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- PDB-8qh1: Crystal structure of the SARS-CoV-2 RBD from the Omicron BA4 vari... -

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Basic information

Entry
Database: PDB / ID: 8qh1
TitleCrystal structure of the SARS-CoV-2 RBD from the Omicron BA4 variant with the antibody Cv2.3194
Components
  • Cv2.3194 heavy chain
  • IGK@ protein
  • Spike glycoprotein
KeywordsVIRAL PROTEIN / Coronavirus Neutralizing Antibody
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 / immune response / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / extracellular space / membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulin / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulin / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / 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 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Spike glycoprotein / IGK@ protein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsFernandez, I. / Rey, F.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Pan-neutralizing antibody isolated from a COVID patient
Authors: Planchais, C. / Fernandez, I. / Rey, F.A. / Mouquet, H.
History
DepositionSep 6, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Spike glycoprotein
H: Cv2.3194 heavy chain
L: IGK@ protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,9204
Polymers74,6983
Non-polymers2211
Water1448
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-21 kcal/mol
Surface area27700 Å2
Unit cell
Length a, b, c (Å)57.793, 85.348, 193.987
Angle α, β, γ (deg.)90.000, 97.480, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)

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Components

#1: Protein Spike glycoprotein


Mass: 27508.818 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: A0A8A5XRG7
#2: Antibody Cv2.3194 heavy chain


Mass: 24379.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein IGK@ protein


Mass: 22810.342 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGK@ / Production host: Homo sapiens (human) / References: UniProt: Q6PJF2
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 3.42 Å3/Da / Density % sol: 64.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2 M sodium malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.919 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919 Å / Relative weight: 1
ReflectionResolution: 2.65→39.01 Å / Num. obs: 27213 / % possible obs: 99.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 69.23 Å2 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.06 / Net I/σ(I): 6.7
Reflection shellResolution: 2.65→2.78 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1.489 / Num. unique obs: 3610 / Rpim(I) all: 0.952 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→39.01 Å / SU ML: 0.4066 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.9626
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2323 1402 5.16 %
Rwork0.1976 25785 -
obs0.1994 27187 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 79.66 Å2
Refinement stepCycle: LAST / Resolution: 2.65→39.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4729 0 14 8 4751
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00184859
X-RAY DIFFRACTIONf_angle_d0.52886612
X-RAY DIFFRACTIONf_chiral_restr0.043739
X-RAY DIFFRACTIONf_plane_restr0.0051853
X-RAY DIFFRACTIONf_dihedral_angle_d10.26211737
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.740.36671390.35042551X-RAY DIFFRACTION99.41
2.74-2.850.37851500.3332575X-RAY DIFFRACTION99.82
2.85-2.980.35961560.30712528X-RAY DIFFRACTION99.7
2.98-3.140.33021510.26372588X-RAY DIFFRACTION99.82
3.14-3.340.29941490.24772550X-RAY DIFFRACTION99.89
3.34-3.60.25611230.21992598X-RAY DIFFRACTION99.71
3.6-3.960.22281360.2092571X-RAY DIFFRACTION99.63
3.96-4.530.18241400.15722591X-RAY DIFFRACTION99.42
4.53-5.70.17151420.14842597X-RAY DIFFRACTION99.6
5.7-39.010.19751160.16232636X-RAY DIFFRACTION98.43
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)
12.99210234110.619759739004-0.08382084746882.070374384620.6822922843212.25099592069-0.07359927422370.4088516195810.614222557572-0.533331824186-0.2314643577290.435535090325-0.882248736202-0.6927142718810.2061084863230.902303063960.0757480470098-0.1061439154840.8579085077580.007488599718720.805282912301-12.83081373544.4740647258216.6312019307
22.18854993362-0.7811294208340.7675220185572.756630313880.5345954041265.482480424060.1373044709480.1011240591640.0559001095626-0.142849054426-0.2074690129130.2115556023070.265247175229-0.5878540355090.08057240283330.464448931623-0.0519164650187-0.001568634581470.548379384036-0.08827868250750.570515651751-7.332077733-4.2797176812531.0912000111
32.349703206550.392011491903-0.5407401095441.200883649951.311225626565.733507231220.00384614575143-0.181200082615-0.1228802097620.1327976298370.245889261273-0.2611492050340.5898023209280.918277637447-0.2032118383630.5008762171380.127093006555-0.02560723115880.526710037065-0.1191962461420.60870987603814.165141701-5.7560633550948.8339661981
43.314207810840.7378117001830.6766527332561.52653729254-0.7478672432240.73042363823-0.001258080817580.350435757774-0.1530298447450.111136992383-0.0164077428494-0.106213328825-0.754248212924-0.534241722945-0.04831779754510.5230739532640.213425379155-0.05162323222080.849327794759-0.05678378545140.67858662643630.945727298.6674559590376.8994856982
54.18565140454-0.101865361503-1.153100239722.517769052690.67826456133.12988831546-0.08358033740930.224432887349-0.4998598049020.4458807787870.186790081351-0.3544921876930.459742537780.381204827074-0.1667563993530.5726002473870.167447738353-0.06754136154970.559615037506-0.1013225144640.5569154647529.13990224643.2569224081881.3511452474
62.50477638409-0.5632991086941.853957120882.83870290321.333488130113.519048947050.0573992656045-0.1924200709310.1094435915180.0432686322455-0.3028855741580.196419699872-0.301159604857-1.211572770720.2102900187210.5264530084820.02018194129270.09706544814330.810947231646-0.1444301991630.659453879491-4.945125071175.5598100633462.8641037576
73.827302461850.323713085467-1.563015456922.295511096921.50220101134.346786008970.0267195441513-0.214706352936-0.05219257534860.254879827337-0.00901482704660.02169435441470.75208145943-0.766783272707-0.00664567060090.635953918663-0.0786323482559-0.004823212793730.61040478578-0.07897162834380.573588063827-2.89215332849-3.844697919862.0283200487
81.561960217861.207005392780.8593778108371.64916021877-0.09841636317251.29389089774-0.2091068605220.227347629985-0.620012010708-0.01858436725670.115423225114-0.2326451038380.2324861605080.05876930511410.07380346387760.5449914781190.05506588240970.0184096554410.597630476127-0.1358355799340.51232233246318.64184952912.279885123281.5215584437
93.959419404343.378900352760.171365507786.14888820411-0.7625972398012.88453056866-0.2813816249640.591512131915-0.06861003031510.6286679007390.539702874339-0.0133499882432-0.168103866161-0.172614646191-0.2243635263890.58675468310.08758278209860.01271623726630.588108185-0.03630786838130.46641569110116.609782615115.254016554977.7552800238
104.060720565481.939468404340.3409504396774.216618946070.4302033838932.27555119612-0.0385332279662-0.1595100598950.6806416004320.291239438888-0.04908338707920.0808028088353-0.07686401233410.4179324157730.1066129465010.6198423846990.0532896962557-0.06982473987080.5955053915070.004130768695070.52184160359923.792127166123.045501322982.1717439661
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'E' and (resid 333 through 393 )EA333 - 3931 - 58
22chain 'E' and (resid 394 through 527 )EA394 - 52759 - 192
33chain 'H' and (resid 1 through 113 )HC1 - 1131 - 113
44chain 'H' and (resid 114 through 138 )HC114 - 138114 - 136
55chain 'H' and (resid 139 through 219 )HC139 - 219137 - 217
66chain 'L' and (resid 1 through 30 )LD1 - 301 - 30
77chain 'L' and (resid 31 through 99 )LD31 - 9931 - 99
88chain 'L' and (resid 100 through 140 )LD100 - 140100 - 140
99chain 'L' and (resid 141 through 171 )LD141 - 171141 - 171
1010chain 'L' and (resid 172 through 210 )LD172 - 210172 - 210

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