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- PDB-7q3q: Crystal structure of SARS-CoV-2 RBD in complex with the neutraliz... -

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Basic information

Entry
Database: PDB / ID: 7q3q
TitleCrystal structure of SARS-CoV-2 RBD in complex with the neutralizing nanobody VHH-12
Components
  • Spike glycoprotein
  • VHH-12
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 / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / 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 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / 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 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesVicugna pacos (alpaca)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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
Revision 1.2Oct 23, 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
B: VHH-12
A: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,45510
Polymers37,5522
Non-polymers9038
Water2,414134
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-45 kcal/mol
Surface area15460 Å2
Unit cell
Length a, b, c (Å)62.451, 62.451, 218.525
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-757-

HOH

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Components

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Antibody / Protein / Sugars , 3 types, 3 molecules BA

#1: Antibody VHH-12


Mass: 15274.132 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Homo sapiens (human)
#2: Protein Spike glycoprotein / 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
#3: 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 , 4 types, 141 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.84 Å3/Da / Density % sol: 56.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% PEG 4000, 0.1 M Tris-HCl (pH 8.5) and 0.2 M Li2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980112 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980112 Å / Relative weight: 1
ReflectionResolution: 2.3→47.41 Å / Num. obs: 20030 / % possible obs: 99.4 % / Redundancy: 52.1 % / Biso Wilson estimate: 49.8 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.016 / Rrim(I) all: 0.116 / Net I/σ(I): 32.4 / Num. measured all: 1043029
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
2.3-2.3855.21.76110617119230.8860.2361.7773.599
8.91-47.4139.90.0341741343610.0050.03489.499.6

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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: 2.3→47.41 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2202 1018 5.09 %
Rwork0.1849 18984 -
obs0.1866 20002 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122.79 Å2 / Biso mean: 52.8057 Å2 / Biso min: 28.33 Å2
Refinement stepCycle: final / Resolution: 2.3→47.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2502 0 54 134 2690
Biso mean--78.15 51.97 -
Num. residues----321
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.420.33911450.28272619276499
2.42-2.570.25431470.22832626277399
2.57-2.770.29161340.23622666280099
2.77-3.050.32411600.2182653281399
3.05-3.490.22891500.19252707285799
3.49-4.40.21480.1627452893100
4.4-47.410.15941340.161929683102100
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)
15.6174-5.39380.79725.55030.26712.9983-1.4638-0.30552.40251.0859-0.0808-2.3537-2.6091.19021.59010.8536-0.2141-0.27290.65120.10290.83798.2387-0.086-18.4795
25.77715.6419-6.38785.5183-6.32737.39130.2709-0.5769-0.3907-0.0798-0.8282-0.76580.13961.25910.49510.4371-0.0806-0.14330.6870.13720.472917.7189-17.6494-4.7263
35.3084-5.40285.85869.0799-4.22467.4095-0.9386-0.75420.82980.14190.2161-0.2588-1.0248-0.29140.670.5678-0.0243-0.11760.4565-0.01020.42292.2815-5.4854-16.1012
48.8555-4.3156-2.7922.32581.72796.00250.05280.7240.5531-0.93320.1627-0.4389-0.4631.3206-0.18230.4847-0.0682-0.00610.83150.02660.450413.8646-16.0933-21.8285
50.37060.1466-1.41447.7453-0.44416.61410.2972-0.1978-0.48360.188-0.20990.1720.3534-0.0316-0.1390.4231-0.0363-0.11050.36470.00990.3711-1.3161-16.6039-20.3435
69.0453-5.61794.20724.3578-4.23734.9838-0.299-0.6706-0.20160.72530.39950.253-0.2128-0.1593-0.08030.4767-0.03-0.05140.38710.05640.35973.1938-14.8954-12.1203
73.3143-4.54943.41937.9735-3.96363.97170.28750.4176-0.4289-0.8493-0.17690.24760.31140.46110.07440.43820.0086-0.07430.55160.03480.424314.0854-18.0026-14.2201
86.54430.6249-0.49063.62723.81544.37680.05930.95170.5783-0.4675-0.4466-0.225-0.80840.58190.35990.4753-0.0025-0.10160.4290.08090.3661-0.9497-12.3994-28.2853
97.8549-2.74375.94025.8141-2.24614.4473-0.67110.31540.06480.16660.2737-0.0766-0.86150.81310.57630.4211-0.0418-0.00020.57680.07130.332712.2328-11.0677-20.6668
105.47550.12822.27492.707-0.16831.7507-0.1586-0.3050.54510.0298-0.19740.3155-0.4253-0.35860.38370.56780.1108-0.07950.4693-0.15020.4664-28.2693-8.382-43.3441
114.30626.35144.92029.41627.16796.3784-0.44040.63541.5533-0.9850.36650.6512-2.01870.07420.15010.96430.0165-0.07480.49110.08650.5508-23.8266-3.3717-56.7015
126.53190.05412.32950.5909-0.20764.59940.20040.3975-0.0298-0.2485-0.10850.0148-0.04630.1227-0.09860.54150.0441-0.06470.2768-0.0650.4107-20.4656-16.1719-51.2713
132.8579-0.7153.19380.6215-0.82646.09090.207-0.0174-0.2926-0.1623-0.11110.06310.3081-0.0954-0.13870.38740.0074-0.02230.3046-0.03110.3614-11.6788-18.9481-36.3459
145.22445.1693-5.5745.1098-5.49367.17490.1925-0.5340.00070.2914-0.0183-0.9397-0.13350.5026-0.01840.5222-0.0757-0.1050.4785-0.00870.5697-3.7672-5.3621-43.224
156.52295.95413.45695.34183.2552.05020.35910.0284-0.1475-0.0448-0.29670.1820.0214-0.1352-0.01270.50020.0842-0.16280.426-0.04530.4366-30.4617-14.9559-49.7158
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 3 through 9 )B3 - 9
2X-RAY DIFFRACTION2chain 'B' and (resid 10 through 19 )B10 - 19
3X-RAY DIFFRACTION3chain 'B' and (resid 20 through 35 )B20 - 35
4X-RAY DIFFRACTION4chain 'B' and (resid 36 through 47 )B36 - 47
5X-RAY DIFFRACTION5chain 'B' and (resid 48 through 62 )B48 - 62
6X-RAY DIFFRACTION6chain 'B' and (resid 63 through 85 )B63 - 85
7X-RAY DIFFRACTION7chain 'B' and (resid 86 through 100 )B86 - 100
8X-RAY DIFFRACTION8chain 'B' and (resid 101 through 112 )B101 - 112
9X-RAY DIFFRACTION9chain 'B' and (resid 113 through 128 )B113 - 128
10X-RAY DIFFRACTION10chain 'A' and (resid 334 through 364 )A334 - 364
11X-RAY DIFFRACTION11chain 'A' and (resid 365 through 375 )A365 - 375
12X-RAY DIFFRACTION12chain 'A' and (resid 376 through 421 )A376 - 421
13X-RAY DIFFRACTION13chain 'A' and (resid 422 through 494 )A422 - 494
14X-RAY DIFFRACTION14chain 'A' and (resid 495 through 506 )A495 - 506
15X-RAY DIFFRACTION15chain 'A' and (resid 507 through 526 )A507 - 526

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