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- PDB-4l3n: Crystal structure of the receptor-binding domain from newly emerg... -

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Basic information

Entry
Database: PDB / ID: 4l3n
TitleCrystal structure of the receptor-binding domain from newly emerged Middle East respiratory syndrome coronavirus
ComponentsS proteinCoronavirus spike protein
KeywordsVIRAL PROTEIN / beta-sheet fold
Function / homology
Function and homology information


: / endocytosis involved in viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane => GO:0016020 / 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
Similarity search - Function
ubp-family deubiquitinating enzyme fold - #30 / Spike protein, C-terminal core receptor binding subdomain / : / ubp-family deubiquitinating enzyme fold / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Single Sheet / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus ...ubp-family deubiquitinating enzyme fold - #30 / Spike protein, C-terminal core receptor binding subdomain / : / ubp-family deubiquitinating enzyme fold / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Single Sheet / 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 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 / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesHuman betacoronavirus 2c Jordan-N3/2012
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.13 Å
AuthorsChen, Y. / Rajashankar, K.R. / Yang, Y. / Agnihothram, S.S. / Liu, C. / Lin, Y.-L. / Baric, R.S. / Li, F.
CitationJournal: J.Virol. / Year: 2013
Title: Crystal structure of the receptor-binding domain from newly emerged middle East respiratory syndrome coronavirus.
Authors: Chen, Y. / Rajashankar, K.R. / Yang, Y. / Agnihothram, S.S. / Liu, C. / Lin, Y.L. / Baric, R.S. / Li, F.
History
DepositionJun 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Database references
Revision 1.2Sep 25, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S protein
B: S protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7128
Polymers47,8902
Non-polymers1,8226
Water5,765320
1
A: S protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8564
Polymers23,9451
Non-polymers9113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: S protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8564
Polymers23,9451
Non-polymers9113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.361, 108.065, 124.287
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 S protein / Coronavirus spike protein


Mass: 23945.010 Da / Num. of mol.: 2 / Fragment: receptor-binding domain (UNP residues 379-588)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human betacoronavirus 2c Jordan-N3/2012
Strain: Jordan-N3/2012 / Gene: S / References: UniProt: M4SVE7
#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.18 Å3/Da / Density % sol: 61.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 27% v/v PEG3350, 0.2 M magnesium chloride, 0.1 M Bis-Tris, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationMonochromator: Cryo-Cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.13→49.552 Å / Num. obs: 34770
Reflection shellHighest resolution: 2.13 Å

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Processing

SoftwareName: REFMAC / Version: 5.7.0029 / Classification: refinement
RefinementMethod to determine structure: MIR / Resolution: 2.13→49.552 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.947 / SU B: 7.33 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20602 1748 5 %RANDOM
Rwork0.14405 ---
obs0.14707 33023 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 43.28 Å2
Baniso -1Baniso -2Baniso -3
1-2.99 Å2-0 Å2-0 Å2
2---0.03 Å20 Å2
3----2.96 Å2
Refinement stepCycle: LAST / Resolution: 2.13→49.552 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3233 0 120 320 3673
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.023477
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3352.0094762
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1375423
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.79425.113133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.68915533
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.772158
X-RAY DIFFRACTIONr_chiral_restr0.0860.2563
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212590
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr2.79733477
X-RAY DIFFRACTIONr_sphericity_free36.9135146
X-RAY DIFFRACTIONr_sphericity_bonded20.48853555
LS refinement shellResolution: 2.13→2.245 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.239 250 -
Rwork0.143 4607 -
obs--96.46 %
Refinement TLS params.Method: refined / Origin x: 26.6679 Å / Origin y: 62.074 Å / Origin z: 86.3257 Å
111213212223313233
T0.0388 Å20.0111 Å2-0.0043 Å2-0.0057 Å20.0081 Å2--0.0371 Å2
L0.052 °2-0.1332 °20.1517 °2-0.3619 °2-0.4013 °2--0.4505 °2
S-0.0021 Å °0.0027 Å °0.0014 Å °0.0333 Å °0.0031 Å °0.0004 Å °-0.023 Å °0.0013 Å °-0.001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A380 - 588
2X-RAY DIFFRACTION1B379 - 588

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