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- PDB-7cdi: Crystal structure of SARS-CoV-2 antibody P2C-1F11 with RBD -

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Basic information

Entry
Database: PDB / ID: 7cdi
TitleCrystal structure of SARS-CoV-2 antibody P2C-1F11 with RBD
Components
  • Spike protein S1
  • antibody P2C-1F11 heavy chain
  • antibody P2C-1F11 light chain
KeywordsVIRAL PROTEIN / spike / receptor binding domain / antibody
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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / 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 / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / 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: 2.96 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

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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-1F11 heavy chain
L: antibody P2C-1F11 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9484
Polymers70,7273
Non-polymers2211
Water0
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)194.880, 85.390, 58.510
Angle α, β, γ (deg.)90.000, 100.290, 90.000
Int Tables number5
Space group name H-MC121

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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-1F11 heavy chain


Mass: 22851.592 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-1F11 light chain


Mass: 23274.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: HEK 293F / 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 / N-Acetylglucosamine


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

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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: 3.39 Å3/Da / Density % sol: 63.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1M sodium citrate tribasic dihydrate, pH 5.8, 20% 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: Mar 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.96→34.98 Å / Num. obs: 19785 / % possible obs: 99.68 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.155 / Net I/σ(I): 10.1
Reflection shellResolution: 2.96→3.04 Å / Rmerge(I) obs: 0.997 / Num. unique obs: 1951 / % possible all: 99.9

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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: 2.96→33.974 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2538 987 4.99 %
Rwork0.202 18778 -
obs0.2046 19765 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 143.07 Å2 / Biso mean: 60.986 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.96→33.974 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4701 0 14 0 4715
Biso mean--99.03 --
Num. residues----615
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.96-3.1160.33151480.2982629100
3.116-3.31110.31721340.26492682100
3.3111-3.56650.31011330.24792668100
3.5665-3.92490.2711450.22352701100
3.9249-4.49170.21921430.17792684100
4.4917-5.65490.21951430.15992675100
5.6549-33.97390.23011410.1783273999
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)
16.6161-0.6356-0.72754.6256-0.8043.28350.23630.80820.0897-0.3279-0.3244-0.6343-0.21750.53410.05440.52650.08050.03450.58250.03970.4404-29.74270.309515.3156
25.3776-0.29120.06611.22170.0124.3077-0.2102-0.8496-0.74060.36030.26690.08940.3587-0.2628-0.0890.51690.085-0.00080.43570.14290.5142-55.7437-3.374635.3652
31.7807-1.13911.11682.16590.42254.5726-0.1424-1.1467-0.97990.42430.22090.61130.40360.0068-0.11010.58260.05770.08760.80350.37130.8006-89.59614.971844.8038
47.2676-3.29420.03012.801-0.85133.15050.23690.9408-0.8998-0.5324-0.23260.46420.2138-0.1820.04940.57050.044-0.07880.4628-0.10570.4113-66.18281.498215.5007
54.2692-1.2926-0.40775.16042.31834.2388-0.0628-0.611-0.15410.17240.17840.2191-0.08380.1888-0.08250.3574-0.04820.02530.51060.19930.407-88.700519.202736.3846
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain EE333 - 601
2X-RAY DIFFRACTION2chain H and resid 2:118H2 - 118
3X-RAY DIFFRACTION3chain H and resid 119:217H119 - 217
4X-RAY DIFFRACTION4chain L and resid 1:108L1 - 108
5X-RAY DIFFRACTION5chain L and resid 109:214L109 - 214

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