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- PDB-4zpt: Structure of MERS-Coronavirus Spike Receptor-binding Domain (Engl... -

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Basic information

Entry
Database: PDB / ID: 4zpt
TitleStructure of MERS-Coronavirus Spike Receptor-binding Domain (England1 Strain) in Complex with Vaccine-Elicited Murine Neutralizing Antibody D12 (Crystal Form 1)
Components
  • D12 Fab Heavy chain
  • D12 Fab Light chain
  • Spike glycoproteinSpike protein
KeywordsViral protein/Immune system / Vaccine / Immunogen / Viral protein-Immune system complex
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 / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesHuman coronavirus EMC
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.591 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: Joyce, M.G.
History
DepositionMay 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D12 Fab Heavy chain
B: D12 Fab Light chain
R: Spike glycoprotein
H: D12 Fab Heavy chain
S: Spike glycoprotein
L: D12 Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,0928
Polymers139,6506
Non-polymers4422
Water5,314295
1
A: D12 Fab Heavy chain
B: D12 Fab Light chain
R: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0464
Polymers69,8253
Non-polymers2211
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: D12 Fab Heavy chain
S: Spike glycoprotein
L: D12 Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0464
Polymers69,8253
Non-polymers2211
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.452, 128.790, 170.871
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: Antibody D12 Fab Heavy chain


Mass: 23118.822 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody D12 Fab Light chain


Mass: 23742.113 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Protein Spike glycoprotein / Spike protein / S glycoprotein / E2 / Peplomer protein


Mass: 22963.977 Da / Num. of mol.: 2 / Fragment: receptor-binging 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
#4: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.96 Å3/Da / Density % sol: 58.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M sodium acetate pH 5.5, 50 mM sodium chloride, 10 % PEG 400, 11 % PEG 8,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.591→37.052 Å / Num. obs: 51227 / % possible obs: 99.7 % / Redundancy: 4.5 % / Net I/σ(I): 9.3
Reflection shellResolution: 2.65→2.72 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 1.86 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.591→37.052 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.34 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2441 2529 4.94 %
Rwork0.2038 --
obs0.2057 51214 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.591→37.052 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9732 0 28 295 10055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059981
X-RAY DIFFRACTIONf_angle_d0.94513581
X-RAY DIFFRACTIONf_dihedral_angle_d13.1533562
X-RAY DIFFRACTIONf_chiral_restr0.0391561
X-RAY DIFFRACTIONf_plane_restr0.0051725
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5908-2.64060.37261470.30872496X-RAY DIFFRACTION93
2.6406-2.69450.3421450.29472650X-RAY DIFFRACTION99
2.6945-2.75310.2981670.27652652X-RAY DIFFRACTION99
2.7531-2.81710.31991430.26742674X-RAY DIFFRACTION100
2.8171-2.88750.34281380.27842685X-RAY DIFFRACTION99
2.8875-2.96560.32451510.25842679X-RAY DIFFRACTION99
2.9656-3.05280.31111560.25222669X-RAY DIFFRACTION100
3.0528-3.15130.30211380.23632714X-RAY DIFFRACTION99
3.1513-3.26380.29841360.23352688X-RAY DIFFRACTION100
3.2638-3.39440.26591360.23072749X-RAY DIFFRACTION99
3.3944-3.54880.2351160.2092718X-RAY DIFFRACTION99
3.5488-3.73570.20741270.19452707X-RAY DIFFRACTION99
3.7357-3.96960.19591410.18572722X-RAY DIFFRACTION99
3.9696-4.27560.20611250.1772736X-RAY DIFFRACTION99
4.2756-4.70510.1881400.15562724X-RAY DIFFRACTION99
4.7051-5.38420.19251430.15452756X-RAY DIFFRACTION99
5.3842-6.77680.24441410.17522786X-RAY DIFFRACTION99
6.7768-37.05590.1971390.17232880X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -21.7544 Å / Origin y: 15.9784 Å / Origin z: -54.329 Å
111213212223313233
T0.2983 Å2-0.0145 Å2-0.0255 Å2-0.3251 Å20.0071 Å2--0.3814 Å2
L0.0937 °2-0.0301 °2-0.0562 °2-0.3198 °2-0.2624 °2--0.8031 °2
S0.001 Å °0.0048 Å °-0.0093 Å °0.1189 Å °-0.0137 Å °-0.0208 Å °-0.0845 Å °0.0233 Å °0.0091 Å °
Refinement TLS groupSelection details: all

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