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- PDB-2yq3: Structure of BVDV1 envelope glycoprotein E2, pH5 -

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Basic information

Entry
Database: PDB / ID: 2yq3
TitleStructure of BVDV1 envelope glycoprotein E2, pH5
ComponentsBVDV1 E2
KeywordsVIRAL PROTEIN / PESTIVIRUS / VIRUS FUSION
Function / homology
Function and homology information


pestivirus NS3 polyprotein peptidase / ribonuclease T2 / serine-type exopeptidase activity / ribonuclease T2 activity / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / clathrin-dependent endocytosis of virus by host cell ...pestivirus NS3 polyprotein peptidase / ribonuclease T2 / serine-type exopeptidase activity / ribonuclease T2 activity / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / clathrin-dependent endocytosis of virus by host cell / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / host cell endoplasmic reticulum membrane / viral protein processing / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / virion attachment to host cell / GTP binding / virion membrane / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane
Similarity search - Function
Alpha-Beta Plaits - #50 / Pestivirus envelope glycoprotein E2, domain B / Alpha-Beta Plaits / Pestivirus envelope glycoprotein E2, domain A / Pestivirus envelope glycoprotein E2, domain B / Capsid protein C, pestivirus / Pestivirus nonstructural protein 2 / Pestivirus NS2, peptidase C74 / Capsid protein C, pestivirus / Pestivirus NS2 peptidase ...Alpha-Beta Plaits - #50 / Pestivirus envelope glycoprotein E2, domain B / Alpha-Beta Plaits / Pestivirus envelope glycoprotein E2, domain A / Pestivirus envelope glycoprotein E2, domain B / Capsid protein C, pestivirus / Pestivirus nonstructural protein 2 / Pestivirus NS2, peptidase C74 / Capsid protein C, pestivirus / Pestivirus NS2 peptidase / Pestivirus nonstructural protein 2 (NS2) protease domain profile. / Pestivirus NS3, peptidase S31 / Pestivirus envelope glycoprotein E2 / Pestivirus envelope glycoprotein E2, domain D / Pestivirus NS3 polyprotein peptidase S31 / Pestivirus envelope glycoprotein E2 / Pestivirus NS3 protease (NS3pro) domain profile. / Peptidase C53, pestivirus Npro, interaction domain / Peptidase C53, pestivirus Npro / Pestivirus Npro endopeptidase C53 / Pestivirus N-terminal protease Npro domain profile. / Ribonuclease T2, His active site 2 / Ribonuclease T2 family histidine active site 2. / Ribonuclease T2-like superfamily / Other non-globular / RNA dependent RNA polymerase, hepatitis C virus / Viral RNA dependent RNA polymerase / : / Flavivirus NS3 helicase, C-terminal helical domain / DEAD box, Flavivirus / Flavivirus DEAD domain / Helicase conserved C-terminal domain / Special / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Biological speciesBOVINE VIRAL DIARRHEA VIRUS 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.29 Å
AuthorsEl Omari, K. / Iourin, O. / Harlos, K. / Grimes, J.M. / Stuart, D.I.
CitationJournal: Cell Rep. / Year: 2013
Title: Structure of a Pestivirus Envelope Glycoprotein E2 Clarifies its Role in Cell Entry.
Authors: El Omari, K. / Iourin, O. / Harlos, K. / Grimes, J.M. / Stuart, D.I.
History
DepositionNov 4, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2Nov 26, 2014Group: Other
Revision 1.3Apr 3, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc ...entity_src_gen / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Dec 20, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BVDV1 E2
B: BVDV1 E2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,93510
Polymers76,1652
Non-polymers1,7708
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6720 Å2
ΔGint-9.6 kcal/mol
Surface area31430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.736, 49.695, 136.422
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein BVDV1 E2


Mass: 38082.441 Da / Num. of mol.: 2 / Fragment: BVDV1 E2 ECTODOMAIN, RESIDUES 1-337 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOVINE VIRAL DIARRHEA VIRUS 1 / Strain: PE515 / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: Q01499*PLUS
#2: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
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
Sequence detailsMUTATION: Y9S, G94E

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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: 3.36 Å3/Da / Density % sol: 63.4 % / Description: NONE
Crystal growpH: 5
Details: 16% PEG 6000, 79 MM CITRIC BUFFER PH 5.0, 20MM MGSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1.0341
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0341 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 17239 / % possible obs: 99.9 % / Observed criterion σ(I): 1.5 / Redundancy: 4.9 % / Biso Wilson estimate: 75.46 Å2 / Rmerge(I) obs: 0.24 / Net I/σ(I): 6.1
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 1.5 / % possible all: 99.8

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YQ2

2yq2


Resolution: 3.29→47.48 Å / Cor.coef. Fo:Fc: 0.8241 / Cor.coef. Fo:Fc free: 0.821 / SU R Cruickshank DPI: 2.592 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 4.522 / SU Rfree Blow DPI: 0.424 / SU Rfree Cruickshank DPI: 0.427
RfactorNum. reflection% reflectionSelection details
Rfree0.2637 873 5.07 %RANDOM
Rwork0.2526 ---
obs0.2531 17209 99.29 %-
Displacement parametersBiso mean: 82.96 Å2
Baniso -1Baniso -2Baniso -3
1--15.1136 Å20 Å20 Å2
2--7.7565 Å20 Å2
3---7.3571 Å2
Refine analyzeLuzzati coordinate error obs: 0.885 Å
Refinement stepCycle: LAST / Resolution: 3.29→47.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4083 0 112 0 4195
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0074304HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.995836HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1979SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes102HARMONIC2
X-RAY DIFFRACTIONt_gen_planes616HARMONIC5
X-RAY DIFFRACTIONt_it4304HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.23
X-RAY DIFFRACTIONt_other_torsion3.11
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion582SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4298SEMIHARMONIC4
LS refinement shellResolution: 3.29→3.49 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.206 148 5.58 %
Rwork0.2395 2506 -
all0.2377 2654 -
obs--99.29 %
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)
10.24650.23140.00170.94471.86885.3911-0.03140.01510.0755-0.27420.0008-0.0970.07-0.28830.03060.11220.04730.0167-0.05320.0512-0.0062-50.72378.9575-27.1014
20.70150.2015-1.21510.0245-0.25983.6253-0.06870.0150.19130.24090.0931-0.19020.1947-0.2224-0.02440.1896-0.01050.0041-0.1150.0083-0.0182-33.7222.9117-104.166
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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