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

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Basic information

Entry
Database: PDB / ID: 8tmz
TitleCrystal structure of MERS-CoV spike stem helix peptide in complex with neutralizing antibody CHM-27
Components
  • Neutralizing antibody CHM-27 Heavy Chain
  • Neutralizing antibody CHM-27 Light Chain
  • Stem helix peptide of Spike glycoprotein
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Antibody / MERS-CoV / Coronavirus / IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


host cell endoplasmic reticulum-Golgi intermediate compartment membrane / 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, 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, 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, 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 speciesMacaca mulatta (Rhesus monkey)
Middle East respiratory syndrome-related coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsYuan, M. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-004923 United States
CitationJournal: Not published
Title: Broad Neutralizing Antibodies Against Coronaviruses.
Authors: Feng, Z. / Wilson, I.A.
History
DepositionJul 31, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 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

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Assembly

Deposited unit
H: Neutralizing antibody CHM-27 Heavy Chain
L: Neutralizing antibody CHM-27 Light Chain
A: Stem helix peptide of Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7454
Polymers48,6833
Non-polymers621
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-28 kcal/mol
Surface area19930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.057, 71.402, 74.571
Angle α, β, γ (deg.)90.00, 106.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Neutralizing antibody CHM-27 Heavy Chain


Mass: 23036.877 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#2: Antibody Neutralizing antibody CHM-27 Light Chain


Mass: 22661.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#3: Protein/peptide Stem helix peptide of Spike glycoprotein


Mass: 2985.236 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Middle East respiratory syndrome-related coronavirus
References: UniProt: A0A0U2MN53
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.26 Å3/Da / Density % sol: 45.66 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.17 M sodium acetate, 0.085 M Tris at pH 8.5, 15% (v/v) glycerol, and 25.5% (w/v) polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97933 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.8→50.587 Å / Num. obs: 39980 / % possible obs: 99.1 % / Redundancy: 3.3 % / CC1/2: 0.995 / Net I/σ(I): 7
Reflection shellResolution: 1.8→1.83 Å / Num. unique obs: 1803 / CC1/2: 0.446

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→35.84 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2942 2016 5.05 %
Rwork0.2445 --
obs0.2469 39898 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→35.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3251 0 4 159 3414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123340
X-RAY DIFFRACTIONf_angle_d1.3224559
X-RAY DIFFRACTIONf_dihedral_angle_d7.255461
X-RAY DIFFRACTIONf_chiral_restr0.077527
X-RAY DIFFRACTIONf_plane_restr0.015580
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.43941340.4292458X-RAY DIFFRACTION91
1.84-1.890.42191380.37712659X-RAY DIFFRACTION97
1.89-1.950.42621340.34532722X-RAY DIFFRACTION100
1.95-2.010.38631470.32182673X-RAY DIFFRACTION100
2.01-2.080.32511560.29792737X-RAY DIFFRACTION100
2.09-2.170.33961920.29212659X-RAY DIFFRACTION100
2.17-2.270.39651490.28262739X-RAY DIFFRACTION100
2.27-2.390.31771360.28992722X-RAY DIFFRACTION100
2.39-2.540.36071520.28232728X-RAY DIFFRACTION100
2.54-2.730.41141270.28132744X-RAY DIFFRACTION100
2.73-3.010.30861310.27152752X-RAY DIFFRACTION100
3.01-3.440.25671350.24662743X-RAY DIFFRACTION100
3.44-4.330.24681490.19592740X-RAY DIFFRACTION100
4.33-35.840.20621360.17352806X-RAY DIFFRACTION99

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