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- PDB-7n3c: Crystal Structure of Human Fab S24-202 in the complex with the N-... -

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Basic information

Entry
Database: PDB / ID: 7n3c
TitleCrystal Structure of Human Fab S24-202 in the complex with the N-terminal Domain of Nucleocapsid protein from SARS CoV-2
Components
  • Nucleoprotein
  • S24-202 Fab heavy chain
  • S24-202 Fab light chain
KeywordsVIRAL PROTEIN / SARS Coronavirus 2 / Nucleocapsid protein / Human antibody Fab / COVID-19 / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


: / response to host immune response / viral RNA genome packaging / negative regulation of interferon-beta production / poly(U) RNA binding / Maturation of nucleoprotein / 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 / poly(U) RNA binding / Maturation of nucleoprotein / 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
IODIDE ION / PHOSPHATE ION / Nucleoprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsKim, Y. / Maltseva, N. / Tesar, C. / Jedrzejczak, R. / Dugan, H. / Stamper, C. / Wilson, P. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Iscience / Year: 2024
Title: Epitopes recognition of SARS-CoV-2 nucleocapsid RNA binding domain by human monoclonal antibodies.
Authors: Kim, Y. / Maltseva, N. / Tesar, C. / Jedrzejczak, R. / Endres, M. / Ma, H. / Dugan, H.L. / Stamper, C.T. / Chang, C. / Li, L. / Changrob, S. / Zheng, N.Y. / Huang, M. / Ramanathan, A. / ...Authors: Kim, Y. / Maltseva, N. / Tesar, C. / Jedrzejczak, R. / Endres, M. / Ma, H. / Dugan, H.L. / Stamper, C.T. / Chang, C. / Li, L. / Changrob, S. / Zheng, N.Y. / Huang, M. / Ramanathan, A. / Wilson, P. / Michalska, K. / Joachimiak, A.
History
DepositionMay 31, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Structure summary / Category: citation / struct / Item: _citation.title / _struct.title
Revision 1.2Oct 18, 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
Revision 1.3Feb 28, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Oct 30, 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
H: S24-202 Fab heavy chain
L: S24-202 Fab light chain
C: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,19325
Polymers62,0163
Non-polymers2,17622
Water6,557364
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8900 Å2
ΔGint-14 kcal/mol
Surface area26140 Å2
Unit cell
Length a, b, c (Å)72.622, 64.020, 89.209
Angle α, β, γ (deg.)90.000, 91.091, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 1 molecules C

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


Mass: 14287.961 Da / Num. of mol.: 1 / Fragment: CoV N NTD domain, residues 47-173
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): gold / References: UniProt: P0DTC9

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Antibody , 2 types, 2 molecules HL

#1: Antibody S24-202 Fab heavy chain


Mass: 24365.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody S24-202 Fab light chain


Mass: 23362.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)

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Non-polymers , 4 types, 386 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: I
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.34 Å3/Da / Density % sol: 63.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M Potassium iodide, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Sep 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.82→50 Å / Num. obs: 73169 / % possible obs: 99.5 % / Redundancy: 5.4 % / Biso Wilson estimate: 28.83 Å2 / CC1/2: 0.969 / Rmerge(I) obs: 0.172 / Net I/σ(I): 14.1
Reflection shellResolution: 1.82→1.85 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.911 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3464 / CC1/2: 0.465 / % possible all: 96.2

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBIDs 6IEB, 6VYO

6ieb

6vyo


Resolution: 1.82→42.51 Å / SU ML: 0.2223 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.6938
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2097 3744 5.15 %
Rwork0.1794 68973 -
obs0.181 72717 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.03 Å2
Refinement stepCycle: LAST / Resolution: 1.82→42.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4357 0 53 364 4774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01184620
X-RAY DIFFRACTIONf_angle_d1.09916288
X-RAY DIFFRACTIONf_chiral_restr0.0729679
X-RAY DIFFRACTIONf_plane_restr0.0096820
X-RAY DIFFRACTIONf_dihedral_angle_d14.16311676
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.840.35911220.31852195X-RAY DIFFRACTION86.29
1.84-1.870.33511300.29622425X-RAY DIFFRACTION93.11
1.87-1.890.31881140.28692451X-RAY DIFFRACTION94.89
1.89-1.920.32621400.26012445X-RAY DIFFRACTION96.13
1.92-1.950.2571150.23492521X-RAY DIFFRACTION96.98
1.95-1.980.26771340.21652549X-RAY DIFFRACTION98.17
1.98-2.010.23041400.20762561X-RAY DIFFRACTION99.7
2.01-2.040.23011330.20752544X-RAY DIFFRACTION99.63
2.04-2.080.2451320.20332604X-RAY DIFFRACTION100
2.08-2.120.2221400.19792545X-RAY DIFFRACTION99.96
2.12-2.170.23091670.20132554X-RAY DIFFRACTION99.96
2.17-2.210.23281280.18552615X-RAY DIFFRACTION100
2.21-2.260.22741230.17472584X-RAY DIFFRACTION100
2.26-2.320.20911360.18152594X-RAY DIFFRACTION100
2.32-2.380.21171290.18182591X-RAY DIFFRACTION99.96
2.38-2.450.24161290.18592597X-RAY DIFFRACTION100
2.45-2.530.23911520.18342561X-RAY DIFFRACTION100
2.53-2.620.23121730.18952576X-RAY DIFFRACTION99.93
2.62-2.730.22431530.18152565X-RAY DIFFRACTION99.96
2.73-2.850.24671450.19042572X-RAY DIFFRACTION100
2.85-30.2161510.18382593X-RAY DIFFRACTION100
3-3.190.22821460.18322596X-RAY DIFFRACTION100
3.19-3.440.19281210.18462621X-RAY DIFFRACTION99.96
3.44-3.780.1781440.1592608X-RAY DIFFRACTION99.96
3.78-4.330.17031450.14312594X-RAY DIFFRACTION99.93
4.33-5.450.14061540.13772622X-RAY DIFFRACTION100
5.45-42.510.22561480.18262690X-RAY DIFFRACTION99.75
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)
14.249850920450.6427103325460.9535013329732.32782767658-0.1763227903551.87514917343-0.0282394037013-0.420967632549-0.2497479943570.184515267441-0.07723402426170.65276003727-0.0288852889086-0.2383372514080.05362596741340.136474908008-0.004784568585160.03577105485460.203949692484-0.02411141129680.39999525436-2.75329635296-9.423369463427.88607613792
22.377787511980.5884200924980.2625223247172.52069519705-1.174649167521.55957112596-0.02192891174980.140109468444-0.0826555159151-0.645712285257-0.04831460709840.855211353270.146593233083-0.189030705812-0.04919527109740.264680697023-0.016371926053-0.07320578884870.320268050319-0.06506496752990.466484297886-6.22562943343-10.6526093728-3.09315648487
36.744571296456.601769648350.2665972330757.39292740171.035570155370.2939121561650.178062718942-0.24298888582-0.6658544095710.469461376498-0.273751560638-1.039203541430.02233140234280.08187621385530.1383882453650.1767248089040.03089097875720.02709419858350.211396985558-0.0164491351090.20990404677440.34855556381.920926301065.80671568322
42.097353297440.2592763517720.273136730493.045617062520.03485750360671.28254210353-0.0137350530182-0.001013454084490.111362693131-0.14628337379-0.05149997802930.0670280055458-0.0969424133238-0.0009854802078090.05201881598590.1651530525410.00844424826120.004854604589190.1897508533630.008037482374710.17153681348527.48044860412.24907735064.57075115652
52.017966045240.8082646365050.3458113255663.85937787838-0.05521114210190.7978860807380.02192341847750.0408151797665-0.0373171171197-0.27141890041-0.0776955718881-0.0245515099647-0.04651932943940.01107977809120.07148248733770.190414143158-0.004211648020860.0244514947870.2189883503270.02810804634850.16681064950134.05180682265.025669659520.394933319483
68.184013174454.157467228433.151148158182.65967421672.43320328592.159642142780.334962111914-0.0741456337759-0.7146043700780.226196567045-0.158725217885-0.2359757624930.215318937652-0.00537993093283-0.1638345842970.1990550745180.0205570992091-0.0213884035590.1961461962780.01194890039720.28111322978522.0811703467-8.224364119178.57213712235
70.692803256359-0.41838072128-0.3815170235760.60458211579-0.09006253313891.061164271320.0632768254546-0.3092343017020.2330518991650.0935599801117-0.05715488697180.00530181316531-0.1339009027610.193256949345-0.03385765701960.221810431387-0.0209442657024-0.0128227172270.3219457283010.01670586454180.20824779174944.74423547067.6334123585415.120996624
82.09846815663-0.002544508472762.379671986014.148833764410.2128300268172.847289959330.0429391687768-0.820148393012-0.2336754392730.888321710963-0.0301664272404-0.281187578665-0.7310056699950.435907974636-0.1019773022510.449924995911-0.0607808603383-0.104061141090.782959055062-0.0489848033230.32593903731455.799016134215.837557762337.6144276933
92.07645249671-0.06057240818610.4926778710242.81463721596-0.5293636530159.4042926227-0.0764513987398-0.422981734436-0.1537414610950.3550359723720.197452208799-0.448483037870.6172705547730.722320415836-0.1812965856560.3289009487970.0984534811197-0.07486090871660.428220682047-0.01453936581640.31989198011754.89636238688.7568318676229.1840014364
102.354018343130.02752836596333.867974662961.79148717007-0.9903398982937.08967417823-0.100064401217-0.6127385765090.166697786433-0.0544224822414-0.172106186458-0.7247774505820.8920707477591.75151132575-0.449005944420.2661219114530.077618503853-0.1811902583011.20192133561-0.1835721819280.71034571083764.163048710610.038016728927.2919837164
115.49445842411-2.109570818364.228032134484.44936046744-2.567342226369.10429150959-0.0495658164981-0.7686594225150.2840713092050.294664277775-0.2030087091720.2080630584540.0375344522733-0.3058511581070.1811854822140.296482350233-0.02188031799210.0544545127620.368649150321-0.03123789986050.16577282877519.44922358084.2493129244829.0377512006
122.033274322640.5338691353520.6204840786361.3101156290.7002521152943.12712905070.0453098445205-0.413095638107-0.1504296231070.25888130199-0.04701273567470.07799194524680.137388429202-0.0541432829648-0.03086969160210.2096323080480.006810539248280.03077679961660.2677409886820.01382669628270.16815998076521.3254165355-1.2137318990923.8502408561
134.426367129661.37817299036-0.2794242148053.712876029740.7759835969475.27450598138-0.0942812051485-0.05973545249420.384127142474-0.2385006008650.151147570291-0.300772044432-0.7412829605970.246541798099-0.05123299496270.4898824762670.0223269269379-0.06114169473790.464432647848-0.1242123181550.34100982547846.342260358822.220869756234.0154810971
144.108062613882.49978929095-1.10708559785.29774366114-0.08210673274715.703940147270.0903799764118-0.499479567070.411276758005-0.0971614839451-0.01035606549240.0267773901182-0.7776132335690.138492248943-0.07207876718860.4093474555760.0546776999569-0.0567664850630.441423816809-0.08254327313510.25195075109345.910498659522.049069759337.259529188
150.9360400588262.220513750540.9748563561525.924973181270.1087302845499.609788560230.573828349584-1.004413301840.8730610213791.63331107455-0.4061846841231.3475158621-1.92792444919-1.560127887310.9950691308480.5837856864720.08984083522460.1204660828340.50705364564-0.1345846496550.757891476985-9.573571058681.557326560423.13432127155
168.23089064431.62794799486-0.1026058842384.484714141851.366531650262.974582465930.00276371541135-0.0906392427068-0.171299425434-0.013380092591-0.01579733247870.5884448700750.0962177820054-0.151356526767-0.01348566361470.15856987610.0124520237005-0.02362131999020.166487740201-0.0386579630260.316524155413-2.68687119401-13.79176193272.05021677766
178.21623045214.51925520104-5.870948080449.02271209246-3.506463341364.27130380446-0.325986520931-0.902547002372-1.54149304616-1.1522349002-0.1031545713690.3583675146921.096751951860.06578493894750.2781892689820.570790411160.00914422515373-0.02896376807660.7632420397160.1028606413451.11233769999-28.1878057773-13.950700399211.0089822361
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'C' and (resid 101 through 144 )CJ101 - 14458 - 101
22chain 'C' and (resid 145 through 173 )CJ145 - 173102 - 130
33chain 'H' and (resid 1 through 17 )HA1 - 171 - 17
44chain 'H' and (resid 18 through 67 )HA18 - 6718 - 67
55chain 'H' and (resid 68 through 91 )HA68 - 9168 - 91
66chain 'H' and (resid 92 through 111 )HA92 - 11192 - 111
77chain 'H' and (resid 112 through 137 )HA112 - 137112 - 137
88chain 'H' and (resid 138 through 158 )HA138 - 158138 - 158
99chain 'H' and (resid 159 through 216 )HA159 - 216159 - 216
1010chain 'H' and (resid 217 through 226 )HA217 - 226217 - 226
1111chain 'L' and (resid 0 through 25 )LG0 - 251 - 26
1212chain 'L' and (resid 26 through 113 )LG26 - 11327 - 114
1313chain 'L' and (resid 114 through 163 )LG114 - 163115 - 164
1414chain 'L' and (resid 164 through 213 )LG164 - 213165 - 214
1515chain 'C' and (resid 44 through 53 )CJ44 - 531 - 10
1616chain 'C' and (resid 54 through 90 )CJ54 - 9011 - 47
1717chain 'C' and (resid 91 through 100 )CJ91 - 10048 - 57

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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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