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- PDB-7c53: Crystal Structure of SARS-CoV-2 HR1 motif in complex with pan-CoV... -

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Basic information

Entry
Database: PDB / ID: 7c53
TitleCrystal Structure of SARS-CoV-2 HR1 motif in complex with pan-CoVs inhibitor EK1
ComponentsSpike protein S2',pan-CoVs inhibitor EK1
KeywordsVIRAL PROTEIN / SARS-CoV-2 HR1 / pan-CoVs inhibitor / EK1 peptide / VIRUS
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 / 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 ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / 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 / 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, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / 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 S1 subunit, receptor binding domain superfamily, 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, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / 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 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 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.278 Å
AuthorsZhu, Y. / Yang, X. / Sun, F.
CitationJournal: Signal Transduct Target Ther / Year: 2021
Title: Structural and functional basis for pan-CoV fusion inhibitors against SARS-CoV-2 and its variants with preclinical evaluation.
Authors: Xia, S. / Lan, Q. / Zhu, Y. / Wang, C. / Xu, W. / Li, Y. / Wang, L. / Jiao, F. / Zhou, J. / Hua, C. / Wang, Q. / Cai, X. / Wu, Y. / Gao, J. / Liu, H. / Sun, G. / Munch, J. / Kirchhoff, F. / ...Authors: Xia, S. / Lan, Q. / Zhu, Y. / Wang, C. / Xu, W. / Li, Y. / Wang, L. / Jiao, F. / Zhou, J. / Hua, C. / Wang, Q. / Cai, X. / Wu, Y. / Gao, J. / Liu, H. / Sun, G. / Munch, J. / Kirchhoff, F. / Yuan, Z. / Xie, Y. / Sun, F. / Jiang, S. / Lu, L.
History
DepositionMay 19, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 19, 2021Provider: 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
A: Spike protein S2',pan-CoVs inhibitor EK1
B: Spike protein S2',pan-CoVs inhibitor EK1
C: Spike protein S2',pan-CoVs inhibitor EK1
D: Spike protein S2',pan-CoVs inhibitor EK1
E: Spike protein S2',pan-CoVs inhibitor EK1
F: Spike protein S2',pan-CoVs inhibitor EK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0418
Polymers69,9606
Non-polymers802
Water2,810156
1
A: Spike protein S2',pan-CoVs inhibitor EK1
B: Spike protein S2',pan-CoVs inhibitor EK1
C: Spike protein S2',pan-CoVs inhibitor EK1


Theoretical massNumber of molelcules
Total (without water)34,9803
Polymers34,9803
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9040 Å2
ΔGint-72 kcal/mol
Surface area13680 Å2
MethodPISA
2
D: Spike protein S2',pan-CoVs inhibitor EK1
E: Spike protein S2',pan-CoVs inhibitor EK1
F: Spike protein S2',pan-CoVs inhibitor EK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0605
Polymers34,9803
Non-polymers802
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9140 Å2
ΔGint-80 kcal/mol
Surface area13410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.815, 138.141, 71.461
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-1108-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 912 through 917 or resid 919...
21(chain B and (resid 912 through 917 or resid 919...
31(chain D and (resid 912 through 917 or resid 919...
12(chain C and (resid 913 through 917 or resid 919...
22(chain E and (resid 913 through 917 or resid 919...
32(chain F and (resid 913 through 917 or resid 919...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 912 through 917 or resid 919...A912 - 917
121(chain A and (resid 912 through 917 or resid 919...A919 - 956
131(chain A and (resid 912 through 917 or resid 919...A912 - 1036
141(chain A and (resid 912 through 917 or resid 919...A965 - 969
151(chain A and (resid 912 through 917 or resid 919...A1005 - 1019
161(chain A and (resid 912 through 917 or resid 919...A1021 - 1023
171(chain A and (resid 912 through 917 or resid 919...A1025 - 1027
181(chain A and (resid 912 through 917 or resid 919...A1029 - 1032
211(chain B and (resid 912 through 917 or resid 919...B912 - 917
221(chain B and (resid 912 through 917 or resid 919...B919 - 956
231(chain B and (resid 912 through 917 or resid 919...B911 - 1035
241(chain B and (resid 912 through 917 or resid 919...B965 - 969
251(chain B and (resid 912 through 917 or resid 919...B1005 - 1019
261(chain B and (resid 912 through 917 or resid 919...B1021 - 1023
271(chain B and (resid 912 through 917 or resid 919...B1025 - 1027
281(chain B and (resid 912 through 917 or resid 919...B1029 - 1032
311(chain D and (resid 912 through 917 or resid 919...D912 - 917
321(chain D and (resid 912 through 917 or resid 919...D919 - 956
331(chain D and (resid 912 through 917 or resid 919...D958 - 963
341(chain D and (resid 912 through 917 or resid 919...D965 - 969
351(chain D and (resid 912 through 917 or resid 919...D1005 - 1019
361(chain D and (resid 912 through 917 or resid 919...D1021 - 1023
371(chain D and (resid 912 through 917 or resid 919...D1025 - 1027
381(chain D and (resid 912 through 917 or resid 919...D1029 - 1032
112(chain C and (resid 913 through 917 or resid 919...C913 - 917
122(chain C and (resid 913 through 917 or resid 919...C919 - 953
132(chain C and (resid 913 through 917 or resid 919...C955 - 963
142(chain C and (resid 913 through 917 or resid 919...C100
152(chain C and (resid 913 through 917 or resid 919...C1007 - 1016
162(chain C and (resid 913 through 917 or resid 919...C10 - 1016
172(chain C and (resid 913 through 917 or resid 919...C1018 - 1023
182(chain C and (resid 913 through 917 or resid 919...C1025 - 1034
212(chain E and (resid 913 through 917 or resid 919...E913 - 917
222(chain E and (resid 913 through 917 or resid 919...E919 - 953
232(chain E and (resid 913 through 917 or resid 919...E955 - 963
242(chain E and (resid 913 through 917 or resid 919...E100
252(chain E and (resid 913 through 917 or resid 919...E1007 - 1016
262(chain E and (resid 913 through 917 or resid 919...E10 - 1016
272(chain E and (resid 913 through 917 or resid 919...E1018 - 1023
282(chain E and (resid 913 through 917 or resid 919...E1025 - 1034
312(chain F and (resid 913 through 917 or resid 919...F913 - 917
322(chain F and (resid 913 through 917 or resid 919...F919 - 953
332(chain F and (resid 913 through 917 or resid 919...F955 - 963
342(chain F and (resid 913 through 917 or resid 919...F100
352(chain F and (resid 913 through 917 or resid 919...F1007 - 1016
362(chain F and (resid 913 through 917 or resid 919...F10 - 1016
372(chain F and (resid 913 through 917 or resid 919...F1018 - 1023
382(chain F and (resid 913 through 917 or resid 919...F1025 - 1034

NCS ensembles :
ID
1
2

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Components

#1: Protein
Spike protein S2',pan-CoVs inhibitor EK1


Mass: 11660.062 Da / Num. of mol.: 6 / Fragment: HR1 motif
Source method: isolated from a genetically manipulated source
Details: The fusion protein of SARS-CoV-2 HR1 motif (UNP residues 910-975) and pan-CoVs inhibitor EK1 (residues 976-1036)
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2, (gene. exp.) synthetic construct (others)
Gene: S, 2 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DTC2
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O
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: 2.36 Å3/Da / Density % sol: 47.82 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 30% MPD, 0.1 M Na Acetate pH 5.0, 0.02 M Calcium Chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.278→48.057 Å / Num. obs: 30691 / % possible obs: 99.7 % / Redundancy: 13.8 % / CC1/2: 0.999 / Net I/σ(I): 17.12
Reflection shellResolution: 2.28→2.42 Å / Num. unique obs: 9427 / CC1/2: 0.502

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZVM

5zvm


Resolution: 2.278→48.057 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2418 1492 4.86 %
Rwork0.1951 29199 -
obs0.1974 30691 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 129.12 Å2 / Biso mean: 46.7751 Å2 / Biso min: 18 Å2
Refinement stepCycle: final / Resolution: 2.278→48.057 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4346 0 2 156 4504
Biso mean--90.05 45.09 -
Num. residues----551
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A648X-RAY DIFFRACTION6.859TORSIONAL
12B648X-RAY DIFFRACTION6.859TORSIONAL
13D648X-RAY DIFFRACTION6.859TORSIONAL
21C657X-RAY DIFFRACTION6.859TORSIONAL
22E657X-RAY DIFFRACTION6.859TORSIONAL
23F657X-RAY DIFFRACTION6.859TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.278-2.35120.3571370.2894260499
2.3512-2.43520.31161210.23862636100
2.4352-2.53270.27881490.24142619100
2.5327-2.6480.30251310.2162614100
2.648-2.78760.27061510.19832606100
2.7876-2.96220.27121360.20492630100
2.9622-3.19090.27021410.20422644100
3.1909-3.51190.25771120.18542685100
3.5119-4.01980.23091120.17352700100
4.0198-5.06370.1831480.15712678100
5.0637-48.0570.21521540.20292783100
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)
12.23930.40851.01270.83860.30881.67630.11110.0025-0.1340.0237-0.042-0.14220.2013-0.0211-0.06640.27110.02670.04750.25330.0360.2296-35.0949-27.9111-20.9213
22.3707-0.04391.19590.620.38941.77580.0241-0.25460.03860.0945-0.0579-0.06750.0969-0.14360.05740.2918-0.00480.03970.21430.04220.2019-40.9983-23.6677-13.0601
33.26590.47181.27030.9595-0.00281.3228-0.09210.23520.47940.0511-0.0809-0.1421-0.0970.20140.17540.23830.01560.02130.20220.06190.3184-37.5577-17.4306-20.6699
40.9211-0.45940.66573.3535-2.11682.7129-0.1594-0.2340.11820.61770.2337-0.0809-0.4384-0.1374-0.03780.25870.00010.02310.3257-0.06950.2584-21.885-25.4198-31.3416
51.7807-1.52140.81931.905-0.83441.20770.0373-0.00280.121-0.157-0.0614-0.34910.19250.06150.06350.2926-0.0321-0.00810.2627-0.02560.2489-16.5322-29.264-39.3747
61.1596-0.32760.30742.5058-1.09011.320.0615-0.0954-0.0827-0.13590.14410.25210.1528-0.1786-0.22470.2082-0.039-0.00130.2451-0.00270.2153-26.8671-30.9153-38.7961
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 912 through 1036)A912 - 1036
2X-RAY DIFFRACTION2(chain 'B' and resid 911 through 1035)B911 - 1035
3X-RAY DIFFRACTION3(chain 'C' and resid 911 through 1035)C911 - 1035
4X-RAY DIFFRACTION4(chain 'D' and resid 912 through 1033)D912 - 1033
5X-RAY DIFFRACTION5(chain 'E' and resid 911 through 1035)E911 - 1035
6X-RAY DIFFRACTION6(chain 'F' and resid 912 through 1035)F912 - 1035

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