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- PDB-5gnb: Crystal Structure of the Receptor Binding Domain of the Spike Gly... -

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Basic information

Entry
Database: PDB / ID: 5gnb
TitleCrystal Structure of the Receptor Binding Domain of the Spike Glycoprotein of Human Betacoronavirus HKU1 (HKU1 1A-CTD, 2.3 angstrom, native-SAD phasing)
ComponentsSpike glycoproteinSpike protein
KeywordsVIRAL PROTEIN / Coronavirus spike protein / S1-CTD / receptor binding domain / receptor binding motif / virus entry / HKU1
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, N-terminal domain, murine hepatitis virus-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 (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-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 speciesHuman coronavirus HKU1
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsGuan, H. / Wojdyla, J.A. / Wang, M. / Cui, S.
CitationJournal: Nat Commun / Year: 2017
Title: Crystal structure of the receptor binding domain of the spike glycoprotein of human betacoronavirus HKU1
Authors: Ou, X. / Guan, H. / Qin, B. / Mu, Z. / Wojdyla, J.A. / Wang, M. / Dominguez, S.R. / Qian, Z. / Cui, S.
History
DepositionJul 20, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Structure summary / Category: struct / struct_keywords / Item: _struct.title / _struct_keywords.text
Revision 1.2Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3105
Polymers41,4251
Non-polymers8854
Water4,216234
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint12 kcal/mol
Surface area18850 Å2
Unit cell
Length a, b, c (Å)86.720, 183.990, 63.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-980-

HOH

21A-1002-

HOH

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Components

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


Mass: 41425.062 Da / Num. of mol.: 1 / Fragment: UNP residues 307-677
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human coronavirus HKU1 (isolate N1) / Strain: isolate N1 / Gene: S, 3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5MQD0
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O

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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: 3.04 Å3/Da / Density % sol: 60 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris, 24%PEG4000, 0.2M MgCl2, 4% v/v Pentaerythritol ethoxylate (3/4 EO/OH)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 2.08 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.08 Å / Relative weight: 1
ReflectionResolution: 2.3→49.2 Å / Num. obs: 43316 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 89.76 % / Biso Wilson estimate: 31.062 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.23 / Net I/σ(I): 28.04
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 30.92 % / Rmerge(I) obs: 1.28 / Mean I/σ(I) obs: 3.37 / CC1/2: 0.894 / % possible all: 93.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→49.2 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.93 / Phase error: 23.97
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2192 2155 4.98 %Random
Rwork0.1728 ---
obs0.1751 43282 99.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 30.16 Å2
Refinement stepCycle: LAST / Resolution: 2.3→49.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2853 0 56 234 3143
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083070
X-RAY DIFFRACTIONf_angle_d0.8544213
X-RAY DIFFRACTIONf_dihedral_angle_d9.9681859
X-RAY DIFFRACTIONf_chiral_restr0.051468
X-RAY DIFFRACTIONf_plane_restr0.005546
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.298-2.35150.30321370.23492595X-RAY DIFFRACTION93
2.3515-2.41030.25661400.21762720X-RAY DIFFRACTION99
2.4103-2.47540.23841450.20562765X-RAY DIFFRACTION100
2.4754-2.54830.28891410.18642762X-RAY DIFFRACTION100
2.5483-2.63050.29931400.18312734X-RAY DIFFRACTION100
2.6305-2.72450.21131480.17062760X-RAY DIFFRACTION100
2.7245-2.83360.22231470.17322745X-RAY DIFFRACTION100
2.8336-2.96250.23721440.18482731X-RAY DIFFRACTION100
2.9625-3.11870.23841440.19142764X-RAY DIFFRACTION100
3.1187-3.31410.23231430.17472762X-RAY DIFFRACTION100
3.3141-3.56990.18691470.16372755X-RAY DIFFRACTION100
3.5699-3.9290.20771480.15452774X-RAY DIFFRACTION100
3.929-4.49720.20861420.1342741X-RAY DIFFRACTION100
4.4972-5.66470.14631430.15082769X-RAY DIFFRACTION100
5.6647-49.20670.23021460.19472750X-RAY DIFFRACTION100

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