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- PDB-4qzv: Bat-derived coronavirus HKU4 uses MERS-CoV receptor human CD26 fo... -

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Basic information

Entry
Database: PDB / ID: 4qzv
TitleBat-derived coronavirus HKU4 uses MERS-CoV receptor human CD26 for cell entry
Components
  • Dipeptidyl peptidase 4
  • Spike protein S1
KeywordsHYDROLASE/VIRAL PROTEIN / 8-BLADED BETA-PROPELLER DOMAIN / ALPHA/BETA HYDROLASE DOMAIN / BLADES IV AND V / CD26 BETA-PROPELLER / HYDROLASE-VIRAL PROTEIN COMPLEX
Function / homology
Function and homology information


glucagon processing / regulation of cell-cell adhesion mediated by integrin / negative regulation of neutrophil chemotaxis / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / dipeptidyl-peptidase IV / negative regulation of extracellular matrix disassembly / psychomotor behavior / chemorepellent activity / intercellular canaliculus / dipeptidyl-peptidase activity ...glucagon processing / regulation of cell-cell adhesion mediated by integrin / negative regulation of neutrophil chemotaxis / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / dipeptidyl-peptidase IV / negative regulation of extracellular matrix disassembly / psychomotor behavior / chemorepellent activity / intercellular canaliculus / dipeptidyl-peptidase activity / peptide hormone processing / behavioral fear response / lamellipodium membrane / locomotory exploration behavior / aminopeptidase activity / endothelial cell migration / endocytic vesicle / T cell costimulation / receptor-mediated endocytosis of virus by host cell / serine-type peptidase activity / T cell activation / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / lamellipodium / virus receptor activity / protease binding / membrane fusion / response to hypoxia / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / cell adhesion / apical plasma membrane / endocytosis involved in viral entry into host cell / membrane raft / serine-type endopeptidase activity / fusion of virus membrane with host plasma membrane / signaling receptor binding / lysosomal membrane / focal adhesion / positive regulation of cell population proliferation / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / cell surface / protein homodimerization activity / proteolysis / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane
Similarity search - Function
ubp-family deubiquitinating enzyme fold - #30 / Spike (S) protein S1 subunit, receptor-binding domain, HKU4-like / Spike protein, C-terminal core receptor binding subdomain / ubp-family deubiquitinating enzyme fold / Dipeptidylpeptidase IV, N-terminal domain / 8 Propeller / Methanol Dehydrogenase; Chain A / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / : / Dipeptidylpeptidase IV, N-terminal domain ...ubp-family deubiquitinating enzyme fold - #30 / Spike (S) protein S1 subunit, receptor-binding domain, HKU4-like / Spike protein, C-terminal core receptor binding subdomain / ubp-family deubiquitinating enzyme fold / Dipeptidylpeptidase IV, N-terminal domain / 8 Propeller / Methanol Dehydrogenase; Chain A / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / : / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Single Sheet / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / 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. / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / 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 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 / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Spike glycoprotein / Dipeptidyl peptidase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Tylonycteris bat coronavirus HKU4
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.592 Å
AuthorsGao, F.G. / Wang, Q.H. / Qi, J.X. / Lu, G.W.
CitationJournal: Cell Host Microbe / Year: 2014
Title: Bat Origins of MERS-CoV Supported by Bat Coronavirus HKU4 Usage of Human Receptor CD26.
Authors: Wang, Q.H. / Qi, J.X. / Yuan, Y. / Xuan, Y. / Han, P. / Wan, Y. / Ji, W. / Li, Y. / Wu, Y. / Wang, J. / Iwamoto, A. / Woo, P.C. / Yuen, K.Y. / Yan, J. / Lu, G.W. / Gao, G.F.
History
DepositionJul 29, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / 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_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dipeptidyl peptidase 4
B: Spike protein S1
C: Dipeptidyl peptidase 4
D: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,45617
Polymers224,6304
Non-polymers4,82613
Water8,575476
1
A: Dipeptidyl peptidase 4
B: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,8389
Polymers112,3152
Non-polymers2,5237
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Dipeptidyl peptidase 4
D: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,6178
Polymers112,3152
Non-polymers2,3026
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.801, 203.166, 207.753
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Dipeptidyl peptidase 4 / ADABP / Adenosine deaminase complexing protein 2 / ADCP-2 / Dipeptidyl peptidase IV / DPP IV / T- ...ADABP / Adenosine deaminase complexing protein 2 / ADCP-2 / Dipeptidyl peptidase IV / DPP IV / T-cell activation antigen CD26 / TP103 / Dipeptidyl peptidase 4 membrane form / Dipeptidyl peptidase IV membrane form / Dipeptidyl peptidase 4 soluble form / Dipeptidyl peptidase IV soluble form


Mass: 85291.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPP4, ADCP2, CD26 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P27487, dipeptidyl-peptidase IV
#2: Protein Spike protein S1


Mass: 27023.508 Da / Num. of mol.: 2 / Fragment: receptor binding domain (UNP RESIDUES 372-611)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tylonycteris bat coronavirus HKU4 / Gene: S, 2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A3EX94

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Sugars , 3 types, 13 molecules

#3: 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.: 6
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
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: 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.: 5
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

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Non-polymers , 1 types, 476 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 476 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.7 Å3/Da / Density % sol: 66.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M sodium citrate, pH 5.5, 15% PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 21, 2013
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.592→50 Å / Num. all: 102311 / Num. obs: 102311 / % possible obs: 98.02 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.6→2.69 Å / % possible all: 95.2

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.592→46.301 Å / SU ML: 0.29 / σ(F): 1.34 / Phase error: 23.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2236 5112 5 %RANDOM
Rwork0.1895 ---
all0.1912 102311 --
obs0.1912 102311 98.02 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.592→46.301 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15108 0 316 476 15900
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00615885
X-RAY DIFFRACTIONf_angle_d0.94421612
X-RAY DIFFRACTIONf_dihedral_angle_d14.2645664
X-RAY DIFFRACTIONf_chiral_restr0.042365
X-RAY DIFFRACTIONf_plane_restr0.0042734
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5917-2.62110.3181330.2808282185
2.6211-2.6520.33511700.2596307696
2.652-2.68430.33821500.2505314396
2.6843-2.71830.2761510.2483316995
2.7183-2.7540.25791780.2472311697
2.754-2.79180.28831550.244316296
2.7918-2.83170.29821530.2462317997
2.8317-2.87390.26881530.2383319898
2.8739-2.91880.26931480.2286324297
2.9188-2.96670.27221740.2373318299
2.9667-3.01780.29721600.2368318597
3.0178-3.07270.28351850.2262318998
3.0727-3.13180.24841890.2161325099
3.1318-3.19570.23331900.221321299
3.1957-3.26510.24541730.2182326799
3.2651-3.34110.28321660.2247325399
3.3411-3.42460.26571640.2107329699
3.4246-3.51720.23751670.2006321999
3.5172-3.62060.22541680.1912328099
3.6206-3.73740.21281550.17823286100
3.7374-3.87090.20021660.17693281100
3.8709-4.02580.19881840.16213307100
4.0258-4.2090.19131830.15153313100
4.209-4.43070.18041860.1393297100
4.4307-4.7080.15091770.13323306100
4.708-5.07110.17291890.13663327100
5.0711-5.58070.19262010.14823349100
5.5807-6.38640.17481880.17313340100
6.3864-8.03940.20611830.18943408100
8.0394-46.30820.22711730.1938354699
Refinement TLS params.Method: refined / Origin x: 180.8006 Å / Origin y: 251.3016 Å / Origin z: 41.2624 Å
111213212223313233
T0.1984 Å2-0.0018 Å20.0173 Å2-0.228 Å20.0002 Å2--0.1936 Å2
L0.1699 °2-0.0349 °20.0989 °2-0.1628 °2-0.0233 °2--0.1481 °2
S-0.0121 Å °0.0135 Å °0.0083 Å °-0.0238 Å °0.0288 Å °-0.0263 Å °-0.0031 Å °0.0075 Å °0 Å °
Refinement TLS groupSelection details: ALL

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