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- PDB-8fax: Fab 1249A8-MERS Stem Helix Complex -

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Basic information

Entry
Database: PDB / ID: 8fax
TitleFab 1249A8-MERS Stem Helix Complex
Components
  • 1249A8-HC
  • 1249A8-LC
  • Spike glycoproteinSpike protein
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / Broadly Neutralizing antibody / MERS S protein / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homology
Function and homology information


endocytosis involved in viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / 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: 2.1 Å
AuthorsDeshpande, A. / Schormann, N. / Piepenbrink, M.S. / Martinez-Sobrido, L. / Kobie, J.J. / Walter, M.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI161175 United States
CitationJournal: Febs J. / Year: 2023
Title: Structure and epitope of a neutralizing monoclonal antibody that targets the stem helix of beta coronaviruses.
Authors: Deshpande, A. / Schormann, N. / Piepenbrink, M.S. / Martinez Sobrido, L. / Kobie, J.J. / Walter, M.R.
History
DepositionNov 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 1249A8-HC
B: 1249A8-LC
L: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,20713
Polymers49,9533
Non-polymers25410
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-102 kcal/mol
Surface area19040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.714, 56.308, 76.124
Angle α, β, γ (deg.)90.000, 91.191, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein/peptide , 1 types, 1 molecules L

#3: Protein/peptide Spike glycoprotein / Spike protein


Mass: 2564.691 Da / Num. of mol.: 1 / Fragment: UNP residues 1223-1245 / Source method: obtained synthetically
Source: (synth.) Middle East respiratory syndrome-related coronavirus
References: UniProt: R9UCW7

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Antibody , 2 types, 2 molecules AB

#1: Antibody 1249A8-HC / 1249A8 heavy chain


Mass: 23463.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody 1249A8-LC / 1249A8 light chain


Mass: 23924.646 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 234 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.33 Å3/Da / Density % sol: 47.21 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M magnesium chloride, 0.1 M Tris, pH 8.5, 20% PEG8000

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Data collection

DiffractionMean temperature: 113 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→45.3 Å / Num. obs: 26255 / % possible obs: 93.9 % / Redundancy: 3 % / Biso Wilson estimate: 29.65 Å2 / CC1/2: 0.967 / Rmerge(I) obs: 0.119 / Net I/σ(I): 5
Reflection shellResolution: 2.1→2.13 Å / Rmerge(I) obs: 0.436 / Num. unique obs: 5954

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
ARP/wARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→43.76 Å / SU ML: 0.249 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.9088
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2397 1410 5.44 %
Rwork0.1822 24489 -
obs0.1853 25899 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.46 Å2
Refinement stepCycle: LAST / Resolution: 2.1→43.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3403 0 10 224 3637
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00773515
X-RAY DIFFRACTIONf_angle_d0.90294779
X-RAY DIFFRACTIONf_chiral_restr0.0498534
X-RAY DIFFRACTIONf_plane_restr0.0057615
X-RAY DIFFRACTIONf_dihedral_angle_d17.7341272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.180.28421410.22662352X-RAY DIFFRACTION96.29
2.18-2.260.27121600.21032453X-RAY DIFFRACTION99.62
2.26-2.370.25661380.18612423X-RAY DIFFRACTION99.49
2.37-2.490.25221320.18192485X-RAY DIFFRACTION99.28
2.49-2.650.25851110.17382473X-RAY DIFFRACTION99
2.65-2.850.24681550.16762402X-RAY DIFFRACTION97.86
2.85-3.140.23691640.16482386X-RAY DIFFRACTION97.33
3.14-3.590.23161330.16752480X-RAY DIFFRACTION99.69
3.59-4.520.20171160.16782542X-RAY DIFFRACTION100
4.52-43.760.24431600.20832493X-RAY DIFFRACTION98.04

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