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- PDB-7cdj: Crystal structure of SARS-CoV-2 antibody P2C-1A3 with RBD -

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Basic information

Entry
Database: PDB / ID: 7cdj
TitleCrystal structure of SARS-CoV-2 antibody P2C-1A3 with RBD
Components
  • Spike protein S1
  • antibody P2C-1A3 heavy chain
  • antibody P2C-1A3 light chain
KeywordsVIRAL PROTEIN / spike / receptor binding domain / antibody
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 / viral translation / 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 / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / 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
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.396 Å
AuthorsWang, X. / Zhang, L. / Ge, J. / Wang, R.
CitationJournal: Nat Commun / Year: 2021
Title: Antibody neutralization of SARS-CoV-2 through ACE2 receptor mimicry.
Authors: Ge, J. / Wang, R. / Ju, B. / Zhang, Q. / Sun, J. / Chen, P. / Zhang, S. / Tian, Y. / Shan, S. / Cheng, L. / Zhou, B. / Song, S. / Zhao, J. / Wang, H. / Shi, X. / Ding, Q. / Liu, L. / Zhao, J. ...Authors: Ge, J. / Wang, R. / Ju, B. / Zhang, Q. / Sun, J. / Chen, P. / Zhang, S. / Tian, Y. / Shan, S. / Cheng, L. / Zhou, B. / Song, S. / Zhao, J. / Wang, H. / Shi, X. / Ding, Q. / Liu, L. / Zhao, J. / Zhang, Z. / Wang, X. / Zhang, L.
History
DepositionJun 19, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 1, 2021Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 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
E: Spike protein S1
H: antibody P2C-1A3 heavy chain
L: antibody P2C-1A3 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2604
Polymers71,0383
Non-polymers2211
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-30 kcal/mol
Surface area27710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.411, 89.411, 437.923
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Spike protein S1 / S glycoprotein / E2 / Peplomer protein


Mass: 24600.631 Da / Num. of mol.: 1 / Fragment: receptor binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0DTC2
#2: Antibody antibody P2C-1A3 heavy chain


Mass: 23172.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293F / Production host: Homo sapiens (human)
#3: Antibody antibody P2C-1A3 light chain


Mass: 23264.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293F / 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: 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
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: 3.56 Å3/Da / Density % sol: 65.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1M lithium sulfate monohydrate, 0.1M citric acid, pH 3.5, 18% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9796 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 3.396→20.312 Å / Num. obs: 15108 / % possible obs: 99.74 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 8.8
Reflection shellResolution: 3.4→3.48 Å / Rmerge(I) obs: 0.933 / Num. unique obs: 1322

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Processing

Software
NameVersionClassification
PHENIX1.15_3459refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M0J

6m0j


Resolution: 3.396→20.312 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2709 707 4.71 %
Rwork0.2314 14318 -
obs0.2334 15025 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 203.41 Å2 / Biso mean: 125.6381 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.396→20.312 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4756 0 14 0 4770
Biso mean--146.29 --
Num. residues----619
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.3963-3.65720.37421250.3529264894
3.6572-4.02260.31841390.2879280899
4.0226-4.59880.27451430.2192284599
4.5988-5.77190.26651390.21752915100
5.7719-20.31190.24031610.19973102100
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)
14.89170.9994-0.56613.8289-1.1238.54160.3075-0.336-0.3837-0.202-0.1105-0.18040.15210.1388-0.21470.73710.0364-0.01731.0161-0.05940.8-35.821828.5826-18.5421
23.7358-0.173-1.57135.1567-0.37323.8540.01480.71780.2915-0.1603-0.2775-0.20190.32510.46090.28870.5705-0.0891-0.05291.16830.08860.9756-61.551419.26294.1683
33.36481.22151.56713.24721.66193.0507-0.0963-0.0063-0.6003-0.23180.16680.4361-0.1769-0.7652-0.08420.9201-0.1405-0.08431.48190.10411.1386-89.973422.308118.0529
42.34090.5445-1.24682.00670.70525.2458-0.107-0.5190.0346-0.19020.0150.08230.3192-0.56820.13770.6726-0.0813-0.14621.03620.19370.9268-56.685722.816325.4844
53.2905-0.57573.08961.42931.84476.67170.51980.0093-0.26590.1414-0.19010.58670.7106-0.7137-0.25940.9746-0.3625-0.1391.54690.33741.303-92.217413.382531.9729
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain EE333 - 601
2X-RAY DIFFRACTION2chain H and resid 1:119H1 - 119
3X-RAY DIFFRACTION3chain H and resid 120:216H120 - 216
4X-RAY DIFFRACTION4chain L and resid -1:106L-1 - 106
5X-RAY DIFFRACTION5chain L and resid 107:211L107 - 211

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