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- PDB-7urq: Crystal Structure of SARS-CoV-2 S delta variant receptor-binding ... -

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Basic information

Entry
Database: PDB / ID: 7urq
TitleCrystal Structure of SARS-CoV-2 S delta variant receptor-binding domain (RBD) in complex CoV11 Fab crystal form 1
Components
  • COV11 Fab HEAVY CHAIN
  • COV11 Fab LIGHT CHAIN
  • Spike protein S1
KeywordsVIRAL PROTEIN/Immune System / SARS-CoV-2 S RBD Fab complex / SARS-CoV-2 S receptor-binding domain antibody Fab complex / COVID-19 spike protein antibody Fab complex / delta variant / 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 / viral translation / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / viral translation / 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 / receptor ligand activity / endocytosis involved in viral entry into host cell / 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 / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / 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
CITRIC ACID / Spike glycoprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsTolbert, W.D. / Pazgier, M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI116274 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI120756 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI129769 United States
CitationJournal: Front Immunol / Year: 2023
Title: The molecular basis of the neutralization breadth of the RBD-specific antibody CoV11.
Authors: Tolbert, W.D. / Chen, Y. / Sun, L. / Benlarbi, M. / Ding, S. / Manickam, R. / Pangaro, E. / Nguyen, D.N. / Gottumukkala, S. / Cote, M. / Gonzalez, F.J. / Finzi, A. / Tehrani, Z.R. / Sajadi, M.M. / Pazgier, M.
History
DepositionApr 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 16, 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: COV11 Fab HEAVY CHAIN
L: COV11 Fab LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2585
Polymers72,8443
Non-polymers4132
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6270 Å2
ΔGint-23 kcal/mol
Surface area26970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.818, 103.551, 112.104
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

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Antibody , 2 types, 2 molecules HL

#2: Antibody COV11 Fab HEAVY CHAIN


Mass: 23362.287 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK 293 / Production host: Homo sapiens (human)
#3: Antibody COV11 Fab LIGHT CHAIN


Mass: 23536.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK 293 / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Spike protein S1


Mass: 25946.182 Da / Num. of mol.: 1 / Mutation: L452R, T478K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Cell (production host): HEK 293 GnT1- / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#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: isolated from a genetically manipulated source
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, 244 molecules

#5: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 3.42 Å3/Da / Density % sol: 64.02 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 10% PEG 4000 0.2 M sodium acetate 0.1 M sodium citrate pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2022
RadiationMonochromator: Si(1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 59785 / % possible obs: 93.3 % / Redundancy: 5.6 % / CC1/2: 0.986 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.056 / Net I/σ(I): 19.9
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.827 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2350 / CC1/2: 0.485 / Rpim(I) all: 0.467 / % possible all: 74.8

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Processing

Software
NameVersionClassification
PHENIX(1.19.1_4122: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7S4S

7s4s


Resolution: 2.05→41.23 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2079 3067 5.13 %
Rwork0.1774 --
obs0.1789 59746 92.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→41.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4805 0 27 243 5075
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084968
X-RAY DIFFRACTIONf_angle_d1.016755
X-RAY DIFFRACTIONf_dihedral_angle_d7.356700
X-RAY DIFFRACTIONf_chiral_restr0.061741
X-RAY DIFFRACTIONf_plane_restr0.006876
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.070.2868850.29041879X-RAY DIFFRACTION68
2.07-2.10.29091200.28192063X-RAY DIFFRACTION76
2.1-2.140.29481030.26892141X-RAY DIFFRACTION78
2.14-2.180.30811400.26542204X-RAY DIFFRACTION81
2.18-2.220.28431200.25212277X-RAY DIFFRACTION84
2.22-2.270.28841200.25952411X-RAY DIFFRACTION87
2.27-2.320.32981230.26542432X-RAY DIFFRACTION88
2.32-2.370.30961240.25172592X-RAY DIFFRACTION94
2.37-2.430.30281420.22732647X-RAY DIFFRACTION96
2.43-2.50.26871510.21232728X-RAY DIFFRACTION99
2.5-2.570.23221660.20682708X-RAY DIFFRACTION100
2.57-2.650.2641490.20332742X-RAY DIFFRACTION100
2.65-2.750.22271410.2072777X-RAY DIFFRACTION100
2.75-2.860.22591580.21472685X-RAY DIFFRACTION97
2.86-2.990.23671630.20832743X-RAY DIFFRACTION100
2.99-3.140.21681450.17932772X-RAY DIFFRACTION100
3.14-3.340.21281600.17592770X-RAY DIFFRACTION100
3.34-3.60.19281480.16632783X-RAY DIFFRACTION100
3.6-3.960.1981320.14742770X-RAY DIFFRACTION98
3.96-4.530.15651520.13042816X-RAY DIFFRACTION100
4.53-5.710.14711500.13062795X-RAY DIFFRACTION98
5.71-41.230.18321750.16792944X-RAY DIFFRACTION99
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)
11.9022-0.2902-0.08195.63190.99713.1822-0.014-0.13780.3542-0.18740.0224-0.0002-0.5933-0.0286-0.00420.3609-0.0064-0.03320.3254-0.00690.264616.487331.95714.3753
20.4618-0.45150.31923.3453-1.41741.7485-0.01040.0983-0.1035-0.2231-0.0599-0.12040.3321-0.01130.07780.2326-0.0010.03180.3097-0.03920.249327.0367-11.163916.2037
30.7077-1.34730.89964.0957-1.9661.81730.0472-0.0352-0.1516-0.05620.08230.28560.2551-0.2144-0.12870.2548-0.05730.02930.3197-0.01090.277111.7022-14.664926.7657
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 334 through 529)
2X-RAY DIFFRACTION2(chain 'H' and resid 1 through 214)
3X-RAY DIFFRACTION3(chain 'L' and resid 1 through 214)

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