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

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Basic information

Entry
Database: PDB / ID: 5kwb
TitleCrystal Structure of the Receptor Binding Domain of the Spike Glycoprotein of Human Betacoronavirus HKU1 (HKU1 1A-CTD, 1.9 angstrom, molecular replacement)
ComponentsSpike glycoprotein
KeywordsVIRAL PROTEIN / Coronavirus spike protein / S1-CTD / receptor binding domain / receptor binding motif / virus entry / HKU1
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, N-terminal domain, murine hepatitis virus-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, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / 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, N-terminal domain, murine hepatitis virus-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, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / 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 / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-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
Similarity search - Domain/homology
sucrose / Spike glycoprotein
Similarity search - Component
Biological speciesHuman coronavirus HKU1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 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 17, 2016Deposition site: RCSB / 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,79812
Polymers41,4251
Non-polymers1,37311
Water6,071337
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint3 kcal/mol
Surface area18730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.556, 183.800, 63.342
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-1031-

HOH

21A-1055-

HOH

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Components

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


Mass: 41425.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human coronavirus HKU1 (isolate N1) / Strain: isolate N1 / Gene: S, 3 / Plasmid: pTIE1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5MQD0
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: 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.: 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
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O
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: 3.04 Å3/Da / Density % sol: 59.55 %
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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97776 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 1.91→50 Å / Num. obs: 75702 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.45 % / Biso Wilson estimate: 28.331 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 9.37
Reflection shellResolution: 1.91→2.02 Å / Redundancy: 3.37 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 1.6 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata processing
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GNB

5gnb


Resolution: 1.91→49.248 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.13 / Phase error: 22.36
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2006 3804 5.03 %Random
Rwork0.1754 ---
obs0.1767 75651 99.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 33.54 Å2
Refinement stepCycle: LAST / Resolution: 1.91→49.248 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2853 0 85 337 3275
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013101
X-RAY DIFFRACTIONf_angle_d1.0464260
X-RAY DIFFRACTIONf_dihedral_angle_d10.031878
X-RAY DIFFRACTIONf_chiral_restr0.057477
X-RAY DIFFRACTIONf_plane_restr0.007548
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.930.33561370.352546X-RAY DIFFRACTION95
1.9324-1.95780.40471430.32592666X-RAY DIFFRACTION100
1.9578-1.98470.3351420.28572651X-RAY DIFFRACTION100
1.9847-2.0130.27371420.27012681X-RAY DIFFRACTION100
2.013-2.04310.25221420.25132636X-RAY DIFFRACTION100
2.0431-2.0750.23131420.24172678X-RAY DIFFRACTION100
2.075-2.1090.25871440.23272698X-RAY DIFFRACTION100
2.109-2.14540.30151390.21632626X-RAY DIFFRACTION100
2.1454-2.18440.28211370.20842666X-RAY DIFFRACTION100
2.1844-2.22640.20711410.20122681X-RAY DIFFRACTION100
2.2264-2.27180.2691430.19382654X-RAY DIFFRACTION100
2.2718-2.32120.23451430.18852669X-RAY DIFFRACTION100
2.3212-2.37520.19241420.18012657X-RAY DIFFRACTION100
2.3752-2.43460.20711420.19132698X-RAY DIFFRACTION100
2.4346-2.50050.19581400.17432646X-RAY DIFFRACTION100
2.5005-2.5740.22321420.17532663X-RAY DIFFRACTION100
2.574-2.65710.18291430.16792697X-RAY DIFFRACTION100
2.6571-2.75210.18751440.16292678X-RAY DIFFRACTION100
2.7521-2.86230.20481400.16032622X-RAY DIFFRACTION100
2.8623-2.99250.18181440.16442703X-RAY DIFFRACTION100
2.9925-3.15030.20531340.15112624X-RAY DIFFRACTION99
3.1503-3.34760.15011420.15012682X-RAY DIFFRACTION100
3.3476-3.6060.15741360.13842672X-RAY DIFFRACTION100
3.606-3.96870.20611380.13722670X-RAY DIFFRACTION100
3.9687-4.54270.11521380.12522653X-RAY DIFFRACTION100
4.5427-5.72190.15511400.14172667X-RAY DIFFRACTION99
5.7219-49.2480.23181440.2042663X-RAY DIFFRACTION100

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