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- PDB-4zpw: Structure of unbound MERS-CoV spike receptor-binding domain (Engl... -

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Basic information

Entry
Database: PDB / ID: 4zpw
TitleStructure of unbound MERS-CoV spike receptor-binding domain (England1 strain).
ComponentsSpike glycoprotein
KeywordsVIRAL PROTEIN / Vaccine / Immunogen
Function / homology
Function and homology information


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 / 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 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal ...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 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / 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 / 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 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Alpha-Beta Plaits / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Spike glycoprotein
Similarity search - Component
Biological speciesHuman coronavirus EMC
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.023 Å
AuthorsJoyce, M.G. / Mascola, J.R. / Graham, B.S. / Kwong, P.D.
CitationJournal: Nat Commun / Year: 2015
Title: Evaluation of candidate vaccine approaches for MERS-CoV.
Authors: Wang, L. / Shi, W. / Joyce, M.G. / Modjarrad, K. / Zhang, Y. / Leung, K. / Lees, C.R. / Zhou, T. / Yassine, H.M. / Kanekiyo, M. / Yang, Z.Y. / Chen, X. / Becker, M.M. / Freeman, M. / Vogel, ...Authors: Wang, L. / Shi, W. / Joyce, M.G. / Modjarrad, K. / Zhang, Y. / Leung, K. / Lees, C.R. / Zhou, T. / Yassine, H.M. / Kanekiyo, M. / Yang, Z.Y. / Chen, X. / Becker, M.M. / Freeman, M. / Vogel, L. / Johnson, J.C. / Olinger, G. / Todd, J.P. / Bagci, U. / Solomon, J. / Mollura, D.J. / Hensley, L. / Jahrling, P. / Denison, M.R. / Rao, S.S. / Subbarao, K. / Kwong, P.D. / Mascola, J.R. / Kong, W.P. / Graham, B.S.
History
DepositionMay 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_oper_list / 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 / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 13, 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
R: Spike glycoprotein
S: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9087
Polymers45,9282
Non-polymers9805
Water1,892105
1
R: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4063
Polymers22,9641
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
S: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5014
Polymers22,9641
Non-polymers5373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.667, 109.887, 125.279
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 Spike glycoprotein / S glycoprotein / E2 / Peplomer protein


Mass: 22963.977 Da / Num. of mol.: 2 / Fragment: receptor-binding domain, UNP residues 381-588
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human coronavirus EMC (isolate United Kingdom/H123990006/2012)
Strain: isolate United Kingdom/H123990006/2012 / Gene: S, 3 / Plasmid: CMVR / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: K9N5Q8
#2: 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
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 3.5 Å3/Da / Density % sol: 64.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris-HCl pH 8.5, 10 % MPD, 29 % PEG 1,500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.023→50 Å / Num. obs: 11975 / % possible obs: 91.7 % / Redundancy: 4.8 % / Net I/σ(I): 5.7
Reflection shellResolution: 3.17→3.31 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 2 / % possible all: 81.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 3.023→43.731 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2589 609 5.09 %
Rwork0.2173 --
obs0.2195 11967 90.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.023→43.731 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3222 0 61 105 3388
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033374
X-RAY DIFFRACTIONf_angle_d0.8074602
X-RAY DIFFRACTIONf_dihedral_angle_d14.4511204
X-RAY DIFFRACTIONf_chiral_restr0.034540
X-RAY DIFFRACTIONf_plane_restr0.005582
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0231-3.32720.361360.26912761X-RAY DIFFRACTION89
3.3272-3.80850.26971510.22282847X-RAY DIFFRACTION93
3.8085-4.79730.21191530.18322875X-RAY DIFFRACTION92
4.7973-43.7360.26461690.22572875X-RAY DIFFRACTION89
Refinement TLS params.Method: refined / Origin x: 19.0416 Å / Origin y: -35.3735 Å / Origin z: -15.8948 Å
111213212223313233
T0.2842 Å20.0088 Å20.0173 Å2-0.45 Å2-0.0438 Å2--0.4154 Å2
L0.403 °20.0413 °20.0703 °2-3.2077 °20.7287 °2--1.054 °2
S0.0403 Å °0.1622 Å °-0.0412 Å °-0.2666 Å °-0.0555 Å °0.0258 Å °0.0253 Å °0.0327 Å °0.0687 Å °
Refinement TLS groupSelection details: all

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