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- PDB-7r98: Structure of the SARS-CoV-2 N protein RNA-binding domain bound to... -

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Basic information

Entry
Database: PDB / ID: 7r98
TitleStructure of the SARS-CoV-2 N protein RNA-binding domain bound to single-domain antibody B6
Components
  • Nanobody B6
  • Nucleoprotein
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / nanobody / nucleocapsid / VIRUS / VIRAL PROTEIN-IMMUNE SYSTEM complex / RNA BINDING PROTEIN
Function / homology
Function and homology information


cytoplasmic capsid assembly / viral RNA genome packaging / response to host immune response / negative regulation of interferon-beta production / Maturation of nucleoprotein / intracellular non-membrane-bounded organelle / positive regulation of NLRP3 inflammasome complex assembly / MHC class I protein binding / CD28 dependent PI3K/Akt signaling / SARS-CoV-2 targets host intracellular signalling and regulatory pathways ...cytoplasmic capsid assembly / viral RNA genome packaging / response to host immune response / negative regulation of interferon-beta production / Maturation of nucleoprotein / intracellular non-membrane-bounded organelle / positive regulation of NLRP3 inflammasome complex assembly / MHC class I protein binding / CD28 dependent PI3K/Akt signaling / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / protein sequestering activity / VEGFR2 mediated vascular permeability / molecular condensate scaffold activity / TAK1-dependent IKK and NF-kappa-B activation / NOD1/2 Signaling Pathway / DDX58/IFIH1-mediated induction of interferon-alpha/beta / MHC class I protein complex / Interleukin-1 signaling / RNA stem-loop binding / Interferon alpha/beta signaling / viral capsid / 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, C-terminal / Nucleocapsid protein, N-terminal / Coronavirus nucleocapsid
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsCorbett, K.D. / Ye, Q.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM128464 United States
Citation
Journal: Front Immunol / Year: 2021
Title: Structural Basis for SARS-CoV-2 Nucleocapsid Protein Recognition by Single-Domain Antibodies.
Authors: Ye, Q. / Lu, S. / Corbett, K.D.
#1: Journal: Biorxiv / Year: 2021
Title: Structural basis for SARS-CoV-2 Nucleocapsid protein recognition by single-domain antibodies.
Authors: Ye, Q. / Lu, S. / Corbett, K.D.
History
DepositionJun 28, 2021Deposition site: RCSB / Processing site: RCSB
SupersessionJul 7, 2021ID: 7N0S
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 1, 2021Group: Database references / Category: citation / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Feb 9, 2022Group: Database references / Category: citation / citation_author
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoprotein
B: Nucleoprotein
C: Nucleoprotein
D: Nanobody B6
E: Nanobody B6
F: Nanobody B6


Theoretical massNumber of molelcules
Total (without water)86,9296
Polymers86,9296
Non-polymers00
Water00
1
A: Nucleoprotein
D: Nanobody B6


Theoretical massNumber of molelcules
Total (without water)28,9762
Polymers28,9762
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nucleoprotein
E: Nanobody B6


Theoretical massNumber of molelcules
Total (without water)28,9762
Polymers28,9762
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Nucleoprotein
F: Nanobody B6


Theoretical massNumber of molelcules
Total (without water)28,9762
Polymers28,9762
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.613, 175.061, 111.964
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 49 through 92 or resid 105 through 174))
d_2ens_1(chain "B" and (resid 49 through 92 or resid 105 through 174))
d_3ens_1(chain "C" and resid 49 through 174)
d_1ens_2chain "D"
d_2ens_2(chain "E" and resid -1 through 127)
d_3ens_2(chain "F" and resid -1 through 127)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1THRARGA1 - 44
d_12ens_1SERGLUA50 - 119
d_21ens_1THRARGB2 - 45
d_22ens_1SERGLUB48 - 117
d_31ens_1THRGLUC2 - 115
d_11ens_2METSERD1 - 129
d_21ens_2METSERE1 - 129
d_31ens_2METSERF1 - 129

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.504500067694, -0.863410435316, -0.0014497878316), (0.863410114928, -0.504495289122, -0.00273435422623), (0.00162945884151, -0.00263124337054, 0.9999952107)-29.1126488592, -99.7054489761, 0.660553085066
2given(-0.499375806254, 0.866233139909, 0.0162465827932), (-0.866346754604, -0.499088375875, -0.0188173817026), (-0.00819175901739, -0.0234721194356, 0.999690929584)71.9008796726, -75.5738102802, -0.854822676528
3given(-0.512999706561, -0.858341023681, -0.0090547299219), (0.8580025285, -0.512423929336, -0.035403075165), (0.0257480514929, -0.0259307483389, 0.999332094018)-28.5522579276, -100.201651386, -1.54252218436
4given(-0.499768018528, 0.865040464822, 0.0440104746365), (-0.865827101814, -0.500338147563, 0.00227329233068), (0.0239866092074, -0.0369693429003, 0.99902848321)71.905097988, -75.4414893932, -2.80150440296

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Components

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


Mass: 13943.570 Da / Num. of mol.: 3 / Fragment: 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: Antibody Nanobody B6


Mass: 15032.604 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)

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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: 2.81 Å3/Da / Density % sol: 56.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium citrate pH 5.6, 0.1 M sodium-potassium tartrate, and 19% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.51→112 Å / Num. obs: 33832 / % possible obs: 100 % / Redundancy: 13.7 % / Biso Wilson estimate: 67.54 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.214 / Rpim(I) all: 0.06 / Net I/σ(I): 9.7
Reflection shellResolution: 2.51→2.61 Å / Mean I/σ(I) obs: 0.7 / Num. unique obs: 3761 / CC1/2: 0.387 / Rpim(I) all: 1.161 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CDZ

7cdz


Resolution: 2.51→87.53 Å / SU ML: 0.482 / Cross valid method: FREE R-VALUE / σ(F): 0.32 / Phase error: 31.1553
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2732 1596 4.76 %
Rwork0.2264 31948 -
obs0.2285 33544 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 82.89 Å2
Refinement stepCycle: LAST / Resolution: 2.51→87.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5599 0 0 0 5599
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01575740
X-RAY DIFFRACTIONf_angle_d1.49347808
X-RAY DIFFRACTIONf_chiral_restr0.0776826
X-RAY DIFFRACTIONf_plane_restr0.01221026
X-RAY DIFFRACTIONf_dihedral_angle_d12.44582018
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.621788638223
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.486332585069
ens_2d_2DX-RAY DIFFRACTIONTorsion NCS0.462245147677
ens_2d_3DX-RAY DIFFRACTIONTorsion NCS0.436389678152
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.590.40271320.38792642X-RAY DIFFRACTION91.82
2.59-2.680.38741810.34972852X-RAY DIFFRACTION99.7
2.68-2.790.37471710.34712865X-RAY DIFFRACTION99.9
2.79-2.920.4321580.35272871X-RAY DIFFRACTION99.97
2.92-3.070.37991460.30572911X-RAY DIFFRACTION100
3.07-3.260.33261310.26192918X-RAY DIFFRACTION99.9
3.26-3.520.32891460.27242900X-RAY DIFFRACTION99.93
3.52-3.870.29641170.23222963X-RAY DIFFRACTION99.81
3.87-4.430.24681490.17982930X-RAY DIFFRACTION100
4.43-5.580.17981420.1672994X-RAY DIFFRACTION100
5.58-87.530.21731230.19013102X-RAY DIFFRACTION99.97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.16239765683-0.9127540717980.4627602167196.07967172833-0.2838344323224.167332242370.0448925508839-0.290098969491-0.8780847315380.43216898376-0.062594930388-0.4571687820520.5378541972520.0181428110573-0.01518657924610.571136621971-0.07849961879440.01888233905510.4037124953680.0198475017510.63639858782834.3450544377-71.47912824970.431346884135
21.10429140567-0.98894564813-0.6818104451511.161696593160.587063490044.25677547311-0.212482102682-1.617353674711.427852722350.2101290306550.269926579388-0.780349500389-0.5069228155170.3973520445010.03703367874880.6431481600090.0471288364124-0.1467041788721.2897905495-0.39856101631.0833682324215.2067407998-34.35070153691.02861274045
32.997438094360.596790498662-0.4733713004542.17667835637-0.6428107462514.22976972808-0.36631568393-0.336700229744-0.6560969758851.074749874020.492933662211.188854045550.107298266726-0.548408361012-0.2814446514461.113177422550.1642249471390.2897366682360.6454854332540.2578078926191.29271043185-6.62042058994-69.49539263210.446703671362
45.9400605956-0.0154853228305-0.2737643899486.74767166011-1.294256834774.44966042809-0.02979015306590.500467037670.33494114211-0.65823932168-0.0711918859729-0.320498069919-0.513021799079-0.079853083050.087717801750.559983442586-0.02290499289940.122467485950.4708192086790.0146992421650.50821473340733.3497603243-43.9785481674-15.782757077
56.51371657293-0.458021259738-0.4039195699194.32797325561-0.08130710186795.30971046627-0.1952115931620.182677735766-0.4992853915710.09780422963520.112090425750.0001493015529120.62708415643-0.4370883710150.08043256222740.422576535863-0.02587984597270.03644233692860.4419640188210.03489079670370.374273386305-7.86918513392-48.5492809463-15.3714262855
64.11373115432-0.2428463225890.2124721968444.01178461319-0.8627512412442.49467205818-0.09171746963730.615350967723-1.4146192481-0.695744677740.1576733150570.1112616094580.270789941880.3157061577070.06102562233840.840368812807-0.0317216873027-0.01862133689020.592856374068-0.2586005624261.201783697116.5984098274-82.4038994636-16.1966659814
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain AAA49 - 1741 - 119
22chain BBB48 - 1741 - 117
33chain CCC48 - 1741 - 115
44chain DDD-1 - 1271 - 129
55chain EEE-1 - 1281 - 130
66chain FFF-1 - 1281 - 130

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