4UD1 | pdb_00004ud1

Structure of the N Terminal domain of the MERS CoV nucleocapsid

PDB DOI: https://doi.org/10.2210/pdb4UD1/pdb

Classification: VIRAL PROTEIN
Organism(s): Middle East respiratory syndrome-related coronavirus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-12-05 Released: 2015-12-02
Deposition Author(s): Papageorgiou, N., Lichiere, J., Ferron, F., Canard, B., Coutard, B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.48 Å
R-Value Free:
0.274 (Depositor), 0.281 (DCC)
R-Value Work:
0.228 (Depositor), 0.241 (DCC)
R-Value Observed:
0.231 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Structural Characterization of the N-Terminal Part of the Mers-Cov Nucleocapsid by X-Ray Diffraction and Small-Angle X-Ray Scattering

Papageorgiou, N., Lichiere, J., Baklouti, A., Ferron, F., Canard, B., Coutard, B.

(2016) Acta Crystallogr D Biol Crystallogr 72: 192

PubMed: 26894667 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S2059798315024328
Primary Citation Related Structures:
4UD1

PubMed Abstract:
The N protein of coronaviruses is a multifunctional protein that is organized into several domains. The N-terminal part is composed of an intrinsically disordered region (IDR) followed by a structured domain called the N-terminal domain (NTD). In this study, the structure determination of the N-terminal region of the MERS-CoV N protein via X-ray diffraction measurements is reported at a resolution of 2.4 Å. Since the first 30 amino acids were not resolved by X-ray diffraction, the structural study was completed by a SAXS experiment to propose a structural model including the IDR. This model presents the N-terminal region of the MERS-CoV as a monomer that displays structural features in common with other coronavirus NTDs.

Organizational Affiliation

CNRS, AFMB UMR 7257, 13288 Marseille, France.

Macromolecule Content

Total Structure Weight: 89.53 kDa
Atom Count: 4,922
Modeled Residue Count: 621
Deposited Residue Count: 820
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N PROTEIN	A, B, C, D, E	164	Middle East respiratory syndrome-related coronavirus	Mutation(s): 0
UniProt
Find proteins for T2B9R0 (Middle East respiratory syndrome-related coronavirus) Explore T2B9R0 Go to UniProtKB: T2B9R0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	T2B9R0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain L [auth C] SDF format, chain I [auth B] MOL2 format, chain M [auth D] MOL2 format, chain L [auth C] MOL2 format, chain I [auth B] mmCIF format, chain M [auth D] mmCIF format, chain L [auth C] mmCIF format, chain I [auth B]	I [auth B], L [auth C], M [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain L [auth C] Focus chain M [auth D] Interactions & Density Focus chain I [auth B] Focus chain L [auth C] Focus chain M [auth D]
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain H [auth B]	H [auth B], K [auth C]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain H [auth B] Focus chain K [auth C] Interactions & Density Focus chain H [auth B] Focus chain K [auth C]
NH4 Query on NH4 Download:Ideal Coordinates CCD File SDF format, chain N [auth E] SDF format, chain J [auth C] SDF format, chain G [auth B] SDF format, chain F [auth A] MOL2 format, chain N [auth E] MOL2 format, chain J [auth C] MOL2 format, chain G [auth B] MOL2 format, chain F [auth A] mmCIF format, chain N [auth E] mmCIF format, chain J [auth C] mmCIF format, chain G [auth B] mmCIF format, chain F [auth A]	F [auth A], G [auth B], J [auth C], N [auth E]	AMMONIUM ION H₄ N QGZKDVFQNNGYKY-UHFFFAOYSA-O		Interactions Focus chain F [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain N [auth E] Interactions & Density Focus chain F [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain N [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.48 Å
R-Value Free: 0.274 (Depositor), 0.281 (DCC)
R-Value Work: 0.228 (Depositor), 0.241 (DCC)
R-Value Observed: 0.231 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 208.648	α = 90
b = 67.021	β = 89.98
c = 60.94	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
PHENIX	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-12-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-12-02
Type: Initial release
Version 1.1: 2016-02-03
Changes: Data collection
Version 1.2: 2016-02-10
Changes: Database references
Version 1.3: 2016-03-02
Changes: Database references
Version 1.4: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description