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- PDB-6l8q: Complex structure of bat CD26 and MERS-RBD -

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Basic information

Entry
Database: PDB / ID: 6l8q
TitleComplex structure of bat CD26 and MERS-RBD
Components
  • Dipeptidyl peptidase 4Dipeptidyl peptidase-4
  • Spike glycoproteinSpike protein
KeywordsSTRUCTURAL PROTEIN / complex / coronavirus / bat / receptor
Function / homology
Function and homology information


: / lamellipodium membrane / endocytosis involved in viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / cell adhesion / fusion of virus membrane with host plasma membrane / serine-type endopeptidase activity ...: / lamellipodium membrane / endocytosis involved in viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / cell adhesion / fusion of virus membrane with host plasma membrane / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
: / ubp-family deubiquitinating enzyme fold - #30 / Spike protein, C-terminal core receptor binding subdomain / ubp-family deubiquitinating enzyme fold / Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Dipeptidylpeptidase IV, N-terminal domain / 8 Propeller / Methanol Dehydrogenase; Chain A / Prolyl endopeptidase family serine active site. ...: / ubp-family deubiquitinating enzyme fold - #30 / Spike protein, C-terminal core receptor binding subdomain / ubp-family deubiquitinating enzyme fold / Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Dipeptidylpeptidase IV, N-terminal domain / 8 Propeller / Methanol Dehydrogenase; Chain A / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / 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 / 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 / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Spike glycoprotein / Spike glycoprotein / Dipeptidyl peptidase 4
Similarity search - Component
Biological speciesMyotis davidii (bat)
Middle East respiratory syndrome-related coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsYuan, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China) China
Citation
Journal: J.Virol. / Year: 2020
Title: Molecular Basis of Binding between Middle East Respiratory Syndrome Coronavirus and CD26 from Seven Bat Species.
Authors: Yuan, Y. / Qi, J. / Peng, R. / Li, C. / Lu, G. / Yan, J. / Wang, Q. / Gao, G.F.
#1: Journal: Nature / Year: 2013
Title: Molecular basis of binding between novel human coronavirus MERS-CoV and its receptor CD26.
Authors: Lu, G. / Hu, Y. / Wang, Q. / Qi, J. / Gao, F. / Li, Y. / Zhang, Y. / Zhang, W. / Yuan, Y. / Bao, J. / Zhang, B. / Shi, Y. / Yan, J. / Gao, G.F.
History
DepositionNov 7, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.country ..._chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / 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 / struct_asym / struct_conn / 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 / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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
Revision 2.1Nov 22, 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

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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 glycoprotein
C: Dipeptidyl peptidase 4
D: Spike glycoprotein
E: Dipeptidyl peptidase 4
F: Spike glycoprotein
G: Dipeptidyl peptidase 4
H: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)457,34936
Polymers447,0528
Non-polymers10,29728
Water0
1
A: Dipeptidyl peptidase 4
B: Spike glycoprotein
C: Dipeptidyl peptidase 4
D: Spike glycoprotein
hetero molecules

E: Dipeptidyl peptidase 4
F: Spike glycoprotein
hetero molecules

G: Dipeptidyl peptidase 4
H: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)457,34936
Polymers447,0528
Non-polymers10,29728
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_656x+1,y,z+11
crystal symmetry operation1_556x,y,z+11
Buried area31800 Å2
ΔGint113 kcal/mol
Surface area151970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.657, 273.674, 115.234
Angle α, β, γ (deg.)90.000, 119.682, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein
Dipeptidyl peptidase 4 / Dipeptidyl peptidase-4


Mass: 84648.586 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myotis davidii (bat) / Gene: MDA_GLEAN10024208 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: L5LQ33
#2: Protein
Spike glycoprotein / Spike protein / S glycoprotein / E2 / Peplomer protein


Mass: 27114.447 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Middle East respiratory syndrome-related coronavirus
Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A0A0Q7F3, UniProt: K9N5Q8*PLUS
#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.: 13
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.: 4
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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 11
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
Has ligand of interestN

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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: 3.54 Å3/Da / Density % sol: 65.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2M imidazole malate, pH 8.5, 7.5% (w/v) PEG 10000

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Data collection

DiffractionMean temperature: 291 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.097→50 Å / Num. obs: 95308 / % possible obs: 85.34 % / Redundancy: 5.7 % / Biso Wilson estimate: 64.28 Å2 / CC1/2: 0.972 / Net I/σ(I): 8.463
Reflection shellResolution: 3.1→3.21 Å / Num. unique obs: 11097 / CC1/2: 0.738

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KR0

4kr0


Resolution: 3.1→49.81 Å / SU ML: 0.2172 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.5973
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2406 4577 4.8 %
Rwork0.1999 90691 -
obs0.202 95268 85.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.05 Å2
Refinement stepCycle: LAST / Resolution: 3.1→49.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30730 0 0 0 30730
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003931574
X-RAY DIFFRACTIONf_angle_d0.65142975
X-RAY DIFFRACTIONf_chiral_restr0.04694740
X-RAY DIFFRACTIONf_plane_restr0.00385461
X-RAY DIFFRACTIONf_dihedral_angle_d17.23511526
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.130.3005970.30141462X-RAY DIFFRACTION41.74
3.13-3.170.3472600.28171739X-RAY DIFFRACTION48.93
3.17-3.210.3127890.2851868X-RAY DIFFRACTION52.38
3.21-3.250.31981070.27772003X-RAY DIFFRACTION57.6
3.25-3.290.39631110.26622157X-RAY DIFFRACTION60.08
3.29-3.340.34931120.25842242X-RAY DIFFRACTION64.21
3.34-3.380.3091020.26012397X-RAY DIFFRACTION66.46
3.38-3.430.30351190.24732496X-RAY DIFFRACTION71.64
3.43-3.490.29661510.24252626X-RAY DIFFRACTION73.78
3.49-3.550.27791640.24292674X-RAY DIFFRACTION77.75
3.55-3.610.27361540.24172921X-RAY DIFFRACTION81.37
3.61-3.670.31271200.23712997X-RAY DIFFRACTION85.26
3.67-3.740.25392070.21883161X-RAY DIFFRACTION90.39
3.74-3.820.22521850.21343367X-RAY DIFFRACTION95.1
3.82-3.90.24911840.2163477X-RAY DIFFRACTION98.97
3.9-3.990.26061780.20373542X-RAY DIFFRACTION99.55
3.99-4.090.23851710.19313542X-RAY DIFFRACTION99.84
4.09-4.20.22831290.19363552X-RAY DIFFRACTION99.89
4.2-4.330.22111880.17253522X-RAY DIFFRACTION99.92
4.33-4.470.20821700.16953571X-RAY DIFFRACTION99.95
4.47-4.630.20011700.15313589X-RAY DIFFRACTION99.89
4.63-4.810.21231670.15333533X-RAY DIFFRACTION99.89
4.81-5.030.20772330.1613480X-RAY DIFFRACTION99.81
5.03-5.290.22941740.16083515X-RAY DIFFRACTION99.78
5.29-5.630.17161230.18493590X-RAY DIFFRACTION99.79
5.63-6.060.24822350.1923545X-RAY DIFFRACTION99.82
6.06-6.670.2261400.20113524X-RAY DIFFRACTION99.65
6.67-7.630.26031780.23568X-RAY DIFFRACTION99.34
7.63-9.60.19021770.18283525X-RAY DIFFRACTION98.96
9.6-49.810.23761820.21783506X-RAY DIFFRACTION97.7
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3586670454810.0273353968611-0.112370693870.5538242329780.0448178287020.3912239661250.02272165805970.0666464339150.0163984967746-0.04902379053130.0363075695796-0.0154597100873-0.0284931554661-0.01034038544576.46611171464E-120.2837179664350.0467128695880.01558972334690.290290021650.03531294064830.27314466867119.60956379631.0894686166411.895909832
20.229821744989-0.0408529347824-0.005561952607950.1576946113040.03906405291530.0719186721470.0595330510776-0.0401991425208-0.0347761000433-0.03417860940190.0469453328314-0.128487112863-0.04508127097160.07328445986318.57011549702E-110.3140888134250.04276150817960.002194443602920.440510148687-0.02829940577710.433235319559152.799561734-7.55956787647404.557197115
30.3463998522150.0250446508210.08164637978930.507452078133-0.04080912249550.4474752267650.02186188985350.0743366247714-0.022883703407-0.04046737737550.02077774565890.001406698769730.01570551065010.022835787739-1.34784470021E-110.2548424785480.0452825030028-0.01904196359780.276796631186-0.03491540652830.27073654589111.900352357-43.8794005251411.861898443
40.174273842143-0.006419798525-0.0102426661320.140323160086-0.05937869836870.08324005786870.0268137381016-0.003454870647820.0683970587710.07767095558540.0611165327780.1234224755630.0528254288546-0.08999133848762.15724535621E-90.3279699036830.05274239274190.01857486775460.4644940389470.02006816568210.4454892695178.6777431932-5.23613824444404.533720024
50.294448321091-0.1029266373880.116093564030.435441901478-0.1461529789030.688494998340.0252661321252-0.01765615156230.009427650654220.0431119348418-0.00575929466739-0.0286247775012-0.1406046266270.0154283379052-2.68879034875E-110.22549682609-0.01064436218510.0002716859761710.2185290541640.01685954907880.22704381329277.40259102637.6961961968366.173447509
60.0868862653603-0.03003271339270.0343335034240.133357825521-0.04993879974590.05589394437560.06831354226740.0873231345174-0.00299112021915-0.1132125047830.0339392294235-0.01774181008320.07272086614020.02810639816051.75991110891E-90.410594019480.0201140577587-0.09202399474720.4004582710410.02241601342470.37062392053281.9946170874-13.1153138469373.652496286
70.248275755577-0.086391743009-0.1641655531180.3377167812960.1983218717930.7288401504910.0166464490129-0.014453136553-0.009884302660710.06975645784510.001889698977430.02018675644820.149347401614-0.00729014101761.96056879493E-110.29834972804-0.0112392893727-0.002602543279970.28841173929-0.01182948969630.296188801505153.941847327-50.4693984879366.116452768
80.111936924650.0118923204277-0.04284280549430.1268512836830.05345139712910.034555471910.1398286249830.05471931137590.024389194059-0.2107138596940.0108375472672-0.108351859684-0.02592000300760.011743509125-3.57098030107E-90.4667780173790.03528563625150.09713060396660.435659532797-0.009200835037860.469016588787149.3366326230.331456812439373.645976485
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F
7X-RAY DIFFRACTION7chain G
8X-RAY DIFFRACTION8chain H

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