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

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Basic information

Entry
Database: PDB / ID: 8dgx
TitleCrystal structure of MERS-CoV spike stem helix peptide in complex with Fab of broadly neutralizing antibody CC68.109 isolated from a vaccinated COVID-19 convalescent
Components
  • Antibody CC68.109 Fab heavy chain
  • Antibody CC68.109 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


membrane fusion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / 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 / 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 / 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. ...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 / 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)
Middle East respiratory syndrome-related coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Antibody CC68.109 Fab heavy chain
L: Antibody CC68.109 Fab light chain
A: Antibody CC68.109 Fab heavy chain
B: Antibody CC68.109 Fab light chain
C: Spike protein S2'
D: Spike protein S2'


Theoretical massNumber of molelcules
Total (without water)100,9226
Polymers100,9226
Non-polymers00
Water00
1
H: Antibody CC68.109 Fab heavy chain
L: Antibody CC68.109 Fab light chain
C: Spike protein S2'


Theoretical massNumber of molelcules
Total (without water)50,4613
Polymers50,4613
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-32 kcal/mol
Surface area19620 Å2
MethodPISA
2
A: Antibody CC68.109 Fab heavy chain
B: Antibody CC68.109 Fab light chain
D: Spike protein S2'


Theoretical massNumber of molelcules
Total (without water)50,4613
Polymers50,4613
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-33 kcal/mol
Surface area19000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.997, 66.499, 94.386
Angle α, β, γ (deg.)90.000, 107.760, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 4 through 18 or (resid 19...
21(chain H and (resid 4 through 12 or (resid 13...
12(chain B and (resid 2 through 17 or (resid 18...
22(chain L and (resid 2 through 126 or (resid 127...
13chain C
23(chain D and (resid 1228 through 1236 or (resid 1237...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LEULEUVALVAL(chain A and (resid 4 through 18 or (resid 19...AC4 - 184 - 18
121LYSLYSLYSLYS(chain A and (resid 4 through 18 or (resid 19...AC1919
131LEULEULYSLYS(chain A and (resid 4 through 18 or (resid 19...AC4 - 2144 - 219
141LEULEULYSLYS(chain A and (resid 4 through 18 or (resid 19...AC4 - 2144 - 219
151LEULEULYSLYS(chain A and (resid 4 through 18 or (resid 19...AC4 - 2144 - 219
161LEULEULYSLYS(chain A and (resid 4 through 18 or (resid 19...AC4 - 2144 - 219
211LEULEULYSLYS(chain H and (resid 4 through 12 or (resid 13...HA4 - 124 - 12
221LYSLYSLYSLYS(chain H and (resid 4 through 12 or (resid 13...HA1313
231LEULEULYSLYS(chain H and (resid 4 through 12 or (resid 13...HA4 - 2144 - 219
241LEULEULYSLYS(chain H and (resid 4 through 12 or (resid 13...HA4 - 2144 - 219
251LEULEULYSLYS(chain H and (resid 4 through 12 or (resid 13...HA4 - 2144 - 219
261LEULEULYSLYS(chain H and (resid 4 through 12 or (resid 13...HA4 - 2144 - 219
112ILEILEGLUGLU(chain B and (resid 2 through 17 or (resid 18...BD2 - 172 - 17
122ARGARGALAALA(chain B and (resid 2 through 17 or (resid 18...BD18 - 1918 - 19
132ILEILEARGARG(chain B and (resid 2 through 17 or (resid 18...BD2 - 2112 - 214
142ILEILEARGARG(chain B and (resid 2 through 17 or (resid 18...BD2 - 2112 - 214
152ILEILEARGARG(chain B and (resid 2 through 17 or (resid 18...BD2 - 2112 - 214
162ILEILEARGARG(chain B and (resid 2 through 17 or (resid 18...BD2 - 2112 - 214
212ILEILELYSLYS(chain L and (resid 2 through 126 or (resid 127...LB2 - 1262 - 129
222SERSERSERSER(chain L and (resid 2 through 126 or (resid 127...LB127130
232ILEILEARGARG(chain L and (resid 2 through 126 or (resid 127...LB2 - 2112 - 214
242ILEILEARGARG(chain L and (resid 2 through 126 or (resid 127...LB2 - 2112 - 214
252ILEILEARGARG(chain L and (resid 2 through 126 or (resid 127...LB2 - 2112 - 214
262ILEILEARGARG(chain L and (resid 2 through 126 or (resid 127...LB2 - 2112 - 214
113GLYGLYVALVALchain CCE1228 - 12428 - 22
213GLYGLYASPASP(chain D and (resid 1228 through 1236 or (resid 1237...DF1228 - 12368 - 16
223GLUGLUGLUGLU(chain D and (resid 1228 through 1236 or (resid 1237...DF123717
233GLYGLYVALVAL(chain D and (resid 1228 through 1236 or (resid 1237...DF1228 - 12428 - 22
243GLYGLYVALVAL(chain D and (resid 1228 through 1236 or (resid 1237...DF1228 - 12428 - 22
253GLYGLYVALVAL(chain D and (resid 1228 through 1236 or (resid 1237...DF1228 - 12428 - 22
263GLYGLYVALVAL(chain D and (resid 1228 through 1236 or (resid 1237...DF1228 - 12428 - 22

NCS ensembles :
ID
1
2
3

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Components

#1: Antibody Antibody CC68.109 Fab heavy chain


Mass: 23606.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Antibody CC68.109 Fab light chain


Mass: 23869.520 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein/peptide Spike protein S2'


Mass: 2985.236 Da / Num. of mol.: 2 / 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
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: 2.04 Å3/Da / Density % sol: 39.8 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.17 M Sodium acetate, 25.5% (w/v) PEG 4000, 15% (v/v) Glycerol, 0.085 M Tris pH 8.5

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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: 2.89→50 Å / Num. obs: 17356 / % possible obs: 94.4 % / Redundancy: 3 % / Biso Wilson estimate: 53.82 Å2 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.056 / Rrim(I) all: 0.1 / Χ2: 0.87 / Net I/σ(I): 6.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.9-2.952.60.7256310.450.5090.890.77173
2.95-32.60.6766920.4850.4740.8290.79975.5
3-3.062.60.557430.7470.3770.670.73682.1
3.06-3.122.70.527760.7660.3570.6330.79684.6
3.12-3.192.70.4138240.7930.2940.5090.84988.8
3.19-3.272.70.4468410.7920.3080.5440.80594.2
3.27-3.352.90.3488860.8910.2410.4250.86196.2
3.35-3.443.10.2958940.9240.1970.3560.89299
3.44-3.543.20.2689260.920.1780.3230.92899.4
3.54-3.653.20.229110.9550.1460.2650.92899.5
3.65-3.783.10.1669050.970.1130.2020.92599.5
3.78-3.942.90.1469280.9630.1010.1791.05399.8
3.94-4.1130.1199100.9740.0810.1450.94299.7
4.11-4.333.20.0929170.9850.0620.1110.99399.6
4.33-4.63.20.0819150.9870.0540.0981.04399
4.6-4.963.10.0689280.9910.0450.0820.96699.3
4.96-5.462.90.0639010.990.0440.0770.86898.9
5.46-6.243.20.0639300.9880.0420.0760.78199.5
6.24-7.863.10.0549410.9910.0360.0650.72799.5
7.86-5030.0439570.9940.0290.0530.57599.1

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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: 2.89→46.69 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2798 651 4.83 %
Rwork0.2327 12835 -
obs0.2351 13486 73.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 177.52 Å2 / Biso mean: 51.5285 Å2 / Biso min: 15.24 Å2
Refinement stepCycle: final / Resolution: 2.89→46.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6507 0 0 0 6507
Num. residues----888
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1298X-RAY DIFFRACTION9.667TORSIONAL
12H1298X-RAY DIFFRACTION9.667TORSIONAL
21B1288X-RAY DIFFRACTION9.667TORSIONAL
22L1288X-RAY DIFFRACTION9.667TORSIONAL
31C84X-RAY DIFFRACTION9.667TORSIONAL
32D84X-RAY DIFFRACTION9.667TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.89-3.120.3251600.3126940100028
3.12-3.430.3715930.2761975206857
3.43-3.930.30411640.25552901306583
3.93-4.950.28241730.20683462363599
4.95-46.690.23261610.22443557371899
Refinement TLS params.Method: refined / Origin x: -28.2564 Å / Origin y: -5.0219 Å / Origin z: -20.2292 Å
111213212223313233
T0.2485 Å20.0094 Å20.0971 Å2-0.1467 Å2-0.0314 Å2--0.1703 Å2
L1.3674 °20.2465 °20.5169 °2-0.841 °20.0427 °2--0.6598 °2
S0.1253 Å °0.1844 Å °0.1552 Å °-0.1707 Å °-0.1033 Å °-0.1983 Å °0.1548 Å °-0.0593 Å °-0.0072 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allH4 - 214
2X-RAY DIFFRACTION1allL2 - 211
3X-RAY DIFFRACTION1allA4 - 214
4X-RAY DIFFRACTION1allB2 - 211
5X-RAY DIFFRACTION1allC1228 - 1242
6X-RAY DIFFRACTION1allD1228 - 1242

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