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- PDB-6x45: SARS-CoV2 spike glycoprotein N-terminal heptad repeat domain + SA... -

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Basic information

Entry
Database: PDB / ID: 6x45
TitleSARS-CoV2 spike glycoprotein N-terminal heptad repeat domain + SARS-CoV2(QEYKKEKE)
Components(Spike protein S2') x 2
KeywordsVIRAL PROTEIN / Coronavirus / COVID-19 / SARS-CoV-2 / spike / antiviral
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 / 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 / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / 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
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKreitler, D.F. / Outlaw, V.K. / Gellman, S.H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32GM122263 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI114736 United States
CitationJournal: To Be Published
Title: Engineered peptides potently block entry of SARS-CoV-2 into human airway cells
Authors: Outlaw, V.K. / Yu, Z. / Kreitler, D.F. / Bovier, F. / Porotto, M. / Moscona, A. / Gellman, S.H.
History
DepositionMay 22, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

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Assembly

Deposited unit
E: Spike protein S2'
D: Spike protein S2'
C: Spike protein S2'
F: Spike protein S2'
B: Spike protein S2'
A: Spike protein S2'


Theoretical massNumber of molelcules
Total (without water)30,4366
Polymers30,4366
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, Formation of helical assembly detected by circular dichroism spectroscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14540 Å2
ΔGint-133 kcal/mol
Surface area12600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.543, 54.458, 80.119
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein/peptide Spike protein S2' / S glycoprotein / E2 / Peplomer protein / spike glycoprotein C-terminal heptad repeat domain (QEYKKEKE)


Mass: 4172.749 Da / Num. of mol.: 3
Mutation: G1171Q, Q1180E, K1181Y, D1184K, R1185K, N1187E, N1192K, N1194E
Source method: obtained synthetically
Details: This compound is derived from the SARS-CoV2 spike glycoprotein C-terminal heptad repeat domain residues 1168-1203 with substitutions G1171Q, Q1180E, K1181Y, D1184K, R1185K, N1187E, N1192K, ...Details: This compound is derived from the SARS-CoV2 spike glycoprotein C-terminal heptad repeat domain residues 1168-1203 with substitutions G1171Q, Q1180E, K1181Y, D1184K, R1185K, N1187E, N1192K, N1194E. It is acetylated at the N-terminus and amidated at the C-terminus.
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC2
#2: Protein Spike protein S2' / S glycoprotein / E2 / Peplomer protein / spike glycoprotein N-terminal heptad repeat domain


Mass: 5972.696 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: This compound is derived from the SARS-CoV2 spike glycoprotein N-terminal heptad repeat domain residues 912-966. It is acetylated at the N-terminus and amidated at the C-terminus.
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 1.92 Å3/Da / Density % sol: 35.9 % / Description: 3D bricks
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: Peptide solution: Lyophilized TFA salt dissolved in 1% w/v beta-D-octylglucoside; HRN (4 mg/mL), HRC-QEYKKEKE (3 mg/mL) Well solution: 0.1 M Tris pH 7.8, 26% w/v PEG3350, 0.3 M MgCl2 Drop: 1 ...Details: Peptide solution: Lyophilized TFA salt dissolved in 1% w/v beta-D-octylglucoside; HRN (4 mg/mL), HRC-QEYKKEKE (3 mg/mL) Well solution: 0.1 M Tris pH 7.8, 26% w/v PEG3350, 0.3 M MgCl2 Drop: 1 uL peptide solution, 1 uL well solution Reservoir: 150 uL in VDXm plate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.920087 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 6, 2020
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920087 Å / Relative weight: 1
ReflectionResolution: 2.2→80.12 Å / Num. obs: 12351 / % possible obs: 99.5 % / Redundancy: 6.5 % / Biso Wilson estimate: 54.79 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.038 / Rrim(I) all: 0.096 / Rsym value: 0.088 / Net I/σ(I): 9
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1047 / CC1/2: 0.475 / Rpim(I) all: 0.666 / Rrim(I) all: 1.705 / Rsym value: 1.565 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
autoPROC1.0.5data scaling
Aimless0.7.4data scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LXT

6lxt


Resolution: 2.2→45.04 Å / SU ML: 0.327 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.8919
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2784 1217 9.88 %
Rwork0.2429 11096 -
obs0.2463 12313 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 88.63 Å2
Refinement stepCycle: LAST / Resolution: 2.2→45.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1976 0 0 8 1984
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00231979
X-RAY DIFFRACTIONf_angle_d0.36482667
X-RAY DIFFRACTIONf_chiral_restr0.0343335
X-RAY DIFFRACTIONf_plane_restr0.0011344
X-RAY DIFFRACTIONf_dihedral_angle_d19.2173738
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.290.40371330.32841208X-RAY DIFFRACTION99.19
2.29-2.390.35941290.31207X-RAY DIFFRACTION99.33
2.39-2.520.2861350.27781205X-RAY DIFFRACTION99.33
2.52-2.680.30551320.26611236X-RAY DIFFRACTION99.27
2.68-2.880.27791330.2511208X-RAY DIFFRACTION99.63
2.88-3.170.281380.24481232X-RAY DIFFRACTION99.13
3.17-3.630.25741420.23391235X-RAY DIFFRACTION99.42
3.63-4.570.24141370.20421251X-RAY DIFFRACTION99
4.58-45.040.29351380.25481314X-RAY DIFFRACTION97.58
Refinement TLS params.Method: refined / Origin x: 14.4060869838 Å / Origin y: 5.33483149575 Å / Origin z: 37.9270700186 Å
111213212223313233
T0.360476346831 Å20.021519463561 Å2-0.00233446670149 Å2-0.370406411045 Å20.013953937288 Å2--0.409330566609 Å2
L0.59000476506 °2-0.63492824488 °20.261145016993 °2-1.47931587103 °2-0.529893780002 °2--2.18644754555 °2
S0.0668264732655 Å °-0.137161724678 Å °0.0342339623568 Å °0.242356343076 Å °0.0833005994134 Å °0.334631692406 Å °-0.168109846833 Å °-0.139319661059 Å °0.0297763634219 Å °
Refinement TLS groupSelection details: all

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