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- PDB-7q3r: Crystal structure of SARS-CoV-2 RBD in complex with the neutraliz... -

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Basic information

Entry
Database: PDB / ID: 7q3r
TitleCrystal structure of SARS-CoV-2 RBD in complex with the neutralizing nanobodies VHH-F04 and VHH-G09
Components
  • Spike glycoproteinSpike protein
  • VHH-F04
  • VHH-G09
KeywordsVIRAL PROTEIN / Coronavirus / nanobody
Function / homology
Function and homology information


endocytosis involved in viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / membrane => GO:0016020 / 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 / 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 speciesSevere acute respiratory syndrome coronavirus 2
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsFernandez, I. / Pederzoli, R. / Rey, F.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: NANOBODIES AGAINST SARS-COV-2 NEUTRALIZE VARIANTS OF CONCERN AND EXPLORE CONFORMATIONAL DIFFERENCES ON THE SPIKE PROTEIN
Authors: Fernandez, I. / Rey, F.A.
History
DepositionOct 28, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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: Spike glycoprotein
F: VHH-F04
G: VHH-G09
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1219
Polymers52,5193
Non-polymers6026
Water4,990277
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-46 kcal/mol
Surface area19630 Å2
Unit cell
Length a, b, c (Å)180.578, 180.578, 48.025
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

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Antibody , 2 types, 2 molecules FG

#2: Antibody VHH-F04


Mass: 15465.069 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Homo sapiens (human)
#3: Antibody VHH-G09


Mass: 14776.256 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Spike glycoprotein / Spike protein / S glycoprotein / E2 / Peplomer protein


Mass: 22277.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Homo sapiens (human) / References: UniProt: A0A6H2EIN2
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 2 types, 282 molecules

#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.3 Å3/Da / Density % sol: 71.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 0.1 M NaAc/HAc (pH 4.5), 0.2 M Li2SO4, 2.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.978565 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 1.92→48.03 Å / Num. obs: 69234 / % possible obs: 99.8 % / Redundancy: 20.7 % / Biso Wilson estimate: 40.05 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.018 / Rrim(I) all: 0.081 / Net I/σ(I): 22.5 / Num. measured all: 1433441
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.92-1.9720.31.45610099949870.860.3271.4932.197.6
8.57-48.0319.10.052162688500.9990.0120.05461.999.4

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YM0

6ym0


Resolution: 1.92→45.91 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.209 3502 5.06 %
Rwork0.1819 65675 -
obs0.1833 69177 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.18 Å2 / Biso mean: 46.6338 Å2 / Biso min: 25.71 Å2
Refinement stepCycle: final / Resolution: 1.92→45.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3392 0 33 277 3702
Biso mean--77.56 50.03 -
Num. residues----441
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.92-1.940.37661330.36172535266897
1.94-1.970.31191330.284525762709100
1.97-20.23841250.2426602785100
2-2.030.22961390.209925912730100
2.03-2.060.22891300.185526102740100
2.06-2.10.21791330.18126392772100
2.1-2.140.21091450.184425692714100
2.14-2.180.19831350.197926682803100
2.18-2.220.2411560.207825702726100
2.22-2.270.251300.221626172747100
2.27-2.320.26771210.205626152736100
2.32-2.380.27331650.215426022767100
2.38-2.450.25781380.200826162754100
2.45-2.520.2261570.196726142771100
2.52-2.60.21681340.202426082742100
2.6-2.690.2491420.212226352777100
2.69-2.80.22191410.217326362777100
2.8-2.930.28881480.234526102758100
2.93-3.080.28931460.212326222768100
3.08-3.280.2411190.197226722791100
3.28-3.530.21451540.176526272781100
3.53-3.880.18711430.162626412784100
3.88-4.450.14061400.134926952835100
4.45-5.60.15071440.138126692813100
5.6-45.910.18391510.169827782929100
Refinement TLS params.Method: refined / Origin x: 57.0235 Å / Origin y: 56.8455 Å / Origin z: 18.1546 Å
111213212223313233
T0.2279 Å20.0028 Å2-0.006 Å2-0.3605 Å2-0.0164 Å2--0.282 Å2
L0.8026 °2-0.4642 °20.0193 °2-0.7848 °2-0.0834 °2--0.8544 °2
S0.0058 Å °-0.0434 Å °-0.0646 Å °0.0074 Å °0.0161 Å °0.175 Å °0.0096 Å °-0.2525 Å °-0.0256 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA334 - 528
2X-RAY DIFFRACTION1allA529 - 530
3X-RAY DIFFRACTION1allF2 - 128
4X-RAY DIFFRACTION1allG1 - 121
5X-RAY DIFFRACTION1allC1 - 5
6X-RAY DIFFRACTION1allW1 - 282

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