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- PDB-5gyq: Putative receptor-binding domain of bat-derived coronavirus HKU9 ... -

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Basic information

Entry
Database: PDB / ID: 5gyq
TitlePutative receptor-binding domain of bat-derived coronavirus HKU9 spike protein
ComponentsSpike glycoproteinSpike protein
KeywordsVIRAL PROTEIN / bat coronavirus HKU9 / putative receptor binding domain (RBD) / spike (S) / SUGAR BINDING PROTEIN
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 / membrane => GO:0016020 / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane
Similarity search - Function
Spike (S) protein S1 subunit, N-terminal domain, HKU9-like / : / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / 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, HKU9-like / : / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / 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 / 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 speciesBat coronavirus HKU9
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsHuang, C. / Qi, J. / Gao, G.F.
CitationJournal: Biochemistry / Year: 2016
Title: Putative Receptor Binding Domain of Bat-Derived Coronavirus HKU9 Spike Protein: Evolution of Betacoronavirus Receptor Binding Motifs
Authors: Huang, C. / Qi, J. / Lu, G. / Wang, Q. / Yuan, Y. / Wu, Y. / Zhang, Y. / Yan, J. / Gao, G.F.
History
DepositionSep 23, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / citation / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_oper_list / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
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)20,2912
Polymers19,8671
Non-polymers4241
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area550 Å2
ΔGint6 kcal/mol
Surface area9040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.752, 35.990, 62.886
Angle α, β, γ (deg.)90.00, 102.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 19866.598 Da / Num. of mol.: 1 / Fragment: UNP residues 355-521
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bat coronavirus HKU9 / Gene: S, 2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A3EXG6
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.38 Å3/Da / Density % sol: 48.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1M sodium citrate tribasic dihydrate pH 7.0, 12% PEG 20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.03906 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03906 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 10822 / % possible obs: 97.1 % / Redundancy: 9.4 % / Net I/σ(I): 34.023
Reflection shellResolution: 2.1→2.18 Å / % possible all: 80.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→41.703 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.57
RfactorNum. reflection% reflection
Rfree0.2006 520 4.81 %
Rwork0.17 --
obs0.1715 10811 97.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→41.703 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1333 0 28 128 1489
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031416
X-RAY DIFFRACTIONf_angle_d0.821942
X-RAY DIFFRACTIONf_dihedral_angle_d12.313499
X-RAY DIFFRACTIONf_chiral_restr0.033219
X-RAY DIFFRACTIONf_plane_restr0.003249
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1005-2.31180.23291040.19752338X-RAY DIFFRACTION89
2.3118-2.64630.18631380.18482627X-RAY DIFFRACTION100
2.6463-3.33390.22621600.17752608X-RAY DIFFRACTION100
3.3339-41.71080.17721180.15362718X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -4.3169 Å / Origin y: -6.861 Å / Origin z: -17.2583 Å
111213212223313233
T0.0908 Å2-0.0214 Å20.0003 Å2-0.0964 Å20.0147 Å2--0.0932 Å2
L0.7254 °20.0195 °20.428 °2-1.1041 °2-0.1729 °2--1.2171 °2
S-0.0229 Å °-0.0096 Å °-0.0305 Å °0.175 Å °-0.0566 Å °-0.0808 Å °-0.1052 Å °0.0872 Å °-0.1139 Å °
Refinement TLS groupSelection details: all

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