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- PDB-7ul1: Crystal structure of SARS-CoV-2 RBD in complex with the neutraliz... -

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Basic information

Entry
Database: PDB / ID: 7ul1
TitleCrystal structure of SARS-CoV-2 RBD in complex with the neutralizing IGHV3-53-encoded antibody EH3 isolated from a nonvaccinated pediatric patient
Components
  • Heavy chain of EH3
  • Light chain of EH3
  • Spike protein S1
KeywordsVIRAL PROTEIN/Immune System / Pediatric neutralizing mAb / IGHV3-53 Ab / / Class-1 RBD-binding antibody / VIRAL PROTEIN / VIRAL PROTEIN-Immune System complex
Function / homology
Function and homology information


symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / membrane fusion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / membrane fusion / entry receptor-mediated virion attachment to host cell / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / endocytosis involved in viral entry into host cell / receptor ligand activity / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / 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 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / 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 (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, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / 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 glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus spike glycoprotein S1, receptor binding / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2 superfamily, coronavirus / 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, coronavirus / Coronavirus spike glycoprotein S2 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsChen, Y. / Tolbert, W.D. / 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
Revision 1.2Nov 13, 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
A: Spike protein S1
H: Heavy chain of EH3
L: Light chain of EH3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3784
Polymers70,1563
Non-polymers2211
Water2,594144
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)86.691, 103.117, 112.344
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein Spike protein S1


Mass: 23593.588 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus
Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#2: Antibody Heavy chain of EH3


Mass: 23282.135 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 EH3


Mass: 23280.729 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#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.: 144 / Source method: isolated from a natural source / Formula: H2O
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: 3.58 Å3/Da / Density % sol: 65.63 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1M sodium citrate pH 5.0, 8% w/v PEG8000 / PH range: 5.0-7.0

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.65→35 Å / Num. obs: 29750 / % possible obs: 99.4 % / Redundancy: 6.6 % / Biso Wilson estimate: 39.62 Å2 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.079 / Rrim(I) all: 0.206 / Χ2: 0.909 / Net I/σ(I): 3.7 / Num. measured all: 197624
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.65-2.746.60.7229380.7720.3010.7820.56799.8
2.74-2.856.20.60428940.8380.260.660.58399
2.85-2.9870.46829550.9030.1910.5060.64299.8
2.98-3.146.90.34929400.9340.1420.3780.74199.8
3.14-3.346.80.28529460.9450.1170.3090.85699.4
3.34-3.66.60.22229390.9610.0930.2411.04499.5
3.6-3.966.60.16729940.9740.070.1811.03799.7
3.96-4.536.90.13529830.9840.0550.1461.27899.9
4.53-5.76.40.1229990.9830.0510.1311.18498.4
5.7-356.50.11931620.9830.0520.131.11999.1

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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: 2.65→34.79 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 21.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2206 2002 6.74 %
Rwork0.174 27698 -
obs0.1772 29700 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 164.95 Å2 / Biso mean: 45.1853 Å2 / Biso min: 14.44 Å2
Refinement stepCycle: final / Resolution: 2.65→34.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4804 0 14 144 4962
Biso mean--99.79 42.48 -
Num. residues----628
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 (%)
2.65-2.720.31461340.24241935206998
2.72-2.790.27971290.23091971210099
2.79-2.870.29851650.24351919208499
2.87-2.960.28621340.226719532087100
2.96-3.070.29711500.208819392089100
3.07-3.190.21921310.198519842115100
3.19-3.340.26951510.19521951210299
3.34-3.510.23241430.19571961210499
3.51-3.730.24161390.18052001214099
3.73-4.020.19931360.152319612097100
4.02-4.430.17591520.133619942146100
4.43-5.060.13011400.12082007214799
5.07-6.370.18871510.14962000215198
6.38-34.790.22721470.17272122226998
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)
12.64390.85880.12444.8540.0451.318-0.154-0.0549-0.6443-0.0280.16670.08420.9912-0.3303-0.12030.7164-0.10170.02320.37340.01890.49419.4841-42.417-3.1512
23.3854-1.58720.24975.31170.40770.78830.0265-0.1162-0.48270.3830.05440.75110.96950.0181-0.11570.71020.09290.01420.2705-0.01790.251416.6782-40.79681.1403
31.7708-0.3763-1.30115.19670.05281.975-0.03560.2219-0.6818-0.34730.1547-0.20810.92030.289-0.06740.860.1165-0.00190.5383-0.13350.549821.6714-45.6352-12.3627
42.90690.1885-0.48634.51981.09953.41560.01880.04470.0267-0.01450.0948-0.23170.24010.4293-0.07080.2568-0.01550.01540.2474-0.02960.215319.8164-28.1079-7.2529
51.76710.38850.16374.94811.26473.5266-0.03230.1537-0.0294-0.0981-0.01310.29610.2481-0.1985-0.00080.2919-0.05790.02060.28120.01920.188813.5496-27.239-6.2888
61.617-0.8559-0.74924.31680.76041.0240.0196-0.1713-0.0030.5784-0.00070.02260.0788-0.1408-0.00660.36660.04250.03620.34680.0310.223316.1324-14.025.3071
71.17011.4206-0.93373.62911.79671.4346-0.3948-0.09410.25330.38440.2284-0.59850.183-0.05020.13140.3880.02940.04640.3683-0.0710.266816.7684-37.307-7.3626
8-0.24860.0899-0.19220.80830.0520.36410.0519-0.16970.06720.1951-0.1498-0.1542-0.18740.2118-00.18490.00340.01270.180.01350.207828.47921.2287-9.7595
90.95260.4034-0.24871.2137-0.3451.1725-0.060.0908-0.0127-0.09450.0102-0.08250.06830.0189-0.2180.1867-0.00270.0130.1878-0.00120.168427.9427-2.0917-14.7575
106.64852.0239-0.36866.803-2.02035.30.0423-0.17971.22580.22570.21351.7203-1.1244-1.4593-0.17660.79640.1615-0.02360.5531-0.0030.715621.310738.1624-26.3916
113.6674-1.7537-0.60633.71770.36112.9493-0.2122-0.28020.07190.23850.03250.0009-0.52760.03080.17220.36320.0225-0.00160.2733-0.02880.233426.10227.9342-20.6643
120.20350.40960.10560.38230.09630.1233-0.05960.391-0.6799-0.1912-0.02690.4774-0.1335-0.1419-0.01060.1559-0.0109-0.03920.34540.1060.28653.77881.8628-25.4755
130.4888-0.59230.74120.5615-0.63390.7995-0.0136-0.0715-0.05160.07570.11070.2302-0.1293-0.248600.2405-0.01680.0350.28660.01950.29875.3976-2.363-15.8735
141.12420.5742-0.28050.67450.18290.9777-0.07750.41070.12420.48550.11720.1832-0.4406-0.02780.04050.03850.03480.01990.19380.0450.17197.20736.1149-21.1923
152.14320.1399-0.50753.5241-1.67863.0756-0.0301-0.22090.1069-0.05040.08360.0217-0.150.1803-0.05030.38970.06440.02740.2656-0.05270.271420.296930.5155-33.6743
161.07640.4555-0.74144.2984-5.18945.59790.2340.2531-0.1318-0.2861-0.17950.2922-0.01420.27130.0860.56360.0264-0.0060.3486-0.04930.315621.536226.975-42.0982
175.03272.9008-3.08122.839-1.24153.104-0.02560.10370.15960.00530.09870.0572-0.2881-0.1038-0.10330.39410.0979-0.01830.2617-0.00930.269417.738231.3187-35.7943
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 334 through 349 )A334 - 349
2X-RAY DIFFRACTION2chain 'A' and (resid 350 through 364 )A350 - 364
3X-RAY DIFFRACTION3chain 'A' and (resid 365 through 393 )A365 - 393
4X-RAY DIFFRACTION4chain 'A' and (resid 394 through 421 )A394 - 421
5X-RAY DIFFRACTION5chain 'A' and (resid 422 through 459 )A422 - 459
6X-RAY DIFFRACTION6chain 'A' and (resid 460 through 494 )A460 - 494
7X-RAY DIFFRACTION7chain 'A' and (resid 495 through 529 )A495 - 529
8X-RAY DIFFRACTION8chain 'H' and (resid 1 through 39 )H1 - 39
9X-RAY DIFFRACTION9chain 'H' and (resid 40 through 119 )H40 - 119
10X-RAY DIFFRACTION10chain 'H' and (resid 120 through 134 )H120 - 134
11X-RAY DIFFRACTION11chain 'H' and (resid 135 through 214 )H135 - 214
12X-RAY DIFFRACTION12chain 'L' and (resid 1 through 18 )L1 - 18
13X-RAY DIFFRACTION13chain 'L' and (resid 19 through 75 )L19 - 75
14X-RAY DIFFRACTION14chain 'L' and (resid 76 through 113 )L76 - 113
15X-RAY DIFFRACTION15chain 'L' and (resid 114 through 150 )L114 - 150
16X-RAY DIFFRACTION16chain 'L' and (resid 151 through 163 )L151 - 163
17X-RAY DIFFRACTION17chain 'L' and (resid 164 through 213 )L164 - 213

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