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- PDB-7vng: Crystal structure of human coronavirus 229E spike protein recepto... -

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Basic information

Entry
Database: PDB / ID: 7vng
TitleCrystal structure of human coronavirus 229E spike protein receptor-binding domain in complex with S11 Fab
Components
  • S11 Fab heavy chain
  • S11 Fab light chain
  • Spike glycoprotein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / human coronavirus 229E / spike protein / RBD / antibody / S11 / 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 / virion membrane / membrane
Similarity search - Function
Spike glycoprotein, Alphacoronavirus / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / 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 S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 ...Spike glycoprotein, Alphacoronavirus / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / 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 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 speciesHuman coronavirus 229E
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsXiang, J.C. / Zhao, W.W. / Yang, B.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32070170 China
CitationJournal: Commun Biol / Year: 2022
Title: Antigenic mapping reveals sites of vulnerability on alpha-HCoV spike protein.
Authors: Xiang, J. / Su, J. / Lan, Q. / Zhao, W. / Zhou, Y. / Xu, Y. / Niu, J. / Xia, S. / Qi, Q. / Sidhu, S. / Lu, L. / Miersch, S. / Yang, B.
History
DepositionOct 11, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Database references / Category: citation / citation_author
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
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 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

Downloads & links

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Assembly

Deposited unit
D: Spike glycoprotein S1
H: S11 Fab heavy chain
L: S11 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2615
Polymers62,8183
Non-polymers4422
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-29 kcal/mol
Surface area26820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.598, 174.678, 97.412
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Space group name HallC22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z
#8: -x+1/2,-y+1/2,z

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Components

#1: Protein Spike glycoprotein S1 / S glycoprotein / E2 / Peplomer protein


Mass: 16194.324 Da / Num. of mol.: 1 / Fragment: receptor binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human coronavirus 229E / Gene: S, 2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P15423
#2: Antibody S11 Fab heavy chain


Mass: 23277.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#3: Antibody S11 Fab light chain


Mass: 23345.889 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
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: 3.85 Å3/Da / Density % sol: 68.02 % / Description: block
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 3.6M Sodium Formate, 10% Glycerol

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3.65→68.1 Å / Num. obs: 20687 / % possible obs: 100 % / Redundancy: 12.5 % / Biso Wilson estimate: 154.9 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.203 / Rpim(I) all: 0.059 / Rrim(I) all: 0.212 / Net I/σ(I): 7.9
Reflection shellResolution: 3.65→4 Å / Redundancy: 13.1 % / Rmerge(I) obs: 3.116 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 2600 / CC1/2: 0.546 / Rpim(I) all: 1.229 / Rrim(I) all: 3.242 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VN9

7vn9


Resolution: 3.8→49.07 Å / SU ML: 0.6579 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.5043
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3176 904 4.92 %
Rwork0.2796 17485 -
obs0.2814 18389 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 182.38 Å2
Refinement stepCycle: LAST / Resolution: 3.8→49.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3929 0 28 0 3957
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034050
X-RAY DIFFRACTIONf_angle_d0.64515497
X-RAY DIFFRACTIONf_chiral_restr0.0442617
X-RAY DIFFRACTIONf_plane_restr0.0053687
X-RAY DIFFRACTIONf_dihedral_angle_d14.3765558
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8-4.040.41811520.38532912X-RAY DIFFRACTION98.68
4.04-4.350.31341410.32672905X-RAY DIFFRACTION99.58
4.35-4.790.3081410.26852937X-RAY DIFFRACTION99.77
4.79-5.480.29341660.25792913X-RAY DIFFRACTION99.84
5.48-6.90.30061580.29932901X-RAY DIFFRACTION99.84
6.9-49.070.32131460.25222917X-RAY DIFFRACTION99.25
Refinement TLS params.Method: refined / Origin x: 2.63474504498 Å / Origin y: 60.272840023 Å / Origin z: 23.4260412009 Å
111213212223313233
T1.25060192614 Å2-0.208656142402 Å2-0.0611893722802 Å2-1.40129972782 Å20.297584985255 Å2--1.12090523346 Å2
L1.39507817443 °2-0.512896395557 °2-0.261452992012 °2-1.10783606188 °20.0730913723678 °2--1.08651545232 °2
S0.102980981615 Å °-0.553787398228 Å °-0.437636261435 Å °0.300700133388 Å °-0.331427023744 Å °-0.0185131388061 Å °0.253399934916 Å °0.536391995947 Å °0.144913463047 Å °
Refinement TLS groupSelection details: all

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