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

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Basic information

Entry
Database: PDB / ID: 5zxv
TitleStructural definition of a unique neutralization epitope on the receptor-binding domain of MERS-CoV spike glycoprotein
Components
  • MERS-CoV RBD
  • heavy chain
  • light chain
KeywordsVIRAL PROTEIN / 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
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 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / 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 (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 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / 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. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus spike glycoprotein S1, receptor binding / Betacoronavirus-like spike glycoprotein S1, N-terminal / 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
Similarity search - Domain/homology
Biological speciesMiddle East respiratory syndrome coronavirus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.482 Å
AuthorsZhang, S. / Wang, X.
Funding support China, 1items
OrganizationGrant numberCountry
China
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
DepositionMay 21, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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


Theoretical massNumber of molelcules
Total (without water)136,8016
Polymers136,8016
Non-polymers00
Water00
1
A: MERS-CoV RBD
H: heavy chain
L: light chain


Theoretical massNumber of molelcules
Total (without water)68,4003
Polymers68,4003
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MERS-CoV RBD
C: heavy chain
D: light chain


Theoretical massNumber of molelcules
Total (without water)68,4003
Polymers68,4003
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.647, 138.647, 228.736
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein MERS-CoV RBD


Mass: 22929.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Middle East respiratory syndrome coronavirus
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: K9N5Q8*PLUS
#2: Antibody heavy chain


Mass: 22745.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody light chain


Mass: 22724.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
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: 3.13 Å3/Da / Density % sol: 60.76 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 2%(v/v) tacsimate pH 5.0, 0.1M sodium citrate tribasic dihydrate pH 5.6, 16%(w/v) polyethylene glycol 3,350 and 2M sodium thiocyanate

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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: May 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 4.482→50 Å / Num. obs: 9351 / % possible obs: 96.8 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 8.4
Reflection shellResolution: 4.5→4.6 Å / Redundancy: 3.1 % / Num. unique obs: 9351 / CC1/2: 0.541 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4L72

4l72


Resolution: 4.482→35.438 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 52.66
RfactorNum. reflection% reflection
Rfree0.343 474 5.07 %
Rwork0.3072 --
obs0.3104 9351 95.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 4.482→35.438 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9488 0 0 0 9488
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069750
X-RAY DIFFRACTIONf_angle_d0.97513326
X-RAY DIFFRACTIONf_dihedral_angle_d12.2495836
X-RAY DIFFRACTIONf_chiral_restr0.0491518
X-RAY DIFFRACTIONf_plane_restr0.0061696
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.4921-5.13640.40441730.39362869X-RAY DIFFRACTION88
5.1364-6.45020.39811340.36773004X-RAY DIFFRACTION93
6.4502-23.88340.32121570.26882978X-RAY DIFFRACTION92
Refinement TLS params.Method: refined / Origin x: -37.7227 Å / Origin y: 91.9355 Å / Origin z: -3.3713 Å
111213212223313233
T2.4933 Å20.1823 Å2-0.092 Å2-2.5291 Å2-0.3317 Å2--2.1425 Å2
L1.7421 °21.1809 °2-0.1946 °2-2.3504 °2-0.2263 °2--1.3357 °2
S0.0536 Å °-0.3159 Å °0.8561 Å °0.1458 Å °0.2548 Å °0.6626 Å °-0.1947 Å °-0.3761 Å °-0 Å °
Refinement TLS groupSelection details: all

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