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- PDB-4njl: Crystal structure of middle east respiratory syndrome coronavirus... -

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Basic information

Entry
Database: PDB / ID: 4njl
TitleCrystal structure of middle east respiratory syndrome coronavirus S2 protein fusion core
ComponentsS proteinCoronavirus spike protein
KeywordsVIRAL PROTEIN / six-helix-bundle / coronavirus / MERS-Cov / fusion inhibitor / fusion core
Function / homology
Function and homology information


endocytosis involved in viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / 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
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #300 / 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 alpha-helices involved in coiled-coils or other helix-helix interfaces / 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 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #300 / 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 alpha-helices involved in coiled-coils or other helix-helix interfaces / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Spike glycoprotein
Similarity search - Component
Biological speciesMiddle East respiratory syndrome coronavirus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZhu, Y. / Lu, L. / Qin, L. / Ye, S. / Jiang, S. / Zhang, R.
CitationJournal: Nat Commun / Year: 2014
Title: Structure-based discovery of Middle East respiratory syndrome coronavirus fusion inhibitor.
Authors: Lu, L. / Liu, Q. / Zhu, Y. / Chan, K.H. / Qin, L. / Li, Y. / Wang, Q. / Chan, J.F. / Du, L. / Yu, F. / Ma, C. / Ye, S. / Yuen, K.Y. / Zhang, R. / Jiang, S.
History
DepositionNov 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1962
Polymers14,0461
Non-polymers1501
Water1,820101
1
A: S protein
hetero molecules

A: S protein
hetero molecules

A: S protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5876
Polymers42,1373
Non-polymers4513
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area12670 Å2
ΔGint-104 kcal/mol
Surface area18360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.510, 43.510, 129.633
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-2129-

HOH

21A-2200-

HOH

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Components

#1: Protein S protein / Coronavirus spike protein


Mass: 14045.628 Da / Num. of mol.: 1 / Fragment: UNP residues 984-1063
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Middle East respiratory syndrome coronavirus
Production host: Escherichia coli (E. coli) / References: UniProt: R9UQ53
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.52 Å3/Da / Density % sol: 51.23 %
Crystal growTemperature: 289 K / pH: 7.5
Details: 0.1 M HEPES-NaOH, 25% (w/v) PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 2, 2013
RadiationMonochromator: MAX-FLUX / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→36.18 Å / Num. obs: 6795 / % possible obs: 99.3 % / Observed criterion σ(I): 1
Reflection shellResolution: 2.3→2.37 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIX(phenix.phaser)model building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WYY

1wyy


Resolution: 2.3→36.18 Å / SU ML: 0.27 / σ(F): 1.34 / Phase error: 31.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.261 336 4.94 %
Rwork0.22 --
obs0.223 6795 99.3 %
all-6843 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→36.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms975 0 10 101 1086
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003997
X-RAY DIFFRACTIONf_angle_d0.5371344
X-RAY DIFFRACTIONf_dihedral_angle_d14.166370
X-RAY DIFFRACTIONf_chiral_restr0.036162
X-RAY DIFFRACTIONf_plane_restr0.001176
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.89770.34831590.25773165X-RAY DIFFRACTION100
2.8977-36.18760.23611770.20853294X-RAY DIFFRACTION99
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)
10.36250.07850.55810.49911.01318.9530.0759-0.08310.02110.04850.03270.00360.4238-0.5257-0.09690.14790.0193-0.00840.15890.0150.192719.25189.169835.0257
23.9693-0.4584-4.56723.5137-0.02488.0622-0.0369-0.5848-0.26070.4104-0.28310.1697-0.8656-0.23990.3770.33230.0516-0.05720.48980.02860.367815.743421.363671.1244
31.5819-1.343-1.70713.47743.65494.5944-0.12630.016-0.0849-0.0776-0.24080.38160.0409-1.19440.47220.2114-0.0755-0.04460.32730.0040.283412.34298.000514.208
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 985 through 1062)
2X-RAY DIFFRACTION2chain 'A' and (resid 1063 through 1257)
3X-RAY DIFFRACTION3chain 'A' and (resid 1258 through 1288)

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