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- PDB-5jil: Crystal structure of rat coronavirus strain New-Jersey Hemaggluti... -

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Basic information

Entry
Database: PDB / ID: 5jil
TitleCrystal structure of rat coronavirus strain New-Jersey Hemagglutinin-Esterase in complex with 4N-acetyl sialic acid
ComponentsHemagglutinin-esterase
KeywordsVIRAL PROTEIN / Hemagglutin / Esterase / Hepatitis virus / Coronavirus / sialic acid
Function / homology
Function and homology information


sialate 9-O-acetylesterase activity / sialate 4-O-acetylesterase activity / sialate O-acetylesterase / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / metal ion binding / plasma membrane
Similarity search - Function
Hemagglutinin-esterase / Haemagglutinin-esterase glycoprotein, haemagglutinin domain / Haemagglutinin-esterase glycoprotein, core / Hemagglutinin domain of haemagglutinin-esterase-fusion glycoprotein / Hemagglutinin esterase / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Chem-6KL / Hemagglutinin-esterase
Similarity search - Component
Biological speciesRat coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsBakkers, M.J.G. / Feitsma, L.J. / de Groot, R.J. / Huizinga, E.G.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organization for Scientific ResearchECHO 711.011.006 Netherlands
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Coronavirus receptor switch explained from the stereochemistry of protein-carbohydrate interactions and a single mutation.
Authors: Bakkers, M.J. / Zeng, Q. / Feitsma, L.J. / Hulswit, R.J. / Li, Z. / Westerbeke, A. / van Kuppeveld, F.J. / Boons, G.J. / Langereis, M.A. / Huizinga, E.G. / de Groot, R.J.
History
DepositionApr 22, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Jun 8, 2016Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Apr 3, 2019Group: Atomic model / Data collection / Source and taxonomy / Category: atom_site / entity_src_gen
Item: _atom_site.occupancy / _entity_src_gen.pdbx_host_org_cell_line
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / 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 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_conn_type / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _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_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 3.2Oct 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: Hemagglutinin-esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,40113
Polymers43,6111
Non-polymers2,79012
Water3,441191
1
A: Hemagglutinin-esterase
hetero molecules

A: Hemagglutinin-esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,80126
Polymers87,2212
Non-polymers5,58024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area8280 Å2
ΔGint36 kcal/mol
Surface area30840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.090, 184.590, 78.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-759-

HOH

21A-791-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Hemagglutinin-esterase / HE protein / E3 glycoprotein


Mass: 43610.688 Da / Num. of mol.: 1 / Fragment: UNP residues 22-400 / Mutation: S40A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rat coronavirus / Gene: HE / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q3HS77, sialate O-acetylesterase

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Sugars , 3 types, 10 molecules

#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.: 1
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: 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.: 7
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
#6: Sugar ChemComp-6KL / methyl 4,5-bisacetamido-3,4,5-trideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid / methyl 4,5-bis(acetylamino)-3,4,5-trideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid / methyl 4,5-bisacetamido-3,4,5-trideoxy-D-glycero-alpha-D-galacto-non-2-ulosidonic acid / methyl 4,5-bisacetamido-3,4,5-trideoxy-D-glycero-D-galacto-non-2-ulosidonic acid / methyl 4,5-bisacetamido-3,4,5-trideoxy-D-glycero-galacto-non-2-ulosidonic acid


Type: D-saccharide / Mass: 364.348 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H24N2O9

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Non-polymers , 3 types, 193 molecules

#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O

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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: 2.47 Å3/Da / Density % sol: 50.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M HEPES pH 7.5, 0.2M NaCl, 20% w/v PEG3000

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 1.85→92.92 Å / Num. obs: 33539 / % possible obs: 94.4 % / Redundancy: 3.2 % / Biso Wilson estimate: 22.5 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.106 / Net I/σ(I): 6.2
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 1.8 / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
MOSFLM7.09data reduction
Aimless0.1.27data scaling
PHASER2.5.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RCoV-HE

Resolution: 1.85→92.29 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.95 / SU B: 6.715 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.126 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2002 1667 5 %RANDOM
Rwork0.18435 ---
obs0.18515 31870 93.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.685 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å2-0 Å20 Å2
2--0.1 Å20 Å2
3----0.32 Å2
Refinement stepCycle: 1 / Resolution: 1.85→92.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2926 0 178 191 3295
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.023362
X-RAY DIFFRACTIONr_bond_other_d0.0020.022967
X-RAY DIFFRACTIONr_angle_refined_deg1.2961.9884634
X-RAY DIFFRACTIONr_angle_other_deg0.9333.0066886
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3475424
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.02724.438160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.18415494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8751512
X-RAY DIFFRACTIONr_chiral_restr0.0750.2516
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213857
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02821
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_it0.3041.2891533
X-RAY DIFFRACTIONr_mcbond_other0.3041.2881532
X-RAY DIFFRACTIONr_mcangle_it0.5571.9311929
X-RAY DIFFRACTIONr_mcangle_other0.5571.9321930
X-RAY DIFFRACTIONr_scbond_it0.3571.3961829
X-RAY DIFFRACTIONr_scbond_other0.3561.3961829
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.6182.0832677
X-RAY DIFFRACTIONr_long_range_B_refined4.48811.3783776
X-RAY DIFFRACTIONr_long_range_B_other4.48811.3783776
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 123 -
Rwork0.284 2342 -
obs--94.73 %
Refinement TLS params.Method: refined / Origin x: -13.6478 Å / Origin y: -26.3082 Å / Origin z: -9.0986 Å
111213212223313233
T0.0642 Å2-0.0128 Å2-0.0026 Å2-0.0079 Å2-0.0046 Å2--0.029 Å2
L0.4453 °2-0.0428 °2-0.0678 °2-1.7951 °2-0.0032 °2--0.7738 °2
S0.0005 Å °-0.025 Å °-0.0625 Å °0.0052 Å °-0.0515 Å °0.1025 Å °0.0713 Å °-0.0378 Å °0.051 Å °

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