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- PDB-7b27: RBD domain SARS-CoV2 in complex with neutralizing nanobody NM1230 -

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Basic information

Entry
Database: PDB / ID: 7b27
TitleRBD domain SARS-CoV2 in complex with neutralizing nanobody NM1230
Components
  • Surface glycoprotein
  • neutralizing nanobody NM1230
KeywordsVIRAL PROTEIN / SARS-CoV2 / receptor binding domain / complex structure / neutralizing nanobody
Function / homology
Function and homology information


: / endocytosis involved in viral entry into host cell / membrane => GO:0016020 / receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane
Similarity search - Function
: / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2 superfamily, coronavirus ...: / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Surface glycoprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.902 Å
AuthorsOstertag, E. / Zocher, G. / Stehle, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)DFG For 2327 Germany
CitationJournal: Embo Rep. / Year: 2021
Title: NeutrobodyPlex-monitoring SARS-CoV-2 neutralizing immune responses using nanobodies.
Authors: Wagner, T.R. / Ostertag, E. / Kaiser, P.D. / Gramlich, M. / Ruetalo, N. / Junker, D. / Haering, J. / Traenkle, B. / Becker, M. / Dulovic, A. / Schweizer, H. / Nueske, S. / Scholz, A. / Zeck, ...Authors: Wagner, T.R. / Ostertag, E. / Kaiser, P.D. / Gramlich, M. / Ruetalo, N. / Junker, D. / Haering, J. / Traenkle, B. / Becker, M. / Dulovic, A. / Schweizer, H. / Nueske, S. / Scholz, A. / Zeck, A. / Schenke-Layland, K. / Nelde, A. / Strengert, M. / Walz, J.S. / Zocher, G. / Stehle, T. / Schindler, M. / Schneiderhan-Marra, N. / Rothbauer, U.
History
DepositionNov 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1May 19, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Surface glycoprotein
aba: Surface glycoprotein
CCC: neutralizing nanobody NM1230
DDD: neutralizing nanobody NM1230
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3196
Polymers80,8774
Non-polymers4422
Water00
1
AAA: Surface glycoprotein
CCC: neutralizing nanobody NM1230
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6603
Polymers40,4392
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-2 kcal/mol
Surface area15660 Å2
MethodPISA
2
aba: Surface glycoprotein
DDD: neutralizing nanobody NM1230
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6603
Polymers40,4392
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-6 kcal/mol
Surface area14450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.290, 63.290, 411.910
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Surface glycoprotein


Mass: 24975.162 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Homo sapiens (human) / Strain (production host): Expi293F(TM) / References: UniProt: A0A6M6B9J6
#2: Antibody neutralizing nanobody NM1230


Mass: 15463.362 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN

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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: 2.55 Å3/Da / Density % sol: 51.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.9 / Details: 200 mM MgCl2, 20% (w/v) PEG 3350, pH 5.9

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999998 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999998 Å / Relative weight: 1
ReflectionResolution: 2.9→46.5 Å / Num. obs: 18493 / % possible obs: 93.5 % / Redundancy: 6.06 % / Biso Wilson estimate: 61 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.207 / Net I/σ(I): 7.8
Reflection shellResolution: 2.9→2.98 Å / Mean I/σ(I) obs: 1.15 / Num. unique obs: 1340 / CC1/2: 0.662 / Rrim(I) all: 1.86 / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0232 2018/13/08refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6XC4, 6Z1Z

6xc4

6z1z


Resolution: 2.902→30.002 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.88 / SU B: 30.768 / SU ML: 0.514 / Cross valid method: FREE R-VALUE / ESU R Free: 0.493
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3051 1293 -
Rwork0.2661 17182 -
all0.269 --
obs-18475 93.44 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 67.189 Å2
Baniso -1Baniso -2Baniso -3
1-4.256 Å2-0 Å2-0 Å2
2--4.256 Å2-0 Å2
3----8.511 Å2
Refinement stepCycle: LAST / Resolution: 2.902→30.002 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4831 0 28 0 4859
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0134977
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174363
X-RAY DIFFRACTIONr_angle_refined_deg1.2171.6556764
X-RAY DIFFRACTIONr_angle_other_deg1.0471.58110098
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0155625
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.60221.887265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.80515731
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1641533
X-RAY DIFFRACTIONr_chiral_restr0.0310.2625
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025731
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021136
X-RAY DIFFRACTIONr_nbd_refined0.1620.2813
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1730.24234
X-RAY DIFFRACTIONr_nbtor_refined0.1640.22341
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0710.22435
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.2128
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2860.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2360.216
X-RAY DIFFRACTIONr_nbd_other0.1590.251
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0540.24
X-RAY DIFFRACTIONr_mcbond_it2.69517.2062515
X-RAY DIFFRACTIONr_mcbond_other2.69117.2062514
X-RAY DIFFRACTIONr_mcangle_it4.56124.8643135
X-RAY DIFFRACTIONr_mcangle_other4.5624.8653136
X-RAY DIFFRACTIONr_scbond_it2.23217.3722462
X-RAY DIFFRACTIONr_scbond_other2.23117.3722462
X-RAY DIFFRACTIONr_scangle_it3.8625.0123629
X-RAY DIFFRACTIONr_scangle_other3.85925.0133630
X-RAY DIFFRACTIONr_lrange_it6.83587.6065175
X-RAY DIFFRACTIONr_lrange_other6.83287.5855173
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)WRfactor Rwork
2.902-2.9770.485920.4271228138295.51370.411
2.977-3.0580.397920.3971221136596.19050.379
3.058-3.1450.382910.41197134395.90470.368
3.145-3.2410.39860.3391146128995.5780.312
3.241-3.3460.315850.3141139128295.47580.288
3.346-3.4620.285820.2991086122395.50290.273
3.462-3.5910.365780.2981039118294.50080.272
3.591-3.7350.397780.2831037117994.57170.256
3.735-3.8980.266720.264950107994.71730.237
3.898-4.0850.307690.248918105493.64330.221
4.085-4.3020.324660.219878101493.09660.201
4.302-4.5570.216640.19785298193.37410.183
4.557-4.8630.207600.18179391793.02070.168
4.863-5.2420.253560.21773986292.22740.199
5.242-5.7240.33500.22767279590.81760.209
5.724-6.3710.308470.24161874289.62260.22
6.371-7.3020.325410.26154364690.40250.24
7.302-8.8140.247360.25748959488.38380.247
8.814-11.9590.232290.23337947486.0760.237
11.959-30.0020.338190.33225833881.95270.358

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