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- PDB-4kqz: structure of the receptor binding domain (RBD) of MERS-CoV spike -

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Basic information

Entry
Database: PDB / ID: 4kqz
Titlestructure of the receptor binding domain (RBD) of MERS-CoV spike
ComponentsS proteinCoronavirus spike protein
KeywordsVIRAL PROTEIN / core subdomain / strand-dominated receptor binding motif / receptor binding / CD26 / viral surface
Function / homology
Function and homology information


host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / symbiont 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 ...host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / symbiont 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
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 / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Single Sheet / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily ...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 / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Single Sheet / 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 / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesHuman betacoronavirus 2c EMC/2012
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.514 Å
AuthorsLu, G. / Hu, Y. / Wang, Q. / Qi, J. / Gao, F. / Li, Y. / Zhang, Y. / Zhang, W. / Yuan, Y. / Bao, J. ...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.
CitationJournal: 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
DepositionMay 15, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Database references
Revision 1.2Dec 18, 2019Group: Database references / Derived calculations / Category: citation / struct_conn / struct_ref_seq_dif
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed ..._citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
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

Downloads & links

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Assembly

Deposited unit
A: S protein
B: S protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6404
Polymers55,1982
Non-polymers4422
Water1,13563
1
A: S protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8202
Polymers27,5991
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: S protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8202
Polymers27,5991
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.977, 108.473, 125.925
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein S protein / Coronavirus spike protein


Mass: 27598.953 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 367-606
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human betacoronavirus 2c EMC/2012 / Gene: S, spike / Cell line (production host): High5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: K0BRG7
#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.: 2
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.: 63 / 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: 2.91 Å3/Da / Density % sol: 57.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M ammonium tartrate dibasic pH7.0, 12% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.03818 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 7, 2013
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03818 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 22587 / Num. obs: 22536 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 21.614
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.659 / Mean I/σ(I) obs: 4.308 / Rsym value: 0.659 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.514→49.813 Å / SU ML: 0.37 / σ(F): 1.35 / Phase error: 26.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2509 1153 5.13 %
Rwork0.2079 --
obs0.2101 22479 99.22 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.726 Å2 / ksol: 0.3 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-19.4021 Å20 Å2-0 Å2
2---13.935 Å20 Å2
3----5.467 Å2
Refinement stepCycle: LAST / Resolution: 2.514→49.813 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3216 0 28 63 3307
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053332
X-RAY DIFFRACTIONf_angle_d0.9364540
X-RAY DIFFRACTIONf_dihedral_angle_d14.9651204
X-RAY DIFFRACTIONf_chiral_restr0.064530
X-RAY DIFFRACTIONf_plane_restr0.005574
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5139-2.62830.40361360.31332521X-RAY DIFFRACTION96
2.6283-2.76680.37141420.29172640X-RAY DIFFRACTION100
2.7668-2.94020.35521530.26232639X-RAY DIFFRACTION100
2.9402-3.16710.29411350.2382648X-RAY DIFFRACTION100
3.1671-3.48580.25391480.21932662X-RAY DIFFRACTION100
3.4858-3.990.26041630.20032661X-RAY DIFFRACTION100
3.99-5.02620.19881360.15712725X-RAY DIFFRACTION100
5.0262-49.82240.20071400.19922830X-RAY DIFFRACTION98
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)
11.65610.38290.95281.97280.14061.1408-0.07950.07180.1112-0.20360.00540.0362-0.29910.0609-0.00060.2813-0.03180.06180.29790.03590.271522.7931-8.5234-10.196
20.89931.354-0.18132.0129-0.33270.0587-0.0584-0.0870.1559-0.03760.1788-0.0129-0.3632-0.04680.00060.26490.03730.02490.3235-0.01710.314318.8761-16.1764-7.9012
31.1572-0.64590.53311.7948-0.00231.01380.00360.0473-0.0159-0.21530.0999-0.0615-0.05590.08660.00070.2153-0.01580.03440.3945-0.03410.359424.9837-34.9649-8.2366
40.3723-0.19980.09752.2057-0.92351.2873-0.39410.09910.3023-0.53340.08240.0392-0.69070.2562-0.05150.4276-0.0810.07880.4243-0.0060.407225.1136-5.9246-8.934
50.5743-0.06140.46770.60140.50620.8888-0.24640.3185-0.2259-0.11620.07760.28591.0062-0.2169-0.00570.7714-0.1088-0.03510.4584-0.12020.60347.3397-60.9243-22.2293
60.6497-0.2004-0.71140.49120.10540.7764-0.3737-0.1902-0.06190.04660.10830.06920.65560.05400.6505-0.00910.04630.3353-0.03920.452711.5191-59.6594-12.2305
70.19060.1123-0.11310.11810.00820.14350.01830.0330.26170.3861-0.0047-0.70360.0860.4882-00.51670.09910.02150.5762-0.09340.433125.3044-49.2632-18.1309
80.13380.1249-0.09270.0991-0.05980.1850.2482-0.068-0.31620.037-0.16540.4583-0.00830.036300.42610.02540.01420.3755-0.06080.401314.587-44.9053-18.3762
91.11690.27330.43620.38920.01360.216-0.14520.0076-0.7281-0.22270.0139-0.03430.72150.0278-01.04190.10610.0790.463-0.08180.697919.887-64.7286-22.4485
100.7573-0.1432-0.65510.32460.23440.88970.5890.37240.2707-1.0406-0.2862-0.2341-0.49530.18190.00380.90580.0750.13370.531-0.01470.440421.5889-36.4345-32.5903
110.3397-0.11870.22920.4161-0.37550.56920.37980.32650.0168-0.7027-0.09410.19060.07020.0278-00.65460.0774-0.03310.6471-0.07270.549417.673-45.463-31.7942
120.0468-0.0353-0.10490.12690.20390.38510.0175-0.19531.0646-0.24060.57280.323-0.5370.6720.02141.39240.00320.16320.8160.16410.856713.9437-34.9224-40.3357
131.25210.89320.52470.63560.52371.3226-0.13280.02770.2131-0.79620.31230.01730.45320.11230.00270.6530.03350.09710.3936-0.00810.424920.2127-53.231-25.7438
140.9046-0.31680.96961.0181-0.21631.04570.0785-0.58810.26450.2218-0.19611.220.5741-1.01660.1870.8802-0.20.28960.6597-0.21150.8626-3.3481-59.3314-8.1682
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 381:456)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 457:495)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 496:562)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 563:588)
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 381:410)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 411:447)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 448:462)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 463:476)
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 477:495)
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 496:515)
11X-RAY DIFFRACTION11CHAIN B AND (RESSEQ 516:539)
12X-RAY DIFFRACTION12CHAIN B AND (RESSEQ 540:552)
13X-RAY DIFFRACTION13CHAIN B AND (RESSEQ 553:576)
14X-RAY DIFFRACTION14CHAIN B AND (RESSEQ 577:588)

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