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- PDB-4dwa: Crystal structure of an active-site mutant of the glycoprotein Er... -

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Basic information

Entry
Database: PDB / ID: 4dwa
TitleCrystal structure of an active-site mutant of the glycoprotein Erns from the pestivirus BVDV-1 in complex with a CpUpC trinucleotide
Components
  • E(rns) glycoprotein
  • RNA (5'-R(*CP*UP*C)-3')
KeywordsVIRAL PROTEIN/RNA / virus glycoprotein / T2 Ribonuclease / VIRAL PROTEIN-RNA complex
Function / homology
Function and homology information


pestivirus NS3 polyprotein peptidase / ribonuclease T2 / serine-type exopeptidase activity / ribonuclease T2 activity / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / 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 ...pestivirus NS3 polyprotein peptidase / ribonuclease T2 / serine-type exopeptidase activity / ribonuclease T2 activity / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / 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 / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / 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
Ribonuclease Rh; Chain A / Ribonuclease T2-like / 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. ...Ribonuclease Rh; Chain A / Ribonuclease T2-like / 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 / Alpha-Beta Complex / P-loop containing nucleoside triphosphate hydrolase / Alpha Beta
Similarity search - Domain/homology
RNA / Genome polyprotein
Similarity search - Component
Biological speciesBovine viral diarrhea virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.01 Å
AuthorsKrey, T. / Bontems, F. / Vonrhein, C. / Vaney, M.-C. / Bricogne, G. / Ruemenapf, T. / Rey, F.A.
CitationJournal: Structure / Year: 2012
Title: Crystal Structure of the Pestivirus Envelope Glycoprotein E(rns) and Mechanistic Analysis of Its Ribonuclease Activity.
Authors: Krey, T. / Bontems, F. / Vonrhein, C. / Vaney, M.C. / Bricogne, G. / Rumenapf, T. / Rey, F.A.
History
DepositionFeb 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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_unobs_or_zero_occ_atoms / 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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 30, 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: E(rns) glycoprotein
B: E(rns) glycoprotein
D: RNA (5'-R(*CP*UP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,58318
Polymers38,8653
Non-polymers4,71815
Water1,13563
1
A: E(rns) glycoprotein
D: RNA (5'-R(*CP*UP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,45411
Polymers19,8682
Non-polymers2,5869
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-21 kcal/mol
Surface area9920 Å2
2
B: E(rns) glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1287
Polymers18,9971
Non-polymers2,1326
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.213, 105.213, 210.904
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein / RNA chain , 2 types, 3 molecules ABD

#1: Protein E(rns) glycoprotein


Mass: 18996.523 Da / Num. of mol.: 2 / Fragment: N-terminal fragment / Mutation: H32K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bovine viral diarrhea virus / Strain: CP7 / Gene: Erns / Plasmid: pMT-BIP-based / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q96662
#2: RNA chain RNA (5'-R(*CP*UP*C)-3')


Mass: 871.572 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Sugars , 4 types, 9 molecules

#3: Polysaccharide beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-6DManpb1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2-2-2/a4-b1_b4-c1_c3-d1_d6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{[(6+1)][b-D-Manp]{}}}}}}LINUCSPDB-CARE
#4: 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.: 3
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
#5: Polysaccharide beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-6DManpb1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-2-2-3/a4-b1_b4-c1_c3-d1_c6-f1_d6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{[(6+1)][b-D-Manp]{}}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: 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.: 4
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

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Non-polymers , 2 types, 69 molecules

#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 4.34 Å3/Da / Density % sol: 71.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 4.6
Details: 33% PEG2000 MME, 100mM Na-Acetate, 140mM (NH4)2SO4, 50mM KH2PO4, pH 4.6, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 26, 2011
RadiationMonochromator: Diamond (001) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 3.01→41.82 Å / Num. all: 14264 / Num. obs: 13636 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 68.71 Å2
Reflection shellResolution: 3.01→3.17 Å / % possible all: 79.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASERphasing
BUSTER-TNTBUSTER 2.9.2refinement
PDB_EXTRACT3.1data extraction
XDSdata scaling
XDSdata reduction
BUSTER2.9.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4DVK

4dvk


Resolution: 3.01→41.82 Å / Cor.coef. Fo:Fc: 0.8851 / Cor.coef. Fo:Fc free: 0.8504 / Occupancy max: 1 / Occupancy min: 0 / SU R Cruickshank DPI: 0.962 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2362 657 4.94 %RANDOM
Rwork0.1949 ---
obs0.197 13291 92.57 %-
all-13903 --
Displacement parametersBiso mean: 47.86 Å2
Baniso -1Baniso -2Baniso -3
1--9.9971 Å20 Å20 Å2
2---9.9971 Å20 Å2
3---19.9942 Å2
Refine analyzeLuzzati coordinate error obs: 0.521 Å
Refinement stepCycle: LAST / Resolution: 3.01→41.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2469 57 303 63 2892
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012930HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.24026HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1074SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes75HARMONIC2
X-RAY DIFFRACTIONt_gen_planes399HARMONIC5
X-RAY DIFFRACTIONt_it2657HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.76
X-RAY DIFFRACTIONt_other_torsion19.81
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion461SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies2HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion30SINUSOIDAL1
X-RAY DIFFRACTIONt_ideal_dist_contact3312SEMIHARMONIC4
LS refinement shellResolution: 3.01→3.25 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2686 107 5.12 %
Rwork0.2256 1983 -
all0.2279 2090 -
obs--92.57 %

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