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- PDB-7n0i: Structure of the SARS-CoV-2 N protein C-terminal domain bound to ... -

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Basic information

Entry
Database: PDB / ID: 7n0i
TitleStructure of the SARS-CoV-2 N protein C-terminal domain bound to single-domain antibody E2
Components
  • Nucleoprotein
  • Single-domain antibody E2
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / nanobody / nucleocapsid / VIRUS / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


: / response to host immune response / viral RNA genome packaging / negative regulation of interferon-beta production / Maturation of nucleoprotein / poly(U) RNA binding / intracellular membraneless organelle / positive regulation of NLRP3 inflammasome complex assembly / MHC class I protein binding / CD28 dependent PI3K/Akt signaling ...: / response to host immune response / viral RNA genome packaging / negative regulation of interferon-beta production / Maturation of nucleoprotein / poly(U) RNA binding / intracellular membraneless 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 / NOD1/2 Signaling Pathway / TAK1-dependent IKK and NF-kappa-B activation / DDX58/IFIH1-mediated induction of interferon-alpha/beta / MHC class I protein complex / RNA stem-loop binding / Interleukin-1 signaling / Interferon alpha/beta signaling / viral capsid / PIP3 activates AKT signaling / viral nucleocapsid / Transcription of SARS-CoV-2 sgRNAs / host cell endoplasmic reticulum-Golgi intermediate compartment / Translation of Structural Proteins / Virion Assembly and Release / host extracellular space / host cell Golgi apparatus / 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 protein, coronavirus / Nucleocapsid protein, C-terminal / Nucleocapsid protein, N-terminal / Nucleocapsid (N) protein, C-terminal domain, coronavirus / Nucleocapsid (N) protein, N-terminal domain, coronavirus / Coronavirus nucleocapsid / Coronavirus nucleocapsid (CoV N) protein N-terminal (NTD) domain profile. / Coronavirus nucleocapsid (CoV N) protein C-terminal (CTD) domain profile. / Immunoglobulins ...Nucleocapsid protein, betacoronavirus / Nucleocapsid protein, coronavirus / Nucleocapsid protein, C-terminal / Nucleocapsid protein, N-terminal / Nucleocapsid (N) protein, C-terminal domain, coronavirus / Nucleocapsid (N) protein, N-terminal domain, coronavirus / Coronavirus nucleocapsid / Coronavirus nucleocapsid (CoV N) protein N-terminal (NTD) domain profile. / Coronavirus nucleocapsid (CoV N) protein C-terminal (CTD) domain profile. / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Nucleoprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsYe, Q. / Corbett, K.D.
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
DepositionMay 25, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 1, 2021Group: Database references / Category: citation / citation_author / 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 / _citation_author.identifier_ORCID / _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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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: Nucleoprotein
E: Nucleoprotein
F: Nucleoprotein
H: Nucleoprotein
I: Single-domain antibody E2
J: Single-domain antibody E2
K: Single-domain antibody E2
L: Single-domain antibody E2
G: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,44315
Polymers148,30112
Non-polymers1423
Water15,529862
1
A: Nucleoprotein
B: Nucleoprotein
I: Single-domain antibody E2


Theoretical massNumber of molelcules
Total (without water)37,0753
Polymers37,0753
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Nucleoprotein
D: Nucleoprotein
J: Single-domain antibody E2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1585
Polymers37,0753
Non-polymers832
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Nucleoprotein
F: Nucleoprotein
K: Single-domain antibody E2


Theoretical massNumber of molelcules
Total (without water)37,0753
Polymers37,0753
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
H: Nucleoprotein
L: Single-domain antibody E2
G: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1344
Polymers37,0753
Non-polymers591
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.846, 131.557, 140.048
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1(chain "C" and resid 269 through 364)
d_3ens_1chain "E"
d_4ens_1(chain "G" and resid 269 through 364)
d_1ens_2chain "B"
d_2ens_2chain "D"
d_3ens_2chain "F"
d_4ens_2chain "H"
d_1ens_3(chain "I" and resid 0 through 128)
d_2ens_3(chain "J" and resid 0 through 128)
d_3ens_3(chain "K" and resid 0 through 128)
d_4ens_3(chain "L" and resid 0 through 128)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASNPROA1 - 96
d_21ens_1ASNPROC1 - 96
d_31ens_1ASNPROF1 - 96
d_41ens_1ASNPRON1 - 96
d_11ens_2ASNPROB1 - 96
d_21ens_2ASNPROE1 - 96
d_31ens_2ASNPROG1 - 96
d_41ens_2ASNPROH1 - 96
d_11ens_3ALAALAI1 - 129
d_21ens_3ALAALAJ1 - 129
d_31ens_3ALAALAK2 - 130
d_41ens_3ALAALAL2 - 130

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(0.999940522558, -0.00415392768972, 0.0100844549362), (0.00413345302378, 0.999989355333, 0.0020503136866), (-0.0100928644453, -0.00200850811843, 0.999947048589)37.7984189257, -4.50537994628, -0.308543711574
2given(0.992463911455, 0.117891242712, 0.0334221386483), (-0.0832285157307, 0.448348967646, 0.889975402683), (0.0899355248463, -0.886050144237, 0.454782083275)-10.3985100913, -12.5310056848, 22.1294337557
3given(0.99908987947, 0.0388998137013, -0.0174990638142), (-0.00167714511955, 0.445758765554, 0.895151557065), (0.0426215898884, -0.894307512786, 0.445418311983)30.2612571599, -13.908779541, 20.6019594522
4given(0.999814178018, -0.0184278025786, 0.00565911003736), (0.0184093036254, 0.999825076055, 0.0033037602034), (-0.0057190011643, -0.0031989660172, 0.999978529591)38.0239106365, -3.94892611441, -0.143249035509
5given(0.98834664212, 0.149869385063, 0.0266473719145), (-0.0932020973741, 0.457398258742, 0.884364292554), (0.120350671183, -0.876542069909, 0.46603617416)-11.3803646677, -13.1917761726, 23.4516208248
6given(0.996384174254, 0.0758796817055, -0.0382210831984), (-0.00194256140234, 0.470088033471, 0.882617395729), (0.0849400008935, -0.879351758224, 0.468535677997)28.7810537344, -14.6222868771, 22.3342506027
7given(0.999606572331, 0.0207727279328, 0.0188465998764), (-0.0207993089278, 0.999782932158, 0.00121544802762), (-0.0188172607144, -0.00160696608981, 0.999821648275)37.0883030598, -5.44631225708, -0.670932536019
8given(0.993143620293, 0.114636026346, 0.0228982736376), (-0.0685406617001, 0.412338169886, 0.908448904093), (0.0946991402582, -0.903789696289, 0.417368251926)-10.1606035369, -10.5047658593, 22.3549974061
9given(0.995733215648, 0.0921943421922, 0.00394544328635), (-0.0418124454708, 0.412649670772, 0.909929650366), (0.0822622796835, -0.906212145405, 0.41474385452)28.7363437312, -14.2336197956, 22.0019598397

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Components

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


Mass: 10820.076 Da / Num. of mol.: 8 / Fragment: C-terminal 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
Single-domain antibody E2


Mass: 15434.994 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 862 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.36 Å3/Da / Density % sol: 47.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20 mM HEPES pH 7.0, 200 mM NaCl, 5 mM MgCl2, 1 mM TCEP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→49.69 Å / Num. obs: 129860 / % possible obs: 99.7 % / Redundancy: 6.5 % / Biso Wilson estimate: 26.6 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.038 / Net I/σ(I): 8.1
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 5.417 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 6374 / CC1/2: 0.344 / Rpim(I) all: 2.282

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WZQ

6wzq


Resolution: 2.2→49.69 Å / SU ML: 0.3036 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 32.7474
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2714 3295 5.15 %
Rwork0.2394 60713 -
obs0.241 64008 89.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.21 Å2
Refinement stepCycle: LAST / Resolution: 2.2→49.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10229 0 9 862 11100
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003310500
X-RAY DIFFRACTIONf_angle_d0.682714238
X-RAY DIFFRACTIONf_chiral_restr0.04671478
X-RAY DIFFRACTIONf_plane_restr0.00521881
X-RAY DIFFRACTIONf_dihedral_angle_d12.01863770
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.616819606011
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.800977639104
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.831520376534
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.683460020595
ens_2d_3BX-RAY DIFFRACTIONTorsion NCS0.887891113967
ens_2d_4BX-RAY DIFFRACTIONTorsion NCS0.932315439893
ens_3d_2IX-RAY DIFFRACTIONTorsion NCS0.624510801451
ens_3d_3IX-RAY DIFFRACTIONTorsion NCS0.767207829819
ens_3d_4IX-RAY DIFFRACTIONTorsion NCS0.737202978091
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.230.39041020.34111995X-RAY DIFFRACTION70.46
2.23-2.260.42611100.33632199X-RAY DIFFRACTION78.91
2.26-2.30.31681100.31172128X-RAY DIFFRACTION75.2
2.3-2.340.33741320.31762088X-RAY DIFFRACTION76.13
2.34-2.380.39841140.32122199X-RAY DIFFRACTION77.41
2.38-2.420.37431220.31142233X-RAY DIFFRACTION80.1
2.42-2.470.36241240.31022309X-RAY DIFFRACTION82.67
2.47-2.520.36641320.30212350X-RAY DIFFRACTION83.4
2.52-2.570.32361380.29342440X-RAY DIFFRACTION86.66
2.57-2.630.29111590.28592434X-RAY DIFFRACTION87.42
2.63-2.70.36291470.28852456X-RAY DIFFRACTION87.94
2.7-2.770.30691330.27592539X-RAY DIFFRACTION90.51
2.77-2.850.34641370.27422568X-RAY DIFFRACTION90.77
2.85-2.950.30141660.25422615X-RAY DIFFRACTION92.7
2.95-3.050.311430.2452628X-RAY DIFFRACTION93.11
3.05-3.170.26281290.24372736X-RAY DIFFRACTION96.08
3.17-3.320.27791710.24822728X-RAY DIFFRACTION96.89
3.32-3.490.27961730.22712751X-RAY DIFFRACTION97.96
3.49-3.710.23441290.21582847X-RAY DIFFRACTION98.61
3.71-40.19491200.19882870X-RAY DIFFRACTION98.84
4-4.40.18241230.18872846X-RAY DIFFRACTION98.38
4.4-5.030.20851910.18022825X-RAY DIFFRACTION99.05
5.04-6.340.23071510.20782918X-RAY DIFFRACTION99.42
6.34-49.690.2281390.21743011X-RAY DIFFRACTION97.86
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)
11.510832219280.2740285271470.07637647945572.674417762920.3154818041934.94763029091-0.1688628641960.1140094205480.0656719601465-0.7253722603730.1099005965980.0172935139078-0.9969349953650.1987743549050.01161054072250.594772363476-0.0307996223954-0.06196303741380.1972988452040.02520070635170.15404372782-37.078706694419.3408072216-19.752210704
21.818037478380.36352006817-1.275272355533.06133542437-0.1118501749784.78300260327-0.1162099365250.009808281810730.02703262090450.03306084251360.0807926037222-0.26195148351-0.176340710950.3402960301310.07282704006250.0374974331867-0.0225310804561-0.07174413553310.164538618302-0.01610803792380.2209861156410.48918498205514.6262195413-19.7179775528
32.58671454064-0.459820075322-0.8361775101754.10796155002-0.6183486103084.57544858116-0.0229485495585-0.247402055281-0.07887509952310.2585757420480.246044283733-0.1805902393481.057144714590.115078134227-0.1433108030770.545016764640.0256811035248-0.02722571004550.2447183956760.06798027173920.320881552703-45.669521151-18.3699730409-7.2069663865
44.60488091452-1.52335081181-1.419043269065.37177047206-0.6079676714914.51913408854-0.410292191003-1.09062768961-0.2220995453981.68046861210.129861332994-0.3008078413391.367254374760.2641923442730.4562729981081.403036260610.02250631347170.5558372320570.5272047574980.2935212030420.387972736625-5.94066604438-22.9503719617-6.99776787178
52.072101774171.042502348340.09051422084673.33621529602-0.7685547540582.65974187090.2587880031150.06941754658140.00155725216003-0.241717300562-0.0996126098727-0.04030471078640.3510176097030.142298481145-0.1273684807880.6160828081950.0538031416208-2.20636768387E-50.199799864732-0.02940774077090.144869914965-36.335235673148.1669542441-15.4337731497
62.419239408380.7781798133670.0134337275493.951271204480.258678368543.968255532150.1475582495260.00623096066942-0.08713942862110.115159729161-0.027317091669-0.2770618138570.1530311892520.126046069708-0.01508376623650.0719065260319-0.00624658880735-0.01938039026270.128386900468-0.02038694750320.1254061580331.4727778030443.4605662515-15.5223593147
71.426296840910.663621318227-0.6259270498132.451965077041.140129260875.30939754535-0.008097549759950.0802557893658-0.133059340811-0.2696087766270.100619887285-0.0956494459570.003027527360410.0756148011311-0.0805189185090.1433354939160.02804818083580.02443658244880.1330796010350.01288188073280.193849708022-40.985242237-2.32717856548-29.6673446314
81.839912501580.383918758148-0.9172948976282.753441600660.5606272132464.12741858338-0.1278139609580.0433960758585-0.1339851158060.06988627633150.0375551629146-0.05050922199540.3831760600040.02339619528440.106882242070.07864919322820.01703050434220.07057775614670.136587836206-0.02007903011650.221289616606-2.96168181206-7.03139855772-29.7620808175
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain A or chain BA - BA - B269 - 3641 - 96
22chain C or chain DC - DC - E269 - 3641 - 96
33chain E or chain FE - FF - G269 - 3641 - 96
44chain G or chain HH - GH - O269 - 4011
55chain III0 - 1351 - 136
66chain JJJ0 - 1341 - 135
77chain KKK-1 - 1281 - 130
88chain LLL-1 - 1291 - 131

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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