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- PDB-8dgv: Crystal structure of MERS-CoV spike stem helix peptide in complex... -

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Basic information

Entry
Database: PDB / ID: 8dgv
TitleCrystal structure of MERS-CoV spike stem helix peptide in complex with Fab of broadly neutralizing antibody CC99.103 isolated from a vaccinated COVID-19 convalescent
Components
  • Antibody CC99.103 Fab heavy chain
  • Antibody CC99.103 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


endocytosis involved in viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / 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 ...Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / 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 speciesHomo sapiens (human)
Middle East respiratory syndrome-related coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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

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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 CC99.103 Fab heavy chain
L: Antibody CC99.103 Fab light chain


Theoretical massNumber of molelcules
Total (without water)50,2813
Polymers50,2813
Non-polymers00
Water50428
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 area4320 Å2
ΔGint-36 kcal/mol
Surface area19970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.208, 68.134, 62.952
Angle α, β, γ (deg.)90.000, 117.190, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein/peptide Spike protein S2'


Mass: 2985.236 Da / Num. of mol.: 1 / Fragment: stem helix domain, residues 1221-1247 / Source method: obtained synthetically
Source: (synth.) Middle East respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012)
References: UniProt: K9N5Q8
#2: Antibody Antibody CC99.103 Fab heavy chain


Mass: 23601.666 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 CC99.103 Fab light chain


Mass: 23694.439 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O

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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: 2.41 Å3/Da / Density % sol: 49.03 %
Crystal growTemperature: 295.15 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: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 19960 / % possible obs: 93.7 % / Redundancy: 5.3 % / Biso Wilson estimate: 39.56 Å2 / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.069 / Rrim(I) all: 0.169 / Χ2: 1.627 / Net I/σ(I): 6.4 / Num. measured all: 104913
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.352.90.629730.6240.3650.7260.57569.8
2.35-2.413.10.61111030.6950.3560.7130.59178.1
2.41-2.483.30.65712310.7180.3730.7620.51887.4
2.48-2.553.50.65813110.6860.3780.7660.51991.7
2.55-2.634.50.68213600.760.3390.7660.54596.8
2.63-2.735.50.58213920.8560.2660.6420.63298.7
2.73-2.8460.50713780.9060.2220.5550.66198.3
2.84-2.9760.39314030.9310.1710.4290.79998.5
2.97-3.125.80.29213840.950.1320.3210.98297.8
3.12-3.326.20.21214010.9780.0910.2311.32698.8
3.32-3.576.40.16414210.9860.070.1791.84799.2
3.57-3.936.20.13313810.9880.0580.1462.28897.7
3.93-4.560.113970.9920.0440.1093.12797.5
4.5-5.676.20.08614000.9940.0370.0943.3797.8
5.67-505.70.07314250.9960.0330.083.37696.9

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Processing

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

7jmw

7kn4


Resolution: 2.3→36.35 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2491 974 4.89 %
Rwork0.2027 18953 -
obs0.205 19927 93.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 137.38 Å2 / Biso mean: 50.1741 Å2 / Biso min: 20.08 Å2
Refinement stepCycle: final / Resolution: 2.3→36.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3308 0 0 28 3336
Biso mean---40.89 -
Num. residues----438
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.420.34791260.29912069219573
2.42-2.580.34791240.3062621274590
2.58-2.770.35371410.28712830297198
2.77-3.050.30521610.25312804296598
3.05-3.490.26541100.22292901301199
3.49-4.40.23211670.16492829299698
4.4-36.350.17571450.15052899304498
Refinement TLS params.Method: refined / Origin x: -4.5138 Å / Origin y: -10.6777 Å / Origin z: 14.5725 Å
111213212223313233
T0.2538 Å2-0.0059 Å20.0232 Å2-0.2597 Å2-0.012 Å2--0.213 Å2
L1.9651 °20.7842 °21.27 °2-1.1103 °20.7004 °2--1.9435 °2
S0.016 Å °-0.2784 Å °0.0471 Å °0.035 Å °-0.0989 Å °0.1392 Å °0.0866 Å °-0.3907 Å °0.0606 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1225 - 1242
2X-RAY DIFFRACTION1allH1 - 213
3X-RAY DIFFRACTION1allL8 - 212
4X-RAY DIFFRACTION1allC1 - 28

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