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- PDB-2yq2: Structure of BVDV1 envelope glycoprotein E2, pH8 -

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Basic information

Entry
Database: PDB / ID: 2yq2
TitleStructure of BVDV1 envelope glycoprotein E2, pH8
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
Pestivirus envelope glycoprotein E2, domain A / Pestivirus envelope glycoprotein E2, domain B / mini-chromosome maintenance (MCM) complex, domain 2 / 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 envelope glycoprotein E2, domain A / Pestivirus envelope glycoprotein E2, domain B / mini-chromosome maintenance (MCM) complex, domain 2 / 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 / 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 / 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 / MAD / Resolution: 2.58 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 1.2Apr 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 1.3Jul 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

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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)77,6448
Polymers76,3172
Non-polymers1,3276
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-17.1 kcal/mol
Surface area38660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.180, 47.593, 159.290
Angle α, β, γ (deg.)90.00, 108.15, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein BVDV1 E2


Mass: 38158.539 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-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMUTATION: Y9S, G94E, N298Q

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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: 3.1 Å3/Da / Density % sol: 61 % / Description: NONE
Crystal growpH: 8
Details: 52.5% METHYL-2,4-PENTANEDIOL (MPD) AND 0.1 M TRIS PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. obs: 29885 / % possible obs: 97 % / Observed criterion σ(I): 1.7 / Redundancy: 5 % / Biso Wilson estimate: 66.73 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 27.6
Reflection shellResolution: 2.59→2.68 Å / Redundancy: 4.5 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.7 / % possible all: 76.1

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXAUTOSOLphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.58→38.08 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.8892 / SU R Cruickshank DPI: 0.497 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.478 / SU Rfree Blow DPI: 0.27 / SU Rfree Cruickshank DPI: 0.276
RfactorNum. reflection% reflectionSelection details
Rfree0.2527 1506 5.04 %RANDOM
Rwork0.2399 ---
obs0.2406 29867 98.85 %-
Displacement parametersBiso mean: 78.07 Å2
Baniso -1Baniso -2Baniso -3
1-7.4158 Å20 Å2-14.5745 Å2
2---5.1856 Å20 Å2
3----2.2302 Å2
Refine analyzeLuzzati coordinate error obs: 0.547 Å
Refinement stepCycle: LAST / Resolution: 2.58→38.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5248 0 84 48 5380
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0085479HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.087438HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2520SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes122HARMONIC2
X-RAY DIFFRACTIONt_gen_planes794HARMONIC5
X-RAY DIFFRACTIONt_it5479HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.71
X-RAY DIFFRACTIONt_other_torsion3.12
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion723SEMIHARMONIC5
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_contact5554SEMIHARMONIC4
LS refinement shellResolution: 2.58→2.67 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2968 129 4.62 %
Rwork0.2848 2661 -
all0.2853 2790 -
obs--98.85 %
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)
16.0324-0.95711.73691.6349-1.09262.14830.0439-0.11440.00020.0904-0.0105-0.0535-0.03890.1683-0.0334-0.24910.1820.01820.18060.0482-0.0512-29.646638.0939-20.4699
25.8682-2.0991-2.90642.77970.17832.07460.01390.0871-0.0131-0.39150.0052-0.1886-0.1568-0.4424-0.0191-0.06020.17130.0279-0.05690.0423-0.01644.411535.2229-40.1193
33.7543-1.0048-1.31484.3695-0.1541.7146-0.0144-0.03630.09430.0236-0.00240.08050.01870.08960.0168-0.08520.13590.1373-0.09270.10510.043144.877525.0058-52.2045
40.03290.01550.01770.0603-0.03760.02680.0011-0.00260.0010.0026-0.00310-0.0014-0.0020.00190.0104-0.0110.00740.02470.01090.00766.90114.4983-56.0511
52.178-1.681-2.07340.06520.07091.59350.0076-0.0541-0.01690.02370.0071-0.01280.0092-0.0181-0.0147-0.03410.12050.22030.01320.12140.037573.329818.0436-74.1843
63.26480.88260.37760.69762.5484.050.00010.0626-0.0393-0.0461-0.01190.02590.09720.04830.0117-0.08380.11440.07270.1824-0.0589-0.1025131.602754.3747-151.8757
73.68452.5757-1.9593.0103-1.23641.7990.01240.3007-0.10190.10480.01910.11820.07130.2597-0.0315-0.1315-0.05960.002-0.0243-0.04780.0047106.557346.1977-124.111
81.77352.674-2.49140.6693-1.34883.0417-0.0072-0.1699-0.0192-0.02460.06430.0562-0.0998-0.0547-0.05710.02130.07970.2447-0.21250.01970.175884.19425.5331-93.3856
90.06440.00040.04450.0662-0.04950.10330.0010.0004-0.0017-0.00160.0011-0.0014-0.0008-0.003-0.00220.00080.0070.01820.01310.01710.047287.537714.1384-66.1603
100.9511-1.7124-1.44840.3294-0.32521.72250.0069-0.03610.0016-0.0330.0112-0.0427-0.01450.0586-0.018-0.10550.19110.1540.08550.05440.030863.489719.2707-63.3179
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 2 - 88
2X-RAY DIFFRACTION2CHAIN A AND RESID 89 - 203
3X-RAY DIFFRACTION3CHAIN A AND RESID 204 - 287
4X-RAY DIFFRACTION4CHAIN A AND RESID 288 - 293
5X-RAY DIFFRACTION5CHAIN A AND RESID 294 - 333
6X-RAY DIFFRACTION6CHAIN B AND RESID 2 - 88
7X-RAY DIFFRACTION7CHAIN B AND RESID 89 - 203
8X-RAY DIFFRACTION8CHAIN B AND RESID 204 - 287
9X-RAY DIFFRACTION9CHAIN B AND RESID 288 - 293
10X-RAY DIFFRACTION10CHAIN B AND RESID 294 - 331

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