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- PDB-6m3m: Crystal structure of SARS-CoV-2 nucleocapsid protein N-terminal R... -

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Basic information

Entry
Database: PDB / ID: 6m3m
TitleCrystal structure of SARS-CoV-2 nucleocapsid protein N-terminal RNA binding domain
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / coronavirus / nucleocapsid protein / RNA binding domain / SARS-CoV 2 / NTD
Function / homology
Function and homology information


cytoplasmic capsid assembly / viral RNA genome packaging / response to host immune response / negative regulation of interferon-beta production / RNA stem-loop binding / Maturation of nucleoprotein / positive regulation of NLRP3 inflammasome complex assembly / intracellular non-membrane-bounded organelle / CD28 dependent PI3K/Akt signaling / MHC class I protein binding ...cytoplasmic capsid assembly / viral RNA genome packaging / response to host immune response / negative regulation of interferon-beta production / RNA stem-loop binding / Maturation of nucleoprotein / positive regulation of NLRP3 inflammasome complex assembly / intracellular non-membrane-bounded organelle / CD28 dependent PI3K/Akt signaling / MHC class I protein binding / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / molecular condensate scaffold activity / protein sequestering activity / VEGFR2 mediated vascular permeability / TAK1-dependent IKK and NF-kappa-B activation / DDX58/IFIH1-mediated induction of interferon-alpha/beta / NOD1/2 Signaling Pathway / MHC class I protein complex / Interleukin-1 signaling / viral capsid / Interferon alpha/beta signaling / PIP3 activates AKT signaling / Transcription of SARS-CoV-2 sgRNAs / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / viral nucleocapsid / Translation of Structural Proteins / Virion Assembly and Release / host extracellular space / Induction of Cell-Cell Fusion / Attachment and Entry / host cell perinuclear region of cytoplasm / ribonucleoprotein complex / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein homodimerization activity / RNA binding / extracellular region / identical protein binding / cytoplasm
Similarity search - Function
Nucleocapsid protein, betacoronavirus / Nucleocapsid (N) protein, C-terminal domain, coronavirus / Nucleocapsid (N) protein, N-terminal domain, coronavirus / Coronavirus nucleocapsid (CoV N) protein N-terminal (NTD) domain profile. / Coronavirus nucleocapsid (CoV N) protein C-terminal (CTD) domain profile. / Nucleocapsid protein, coronavirus / Nucleocapsid protein, N-terminal / Coronavirus nucleocapsid / Nucleocapsid protein, C-terminal
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsChen, S. / Kang, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770801 China
CitationJournal: Acta Pharm Sin B / Year: 2020
Title: Crystal structure of SARS-CoV-2 nucleocapsid protein RNA binding domain reveals potential unique drug targeting sites.
Authors: Kang, S. / Yang, M. / Hong, Z. / Zhang, L. / Huang, Z. / Chen, X. / He, S. / Zhou, Z. / Zhou, Z. / Chen, Q. / Yan, Y. / Zhang, C. / Shan, H. / Chen, S.
History
DepositionMar 4, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Structure summary / Category: entity / Item: _entity.pdbx_description
Revision 1.2May 27, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Sep 9, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Feb 24, 2021Group: Database references / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_name_com / entity_src_gen / pdbx_entry_details / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.country / _entity.pdbx_description ..._citation.country / _entity.pdbx_description / _entity_src_gen.gene_src_common_name / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg
Revision 1.5Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleoprotein
B: Nucleoprotein
C: Nucleoprotein
D: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)59,5784
Polymers59,5784
Non-polymers00
Water2,342130
1
A: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)14,8951
Polymers14,8951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)14,8951
Polymers14,8951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)14,8951
Polymers14,8951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)14,8951
Polymers14,8951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.888, 92.685, 97.325
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Nucleoprotein / / N / Nucleocapsid protein / Protein N


Mass: 14894.591 Da / Num. of mol.: 4 / Fragment: N-terminal RNA binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Escherichia coli (E. coli) / References: UniProt: P0DTC9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.35 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20 mM sodium acetate, 100 mM sodium cacodylate (pH 6.5), 26 % PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: OXFORD RUBY CCD / Detector: CCD / Date: Feb 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→20.92 Å / Num. obs: 15133 / % possible obs: 99.5 % / Redundancy: 6.5 % / Biso Wilson estimate: 33.94 Å2 / CC1/2: 0.99 / CC star: 0.99 / Rmerge(I) obs: 0.1043 / Rpim(I) all: 0.044 / Rrim(I) all: 0.1135 / Net I/σ(I): 14.97
Reflection shellResolution: 2.7→2.796 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.3172 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 1481 / CC1/2: 0.96 / CC star: 0.99 / Rpim(I) all: 0.1303 / Rrim(I) all: 0.3436 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CrysalisProdata collection
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing
PHENIXphenix.refinerefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OG3

2og3


Resolution: 2.7→20.92 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2934 1481 -
Rwork0.2578 --
obs-15131 99 %
Displacement parametersBiso mean: 31.6 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3822 0 0 130 3952
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00413931
X-RAY DIFFRACTIONf_angle_d0.7175363
X-RAY DIFFRACTIONf_chiral_restr0.0474559
X-RAY DIFFRACTIONf_plane_restr0.005712
X-RAY DIFFRACTIONf_dihedral_angle_d15.52911401
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.80.40581380.355113431481100
2.8-2.910.35541600.330213121472100
2.91-3.040.36761470.311813541501100
3.04-3.20.32911530.298113371490100
3.2-3.40.35791480.27213471495100
3.4-3.660.26511510.258613671518100
3.66-4.030.24971500.223313481498100
4.03-4.60.28511530.225713741527100
4.6-5.780.25371500.229113881538100
5.78-21.220.24631640.23241443160799

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