N-terminal residues, metal ions and robustness of the assembly process.

Organizational Affiliation

Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.

Macromolecule Content

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunoglobulin G-binding protein A,Coat protein	A AA [auth a] B BA [auth b] C A, AA [auth a], B, BA [auth b], C, CA [auth c], D, DA [auth d], E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z	282	Staphylococcus aureus subsp. aureus NCTC 8325, Sesbania mosaic virus This entity is chimeric	Mutation(s): 0 Gene Names: spa, SAOUHSC_00069
UniProt
Find proteins for P38507 (Staphylococcus aureus) Explore P38507 Go to UniProtKB: P38507
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P38507
Sequence Annotations Expand
Reference Sequence

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain FA [auth H] SDF format, chain GA [auth L] SDF format, chain IA [auth S] SDF format, chain JA [auth V] SDF format, chain HA [auth M] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth H] MOL2 format, chain GA [auth L] MOL2 format, chain IA [auth S] MOL2 format, chain JA [auth V] MOL2 format, chain HA [auth M] mmCIF format, chain EA [auth D] mmCIF format, chain FA [auth H] mmCIF format, chain GA [auth L] mmCIF format, chain IA [auth S] mmCIF format, chain JA [auth V] mmCIF format, chain HA [auth M]	EA [auth D] FA [auth H] GA [auth L] HA [auth M] IA [auth S] EA [auth D], FA [auth H], GA [auth L], HA [auth M], IA [auth S], JA [auth V]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain EA [auth D] Focus chain FA [auth H] Focus chain GA [auth L] Focus chain HA [auth M] Focus chain IA [auth S] Focus chain JA [auth V] Interactions & Density Focus chain EA [auth D] Focus chain FA [auth H] Focus chain GA [auth L] Focus chain HA [auth M] Focus chain IA [auth S] Focus chain JA [auth V]

Space Group: C 1 2 1

Unit Cell:

Software Package:

& Funding Information

Deposition Author(s):

Gulati, A.

Funding Organization	Location	Grant Number
DST, DBT, J.C Bose	India	--

Version 1.0: 2016-01-20
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-10-23
Changes: Structure summary