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- PDB-7voa: Crystal structure of SARS-CoV-2 RBD in complex with aRBD5 -

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Basic information

Entry
Database: PDB / ID: 7voa
TitleCrystal structure of SARS-CoV-2 RBD in complex with aRBD5
Components
  • Spike glycoprotein
  • alpaca nanobody
KeywordsVIRAL PROTEIN/ANTIVIRAL PROTEIN / VIRAL PROTEIN-ANTIVIRAL PROTEIN COMPLEX
Function / homology
Function and homology information


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / symbiont-mediated suppression of host innate immune response / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma 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 / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / 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 ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / 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, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / 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
Biological speciesVicugna pacos (alpaca)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMa, H. / Zeng, W.H. / Jin, T.C.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870731 China
National Natural Science Foundation of China (NSFC)U1732109 China
CitationJournal: Cell Res. / Year: 2022
Title: Hetero-bivalent nanobodies provide broad-spectrum protection against SARS-CoV-2 variants of concern including Omicron.
Authors: Ma, H. / Zhang, X. / Zheng, P. / Dube, P.H. / Zeng, W. / Chen, S. / Cheng, Q. / Yang, Y. / Wu, Y. / Zhou, J. / Hu, X. / Xiang, Y. / Zhang, H. / Chiu, S. / Jin, T.
History
DepositionOct 13, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 14, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: alpaca nanobody
B: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2063
Polymers36,9842
Non-polymers2211
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-6 kcal/mol
Surface area15540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.440, 87.700, 89.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody alpaca nanobody


Mass: 13598.057 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Plasmid: pET22b / Production host: Escherichia coli (E. coli)
#2: Protein Spike glycoprotein / S glycoprotein / E2 / Peplomer protein


Mass: 23386.246 Da / Num. of mol.: 1 / Fragment: UNP residues 321-528
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Plasmid: pTT5 / Cell line (production host): 293F / Production host: Eukaryota sp. (eukaryote) / References: UniProt: P0DTC2
#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.: 1 / 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
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: 2.82 Å3/Da / Density % sol: 56.4 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1M Sodium cacodylate pH 5.5, 25%(w/v) PEG 4000

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Data collection

DiffractionMean temperature: 190 K / Ambient temp details: Liquid Nitrogen Steam / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→45.822 Å / Num. obs: 38650 / % possible obs: 97.8 % / Redundancy: 12.938 % / Biso Wilson estimate: 36.27 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.102 / Rrim(I) all: 0.107 / Χ2: 0.83 / Net I/σ(I): 13.34 / Num. measured all: 500053 / Scaling rejects: 100
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.8512.6422.4241.1734828288827550.5892.52595.4
1.85-1.913.9761.8971.6537540278226860.7271.96896.5
1.9-1.9513.8881.2472.5936831274126520.8961.29496.8
1.95-2.0113.6580.9173.4835537267526020.9420.95297.3
2.01-2.0813.4460.7114.3833616256925000.9570.73997.3
2.08-2.1512.9420.5195.6831487249624330.9720.5497.5
2.15-2.2312.5330.3677.4329754244023740.9810.38397.3
2.23-2.3213.6810.3079.3631014231422670.9910.31998
2.32-2.4313.4860.25510.8229466223121850.9910.26497.9
2.43-2.5513.240.18313.727870214221050.9950.1998.3
2.55-2.6812.8180.14416.1525469202219870.9960.1598.3
2.68-2.8511.7050.10919.422158193218930.9960.11498
2.85-3.0413.0390.09423.6323666183818150.9970.09898.7
3.04-3.2912.8260.08127.8821419168916700.9980.08498.9
3.29-3.612.5250.07430.1919664158215700.9970.07799.2
3.6-4.0211.5810.07131.4516445143314200.9970.07499.1
4.02-4.6511.8050.06933.5715052128412750.9970.07299.3
4.65-5.6912.2620.06934.6113316108810860.9970.07299.8
5.69-8.0510.9530.0732.4995078728680.9970.07499.5
8.05-45.82210.6790.06833.6354145155070.9950.07298.4

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Processing

Software
NameVersionClassification
PHENIXdev_2481refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6W41

6w41


Resolution: 1.8→45.822 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2262 2013 5.21 %
Rwork0.1863 36601 -
obs0.1884 38614 97.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130 Å2 / Biso mean: 50.3602 Å2 / Biso min: 26.16 Å2
Refinement stepCycle: final / Resolution: 1.8→45.822 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2507 0 14 175 2696
Biso mean--78.43 52.18 -
Num. residues----324
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162631
X-RAY DIFFRACTIONf_angle_d1.3563596
X-RAY DIFFRACTIONf_chiral_restr0.09387
X-RAY DIFFRACTIONf_plane_restr0.009467
X-RAY DIFFRACTIONf_dihedral_angle_d6.4382064
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8001-1.84510.32491360.3477249495
1.8451-1.8950.30941380.3008256297
1.895-1.95070.28141360.2618252896
1.9507-2.01370.30881420.2305257297
2.0137-2.08570.2881450.2217256197
2.0857-2.16920.23681440.2085258098
2.1692-2.26790.2371440.1973258397
2.2679-2.38740.21281430.1934260198
2.3874-2.5370.22471370.1858262898
2.537-2.73290.23131460.1922261998
2.7329-3.00790.21041510.1958264598
3.0079-3.4430.20541460.1889266999
3.443-4.33730.22791460.1664271599
4.3373-45.820.21451590.1644284499
Refinement TLS params.Method: refined / Origin x: -31.2504 Å / Origin y: -34.6142 Å / Origin z: 32.1937 Å
111213212223313233
T0.3131 Å20.0238 Å20.0061 Å2-0.3063 Å2-0.0031 Å2--0.1937 Å2
L1.2873 °21.6189 °20.5487 °2-3.4124 °21.1493 °2--1.0821 °2
S0.0915 Å °-0.1218 Å °-0.0058 Å °0.1507 Å °-0.2183 Å °0.1303 Å °0.0643 Å °-0.1168 Å °0.125 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 128
2X-RAY DIFFRACTION1allB333 - 601
3X-RAY DIFFRACTION1allS1 - 179

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