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- PDB-7ul0: Crystal structure of SARS-CoV-2 RBD in complex with the ridge-bin... -

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Basic information

Entry
Database: PDB / ID: 7ul0
TitleCrystal structure of SARS-CoV-2 RBD in complex with the ridge-binding nAb EH8 isolated from a nonvaccinated pediatric patient
Components
  • Heavy chain of EH8
  • Light chain of EH8
  • Spike protein S1
KeywordsVIRAL PROTEIN/Immune System / Pediatric neutralizing mAb / RBD-ridge-targeting / bind to both closed and open SARS-CoV-2 spike / Class-2 RBD-binding antibody / VIRAL PROTEIN / VIRAL PROTEIN-Immune System 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 speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsChen, Y. / Tolbert, W.D. / Bai, X. / Pazgier, M.
Funding support United States, 1items
OrganizationGrant numberCountry
Other governmentStart-up funds from the Uniformed Services University of the Health Sciences United States
CitationJournal: Iscience / Year: 2023
Title: Molecular basis for antiviral activity of two pediatric neutralizing antibodies targeting SARS-CoV-2 Spike RBD.
Authors: Chen, Y. / Prevost, J. / Ullah, I. / Romero, H. / Lisi, V. / Tolbert, W.D. / Grover, J.R. / Ding, S. / Gong, S.Y. / Beaudoin-Bussieres, G. / Gasser, R. / Benlarbi, M. / Vezina, D. / Anand, S. ...Authors: Chen, Y. / Prevost, J. / Ullah, I. / Romero, H. / Lisi, V. / Tolbert, W.D. / Grover, J.R. / Ding, S. / Gong, S.Y. / Beaudoin-Bussieres, G. / Gasser, R. / Benlarbi, M. / Vezina, D. / Anand, S.P. / Chatterjee, D. / Goyette, G. / Grunst, M.W. / Yang, Z. / Bo, Y. / Zhou, F. / Beland, K. / Bai, X. / Zeher, A.R. / Huang, R.K. / Nguyen, D.N. / Sherburn, R. / Wu, D. / Piszczek, G. / Pare, B. / Matthies, D. / Xia, D. / Richard, J. / Kumar, P. / Mothes, W. / Cote, M. / Uchil, P.D. / Lavallee, V.P. / Smith, M.A. / Pazgier, M. / Haddad, E. / Finzi, A.
History
DepositionApr 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 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: Spike protein S1
H: Heavy chain of EH8
L: Light chain of EH8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2636
Polymers71,5953
Non-polymers6693
Water1,838102
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.771, 100.709, 106.019
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Spike protein S1


Mass: 24658.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2

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Antibody , 2 types, 2 molecules HL

#2: Antibody Heavy chain of EH8


Mass: 23636.473 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: Antibody Light chain of EH8


Mass: 23299.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Sugars , 2 types, 2 molecules

#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
#5: 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

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Non-polymers , 2 types, 103 molecules

#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 3.05 Å3/Da / Density % sol: 59.65 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M sodium chloride, 0.1 M Na HEPES pH 7.5, 12% w/v PEG 8000
PH range: 7.0-7.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Oct 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.49→50 Å / Num. obs: 31070 / % possible obs: 99.9 % / Redundancy: 18.8 % / Biso Wilson estimate: 57.01 Å2 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.034 / Rrim(I) all: 0.148 / Χ2: 1.193 / Net I/σ(I): 5.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.49-2.5916.61.03730140.8770.2591.070.432100
2.59-2.6916.90.80530270.940.1970.8290.48499.9
2.69-2.8220.20.63830210.9660.1460.6550.521100
2.82-2.9620.30.44230330.9840.1010.4540.606100
2.96-3.1519.90.31130390.9880.0720.320.787100
3.15-3.3919.50.21930490.9930.0510.2251.062100
3.39-3.7318.40.16530540.9950.040.171.426100
3.73-4.2718.50.12130810.9960.0280.1251.9799.8
4.27-5.3819.80.10131170.9980.0230.1042.38899.9
5.38-5017.90.08432540.9980.020.0862.09399.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7S4S, 7NAB

7s4s

7nab


Resolution: 2.49→46.91 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2559 2008 6.46 %
Rwork0.2246 29062 -
obs0.2266 31070 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 167.62 Å2 / Biso mean: 62.5875 Å2 / Biso min: 26.96 Å2
Refinement stepCycle: final / Resolution: 2.49→46.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4826 0 43 102 4971
Biso mean--96.86 49.96 -
Num. residues----632
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.49-2.550.42031290.42531803193288
2.55-2.620.42191400.369820682208100
2.62-2.70.40491350.323320552190100
2.7-2.790.341420.293520842226100
2.79-2.880.34451460.272320642210100
2.88-30.32391470.275620512198100
3-3.140.32711400.286320802220100
3.14-3.30.35591440.290320822226100
3.3-3.510.29351490.231220782227100
3.51-3.780.23691440.220620852229100
3.78-4.160.22941380.201721042242100
4.16-4.760.16921540.165421222276100
4.76-60.21851440.181521412285100
6-46.910.21331560.193622452401100
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)
11.3233-0.4694-0.19340.43260.34010.96290.13940.4159-0.1545-0.38470.1252-0.01880.5440.02050.12150.61710.0847-0.04490.4544-0.15280.420922.5751-49.2248-10.6996
20.86770.0721-0.9471.18740.391.9746-0.1354-0.6758-0.74340.13460.2038-0.11341.13710.4310.25480.77940.06-0.04120.53070.27240.783723.1797-56.00532.8684
31.7014-0.10290.9492.6047-1.631.2293-0.08550.00580.1028-0.15050.1373-0.07550.02950.27180.00090.3280.00810.03890.3985-0.03560.302725.76-37.3145-5.0104
40.16620.3045-0.47260.8298-0.90540.4269-0.0270.81520.5121-0.30630.0519-0.1149-0.11830.26410.00440.5076-0.05260.01580.50350.10840.569923.6726-18.0578-14.7233
51.3309-1.48340.56741.99850.19271.37890.4127-0.66090.23730.1902-0.39670.4858-0.07810.28590.00050.33520.07060.05750.5274-0.01020.429326.0794-45.8964-3.9748
60.26012.6043-0.61613.8642-0.45341.14760.062-0.0753-0.15970.7079-0.2534-0.6698-0.09510.102-0.00050.5056-0.0097-0.08770.4610.10910.729534.9054.1575-13.3434
70.2345-0.1991-0.38980.47080.29650.47530.1370.15430.3411-0.0729-0.38571.1118-0.3367-0.38650.00350.78140.1799-0.12990.5794-0.00890.483634.771442.4093-30.169
80.97661.24090.5632.4814-0.78351.37680.0652-0.5582-0.03710.66820.13290.0804-0.3265-0.2890.60490.59750.10360.07630.55810.02430.209635.040633.0066-22.3693
90.84690.5284-0.65090.87340.2650.7773-0.10010.1503-0.2892-0.89210.20610.34420.6942-0.2089-0.00020.6885-0.07650.0640.65710.15870.568927.74563.6532-38.9764
101.08630.7766-0.47821.2111-1.45721.95820.0160.15110.11440.14360.01660.26370.0242-0.230800.42-0.1174-0.03490.44520.09340.680622.12381.1252-28.3046
11-0.8281-0.325-0.37310.4855-0.66160.8862-0.15610.17940.0229-0.48710.18680.06090.3411-0.151-0.00050.4027-0.068-0.02810.38750.15950.492425.54585.3374-34.5153
121.5014-0.335-0.08432.0982-0.97560.8240.0205-0.071-0.11690.32320.0665-0.1144-0.1586-0.07130.00050.46660.05130.02970.46290.02120.271539.869432.7801-36.2572
131.23530.9893-0.59840.3931-0.32231.07040.12480.07560.12740.01030.0781-0.157-0.29510.29660.00040.47520.0158-0.0060.4321-0.02830.383344.612240.4317-38.9474
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 334 through 358 )A334 - 358
2X-RAY DIFFRACTION2chain 'A' and (resid 359 through 393 )A359 - 393
3X-RAY DIFFRACTION3chain 'A' and (resid 394 through 469 )A394 - 469
4X-RAY DIFFRACTION4chain 'A' and (resid 470 through 494 )A470 - 494
5X-RAY DIFFRACTION5chain 'A' and (resid 495 through 527 )A495 - 527
6X-RAY DIFFRACTION6chain 'H' and (resid 1 through 119 )H1 - 119
7X-RAY DIFFRACTION7chain 'H' and (resid 120 through 134 )H120 - 134
8X-RAY DIFFRACTION8chain 'H' and (resid 135 through 215 )H135 - 215
9X-RAY DIFFRACTION9chain 'L' and (resid 1 through 24 )L1 - 24
10X-RAY DIFFRACTION10chain 'L' and (resid 25 through 61 )L25 - 61
11X-RAY DIFFRACTION11chain 'L' and (resid 62 through 112 )L62 - 112
12X-RAY DIFFRACTION12chain 'L' and (resid 113 through 173 )L113 - 173
13X-RAY DIFFRACTION13chain 'L' and (resid 174 through 213 )L174 - 213

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