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- PDB-8dgu: Crystal structure of SARS-CoV-2 spike stem helix peptide in compl... -

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Basic information

Entry
Database: PDB / ID: 8dgu
TitleCrystal structure of SARS-CoV-2 spike stem helix peptide in complex with Fab of broadly neutralizing antibody CC25.106 isolated from a vaccinated COVID-19 convalescent
Components
  • Antibody CC25.106 Fab heavy chain
  • Antibody CC25.106 Fab light chain
  • Spike protein S2'
KeywordsIMMUNE SYSTEM / broadly neutralizing antibody / pan-betacoronavirus / S2 stem helix / spike / SARS-CoV-2 / MERS-CoV / HCoV-HKU1 / sarbecovirus / cross-reactive / cross-neutralizing
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
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsLiu, H. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-004923 United States
CitationJournal: Immunity / Year: 2023
Title: Broadly neutralizing anti-S2 antibodies protect against all three human betacoronaviruses that cause deadly disease.
Authors: Zhou, P. / Song, G. / Liu, H. / Yuan, M. / He, W.T. / Beutler, N. / Zhu, X. / Tse, L.V. / Martinez, D.R. / Schafer, A. / Anzanello, F. / Yong, P. / Peng, L. / Dueker, K. / Musharrafieh, R. / ...Authors: Zhou, P. / Song, G. / Liu, H. / Yuan, M. / He, W.T. / Beutler, N. / Zhu, X. / Tse, L.V. / Martinez, D.R. / Schafer, A. / Anzanello, F. / Yong, P. / Peng, L. / Dueker, K. / Musharrafieh, R. / Callaghan, S. / Capozzola, T. / Limbo, O. / Parren, M. / Garcia, E. / Rawlings, S.A. / Smith, D.M. / Nemazee, D. / Jardine, J.G. / Safonova, Y. / Briney, B. / Rogers, T.F. / Wilson, I.A. / Baric, R.S. / Gralinski, L.E. / Burton, D.R. / Andrabi, R.
History
DepositionJun 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_DOI
Revision 1.2Mar 22, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 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 S2'
H: Antibody CC25.106 Fab heavy chain
L: Antibody CC25.106 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4735
Polymers49,2893
Non-polymers1842
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, The assembly prediction is based on previous structures, i.e. PDB IDs: 7SJS and 7RNJ.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-32 kcal/mol
Surface area19430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.934, 70.719, 76.551
Angle α, β, γ (deg.)90.000, 95.310, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide Spike protein S2'


Mass: 2981.267 Da / Num. of mol.: 1 / Fragment: Stem helix peptide, residues 1140-1164 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC2
#2: Antibody Antibody CC25.106 Fab heavy chain


Mass: 23477.467 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 Antibody CC25.106 Fab light chain


Mass: 22830.199 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.24 Å3/Da / Density % sol: 45.05 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 19% (v/v) Isopropanol, 19% (w/v) PEG 4000, 5% (v/v) Glycerol, 0.095 M Sodium citrate pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 31, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. obs: 33702 / % possible obs: 98.2 % / Redundancy: 4.5 % / Biso Wilson estimate: 18.64 Å2 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.046 / Rrim(I) all: 0.103 / Χ2: 0.916 / Net I/σ(I): 7.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.932.60.71714140.5180.5160.8910.79283.1
1.93-1.972.90.67715800.5620.4370.8120.77891.4
1.97-2.013.60.60416230.7340.350.7030.8296.7
2.01-2.0540.52616970.7980.2860.6020.82298
2.05-2.094.40.47916770.8590.2480.5420.88399.1
2.09-2.144.50.40516820.8820.2090.4580.90199.2
2.14-2.194.50.37916960.8860.1950.4280.92499.6
2.19-2.254.50.31717070.9340.1650.3590.96599.4
2.25-2.324.40.27716990.9290.1430.3130.95299.3
2.32-2.394.60.25317010.9390.1320.2870.97999.6
2.39-2.484.80.22117070.9520.1110.2490.97999.6
2.48-2.584.90.18817290.9570.0940.210.99399.8
2.58-2.74.80.1516700.9750.0760.1681.01899.5
2.7-2.844.70.12817280.9770.0660.1451.06699.8
2.84-3.024.90.10617140.9860.0530.1191.03599.8
3.02-3.255.10.0917110.9860.0440.1011.06299.8
3.25-3.584.90.07417210.990.0370.0830.94999.8
3.58-4.0950.06417450.9930.0320.0720.8699.8
4.09-5.1650.05617300.9940.0270.0630.722100
5.16-504.90.05317710.9950.0270.060.654100

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7JMW; 7KN4

7jmw

7kn4


Resolution: 1.89→40.76 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2451 1545 4.95 %
Rwork0.2144 29656 -
obs0.2159 31201 88.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.19 Å2 / Biso mean: 25.4309 Å2 / Biso min: 5.95 Å2
Refinement stepCycle: final / Resolution: 1.89→40.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3306 0 12 190 3508
Biso mean--36.5 27.57 -
Num. residues----445
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.89-1.950.2957370.307173276924
1.95-2.020.281240.26362038216269
2.02-2.10.30311490.24912776292592
2.1-2.190.28941420.23832923306597
2.19-2.310.25471470.24412966311398
2.31-2.450.27251520.25443011316399
2.45-2.640.2831560.244830193175100
2.64-2.910.25441570.237430373194100
2.91-3.330.26141480.21730243172100
3.33-4.190.23361750.182430253200100
4.2-40.760.17761580.167331053263100
Refinement TLS params.Method: refined / Origin x: -14.1741 Å / Origin y: -18.8238 Å / Origin z: -19.3945 Å
111213212223313233
T0.0788 Å2-0.0164 Å2-0.0298 Å2-0.0643 Å2-0.0075 Å2--0.1033 Å2
L0.8141 °2-0.1333 °2-0.1967 °2-0.6275 °2-0.1703 °2--1.189 °2
S-0.0669 Å °-0.0795 Å °-0.0015 Å °0.0834 Å °0.0768 Å °-0.0169 Å °0.0703 Å °0.0008 Å °-0.0012 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1145 - 1158
2X-RAY DIFFRACTION1allH1 - 214
3X-RAY DIFFRACTION1allL1 - 210
4X-RAY DIFFRACTION1allS1 - 2
5X-RAY DIFFRACTION1allW1 - 190

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