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- PDB-5yy5: Structural definition of a unique neutralization epitope on the r... -

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Basic information

Entry
Database: PDB / ID: 5yy5
TitleStructural definition of a unique neutralization epitope on the receptor-binding domain of MERS-CoV spike glycoprotein
Components
  • (Heavy chain) x 2
  • (Light chain) x 2
  • MERS-CoV RBD
KeywordsVIRAL PROTEIN / MERS-CoV / spike glycorptotein / neutralizing antibody
Function / homology
Function and homology information


membrane fusion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / 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
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
Biological speciesMiddle East respiratory syndrome coronavirus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsZhang, S. / Wang, P. / Zhou, P. / Wang, X. / Zhang, L.
CitationJournal: Cell Rep / Year: 2018
Title: Structural Definition of a Unique Neutralization Epitope on the Receptor-Binding Domain of MERS-CoV Spike Glycoprotein
Authors: Zhang, S. / Zhou, P. / Wang, P. / Li, Y. / Jiang, L. / Jia, W. / Wang, H. / Fan, A. / Wang, D. / Shi, X. / Fang, X. / Hammel, M. / Wang, S. / Wang, X. / Zhang, L.
History
DepositionDec 8, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Structure summary
Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 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
Revision 1.3Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MERS-CoV RBD
B: MERS-CoV RBD
H: Heavy chain
L: Light chain
C: Heavy chain
D: Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,8698
Polymers93,4266
Non-polymers4422
Water00
1
A: MERS-CoV RBD
H: Heavy chain
L: Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4044
Polymers47,1833
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-11 kcal/mol
Surface area19200 Å2
MethodPISA
2
B: MERS-CoV RBD
C: Heavy chain
D: Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4654
Polymers46,2443
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-12 kcal/mol
Surface area18780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.315, 152.315, 148.535
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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Antibody , 4 types, 4 molecules HLCD

#2: Antibody Heavy chain


Mass: 12474.881 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Antibody Light chain


Mass: 11720.712 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody Heavy chain


Mass: 12216.610 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: Antibody Light chain


Mass: 11039.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein MERS-CoV RBD


Mass: 22987.012 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Middle East respiratory syndrome coronavirus
Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: K9N5Q8*PLUS
#6: 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.: 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

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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: 3.5 Å3/Da / Density % sol: 64.9 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / pH: 7
Details: tris pH7.5, polyethylene glycol 8000, ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 31541 / % possible obs: 99.2 % / Redundancy: 5.5 % / Net I/σ(I): 16.2
Reflection shellResolution: 2.8→2.88 Å / Num. unique obs: 31541 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→41.51 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 40.11
RfactorNum. reflection% reflection
Rfree0.2793 1546 4.9 %
Rwork0.2459 --
obs0.2476 31541 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→41.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6564 0 28 0 6592
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096764
X-RAY DIFFRACTIONf_angle_d1.3329231
X-RAY DIFFRACTIONf_dihedral_angle_d14.4124001
X-RAY DIFFRACTIONf_chiral_restr0.0641033
X-RAY DIFFRACTIONf_plane_restr0.0081178
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.89040.50671270.42392711X-RAY DIFFRACTION99
2.8904-2.99370.40311450.36782708X-RAY DIFFRACTION100
2.9937-3.11350.37081280.33882738X-RAY DIFFRACTION100
3.1135-3.25510.39971150.31982779X-RAY DIFFRACTION100
3.2551-3.42670.37661360.27452722X-RAY DIFFRACTION100
3.4267-3.64120.32141710.26772692X-RAY DIFFRACTION100
3.6412-3.92220.35021620.25232711X-RAY DIFFRACTION100
3.9222-4.31650.28991360.23932731X-RAY DIFFRACTION100
4.3165-4.94020.21161450.20632736X-RAY DIFFRACTION100
4.9402-6.22080.23081540.22432716X-RAY DIFFRACTION100
6.2208-41.5150.21171270.19962751X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 4.1861 Å / Origin y: 42.723 Å / Origin z: -102.7992 Å
111213212223313233
T0.8841 Å2-0.0093 Å20.0481 Å2-0.9316 Å20.0323 Å2--0.7968 Å2
L1.8835 °2-0.666 °2-0.0962 °2-2.9215 °2-0.1083 °2--0.2657 °2
S0.1502 Å °-0.1943 Å °0.4555 Å °-0.0574 Å °-0.1795 Å °-0.4634 Å °-0.0719 Å °0.1312 Å °0.0012 Å °
Refinement TLS groupSelection details: all

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