2WJ8 | pdb_00002wj8

Respiratory Syncitial Virus RiboNucleoProtein

PDB DOI: https://doi.org/10.2210/pdb2WJ8/pdb
NAKB: 2WJ8

Classification: RNA BINDING PROTEIN/RNA
Organism(s): Human respiratory syncytial virus A strain Long, Escherichia coli BL21(DE3)
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-05-25 Released: 2009-12-08
Deposition Author(s): Tawar, R.G., Duquerroy, S., Vonrhein, C., Varela, P.F., Damier-Piolle, L., Castagne, N., MacLellan, K., Bedouelle, H., Bricogne, G., Bhella, D., Eleouet, J., Rey, F.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.29 Å
R-Value Free:
0.226 (Depositor), 0.220 (DCC)
R-Value Work:
0.205 (Depositor)
R-Value Observed:
0.206 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal Structure of a Nucleocapsid-Like Nucleoprotein-RNA Complex of Respiratory Syncytial Virus

Tawar, R.G., Duquerroy, S., Vonrhein, C., Varela, P.F., Damier-Piolle, L., Castagne, N., Maclellan, K., Bedouelle, H., Bricogne, G., Bhella, D., Eleouet, J., Rey, F.A.

(2009) Science 326: 1279

PubMed: 19965480 Search on PubMed
DOI: https://doi.org/10.1126/science.1177634
Primary Citation Related Structures:
2WJ8

PubMed Abstract:
The respiratory syncytial virus (RSV) is an important human pathogen, yet neither a vaccine nor effective therapies are available to treat infection. To help elucidate the replication mechanism of this RNA virus, we determined the three-dimensional (3D) crystal structure at 3.3 A resolution of a decameric, annular ribonucleoprotein complex of the RSV nucleoprotein (N) bound to RNA. This complex mimics one turn of the viral helical nucleocapsid complex, which serves as template for viral RNA synthesis. The RNA wraps around the protein ring, with seven nucleotides contacting each N subunit, alternating rows of four and three stacked bases that are exposed and buried within a protein groove, respectively. Combined with electron microscopy data, this structure provides a detailed model for the RSV nucleocapsid, in which the bases are accessible for readout by the viral polymerase. Furthermore, the nucleoprotein structure highlights possible key sites for drug targeting.

Organizational Affiliation

Institut Pasteur, Unité de Virologie Structurale, Département de Virologie and CNRS Unité de Recherche Associée (URA) 3015, 25 Rue du Dr Roux, 75724 Paris Cedex 15, France.

Macromolecule Content

Total Structure Weight: 912.93 kDa
Atom Count: 61,928
Modeled Residue Count: 7,639
Deposited Residue Count: 7,960
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NUCLEOPROTEIN	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T	391	Human respiratory syncytial virus A strain Long	Mutation(s): 0
UniProt
Find proteins for P03418 (Human respiratory syncytial virus A (strain A2)) Explore P03418 Go to UniProtKB: P03418
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03418
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 2
RNA (5'-R(CPCPCPCPCPC)-3')	AA [auth g] BA [auth h] CA [auth i] DA [auth j] EA [auth k] AA [auth g], BA [auth h], CA [auth i], DA [auth j], EA [auth k], FA [auth l], GA [auth m], HA [auth n], IA [auth o], JA [auth p], KA [auth q], LA [auth r], MA [auth s], NA [auth t], U [auth a], V [auth b], W [auth c], X [auth d], Y [auth e], Z [auth f]	7	Escherichia coli BL21(DE3)
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BO4 Query on BO4 Download:Ideal Coordinates CCD File SDF format, chain OA [auth A] SDF format, chain PA [auth B] SDF format, chain RA [auth D] SDF format, chain TA [auth I] SDF format, chain VA [auth L] SDF format, chain WA [auth M] SDF format, chain YA [auth O] SDF format, chain ZA [auth T] SDF format, chain XA [auth N] SDF format, chain UA [auth K] SDF format, chain SA [auth H] SDF format, chain QA [auth C] MOL2 format, chain OA [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain RA [auth D] MOL2 format, chain TA [auth I] MOL2 format, chain VA [auth L] MOL2 format, chain WA [auth M] MOL2 format, chain YA [auth O] MOL2 format, chain ZA [auth T] MOL2 format, chain XA [auth N] MOL2 format, chain UA [auth K] MOL2 format, chain SA [auth H] MOL2 format, chain QA [auth C] mmCIF format, chain OA [auth A] mmCIF format, chain PA [auth B] mmCIF format, chain RA [auth D] mmCIF format, chain TA [auth I] mmCIF format, chain VA [auth L] mmCIF format, chain WA [auth M] mmCIF format, chain YA [auth O] mmCIF format, chain ZA [auth T] mmCIF format, chain XA [auth N] mmCIF format, chain UA [auth K] mmCIF format, chain SA [auth H] mmCIF format, chain QA [auth C]	OA [auth A] PA [auth B] QA [auth C] RA [auth D] SA [auth H] OA [auth A], PA [auth B], QA [auth C], RA [auth D], SA [auth H], TA [auth I], UA [auth K], VA [auth L], WA [auth M], XA [auth N], YA [auth O], ZA [auth T]	BORATE ION B H₄ O₄ KCFLOKKYWBPKFN-UHFFFAOYSA-N		Interactions Focus chain OA [auth A] Focus chain PA [auth B] Focus chain QA [auth C] Focus chain RA [auth D] Focus chain SA [auth H] Focus chain TA [auth I] Focus chain UA [auth K] Focus chain VA [auth L] Focus chain WA [auth M] Focus chain XA [auth N] Focus chain YA [auth O] Focus chain ZA [auth T] Interactions & Density Focus chain OA [auth A] Focus chain PA [auth B] Focus chain QA [auth C] Focus chain RA [auth D] Focus chain SA [auth H] Focus chain TA [auth I] Focus chain UA [auth K] Focus chain VA [auth L] Focus chain WA [auth M] Focus chain XA [auth N] Focus chain YA [auth O] Focus chain ZA [auth T]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.29 Å
R-Value Free: 0.226 (Depositor), 0.220 (DCC)
R-Value Work: 0.205 (Depositor)
R-Value Observed: 0.206 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 218.2	α = 90
b = 220.99	β = 93.09
c = 218.1	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
SCALA	data scaling
AMoRE	phasing
MOLREP	phasing
BUSTER-TNT	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-12-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-12-08
Type: Initial release
Version 1.1: 2013-04-17
Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Version format compliance
Version 1.2: 2018-11-21
Changes: Data collection, Derived calculations
Version 1.3: 2019-10-30
Changes: Advisory, Data collection, Derived calculations, Other
Version 1.4: 2019-11-13
Changes: Data collection, Database references
Version 1.5: 2024-05-01
Changes: Data collection, Database references, Derived calculations, Refinement description