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- PDB-4ild: Crystal structure of truncated Bovine viral diarrhea virus 1 E2 e... -

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Basic information

Entry
Database: PDB / ID: 4ild
TitleCrystal structure of truncated Bovine viral diarrhea virus 1 E2 envelope protein
ComponentsEnvelope glycoprotein E2
KeywordsVIRAL PROTEIN / BVDV1 / viral envelope protein / viral membrane fusion / E1 envelope protein / viral surface membrane
Function / homology
Function and homology information


dopamine receptor binding / pestivirus NS3 polyprotein peptidase / ribonuclease T2 / RNA stabilization / DNA/DNA annealing activity / serine-type exopeptidase activity / ribonuclease T2 activity / RNA strand annealing activity / viral genome packaging / host cell cytoplasmic vesicle ...dopamine receptor binding / pestivirus NS3 polyprotein peptidase / ribonuclease T2 / RNA stabilization / DNA/DNA annealing activity / serine-type exopeptidase activity / ribonuclease T2 activity / RNA strand annealing activity / viral genome packaging / host cell cytoplasmic vesicle / protein-DNA complex / nucleoside-triphosphate phosphatase / channel activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / viral protein processing / RNA helicase activity / host cell endoplasmic reticulum membrane / RNA helicase / ribonucleoprotein complex / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / chromatin extrusion motor activity / ATP-dependent H2AZ histone chaperone activity / ATP-dependent H3-H4 histone complex chaperone activity / cohesin loader activity / cysteine-type endopeptidase activity / viral RNA genome replication / serine-type endopeptidase activity / DNA clamp loader activity / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / : / GTP binding / virion attachment to host cell / virion membrane / ATP hydrolysis activity / proteolysis / DNA binding / RNA binding / ATP binding / identical protein binding / membrane
Similarity search - Function
Pestivirus envelope glycoprotein E2, C-terminal domain / Pestivirus envelope glycoprotein E2, domain B / Cleavage inducing molecular chaperone, Jiv / : / Cleavage inducing molecular chaperone / Pestivirus envelope glycoprotein E2, domain A / Pestivirus envelope glycoprotein E2, domain B / Capsid protein C, pestivirus / Pestivirus nonstructural protein 2 / Pestivirus NS2, peptidase C74 ...Pestivirus envelope glycoprotein E2, C-terminal domain / Pestivirus envelope glycoprotein E2, domain B / Cleavage inducing molecular chaperone, Jiv / : / Cleavage inducing molecular chaperone / 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
URANYL (VI) ION / Genome polyprotein
Similarity search - Component
Biological speciesBovine viral diarrhea virus 1-NADL
MethodX-RAY DIFFRACTION / SYNCHROTRON / INITIAL SAD PLUS MULTIPLE HA SITE REFINEMENT / Resolution: 3.27 Å
AuthorsModis, Y. / Li, Y. / Wang, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Crystal structure of glycoprotein E2 from bovine viral diarrhea virus.
Authors: Li, Y. / Wang, J. / Kanai, R. / Modis, Y.
History
DepositionDec 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Database references
Revision 1.2May 8, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_struct_conn_angle / pdbx_validate_close_contact / 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.id / _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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Envelope glycoprotein E2
B: Envelope glycoprotein E2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,06918
Polymers57,4342
Non-polymers4,63616
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.720, 54.450, 95.920
Angle α, β, γ (deg.)90.00, 92.23, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Envelope glycoprotein E2 / gp55


Mass: 28716.760 Da / Num. of mol.: 2
Fragment: N-terminal truncated BVDV1 E2 envelope protein, UNP residues 781-1030
Source method: isolated from a genetically manipulated source
Details: N-terminal His-tagged / Source: (gene. exp.) Bovine viral diarrhea virus 1-NADL / Plasmid: pAcgp67a / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P19711
#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.: 8
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-IUM / URANYL (VI) ION


Mass: 270.028 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O2U
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: 3.11 Å3/Da / Density % sol: 60.4 %
Crystal growTemperature: 294 K / pH: 5.5
Details: 10% polyethylene glycol 3350, 0.1 M Bis-tris pH 5.5, 0.05 M cesium chloride, 0.04 M calcium acetate, 10% glycerol., VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 195 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.2142
DetectorType: S/N 60-0107 / Detector: PILATUS 6M / Date: Oct 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2142 Å / Relative weight: 1
ReflectionResolution: 3.27→50 Å / Num. obs: 11169 / % possible obs: 98.4 % / Observed criterion σ(I): 1.9 / Rsym value: 0.086 / Net I/σ(I): 12.08
Reflection shellResolution: 3.27→3.36 Å / Redundancy: 1.72 % / Mean I/σ(I) obs: 69.4 / % possible all: 89.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
MLPHAREphasing
REFMAC5.7.0029refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: INITIAL SAD PLUS MULTIPLE HA SITE REFINEMENT
Resolution: 3.27→47.97 Å / Cor.coef. Fo:Fc: 0.843 / Cor.coef. Fo:Fc free: 0.801 / SU B: 56.081 / SU ML: 0.469 / Cross valid method: THROUGHOUT / ESU R Free: 0.591
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.289 555 5 %RANDOM
Rwork0.246 ---
obs0.248 10539 99.1 %-
all-21043 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.92 Å2
Baniso -1Baniso -2Baniso -3
1-1.88 Å20 Å20.44 Å2
2---3.41 Å2-0 Å2
3---1.51 Å2
Refinement stepCycle: LAST / Resolution: 3.27→47.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3734 0 240 0 3974
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.024087
X-RAY DIFFRACTIONr_bond_other_d0.0020.023739
X-RAY DIFFRACTIONr_angle_refined_deg1.8952.0255551
X-RAY DIFFRACTIONr_angle_other_deg1.2443.0068566
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2915468
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.7724.32169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.06715658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2431518
X-RAY DIFFRACTIONr_chiral_restr0.0880.2626
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214408
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02882
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_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.27→3.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 39 -
Rwork0.325 740 -
obs--94.08 %
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)
13.4141-0.9429-1.06770.98881.80343.78240.11590.18860.128-0.27370.1808-0.1355-0.49150.1759-0.29670.1802-0.08030.05290.26220.10250.311275.72278.101-63.3022
26.43450.6676-5.54080.1498-0.60784.86250.28650.63510.3636-0.094-0.0342-0.0006-0.2011-0.6412-0.25240.20790.16450.05320.41370.05990.323246.877311.1301-43.5652
36.9107-0.2266-3.8311.7948-1.86514.3608-0.2515-0.1022-0.0008-0.04310.1105-0.10450.2183-0.15590.1410.0861-0.07220.00680.4101-0.17930.134726.09982.0212-17.7771
43.5163-1.2382-1.47164.55450.23534.05380.1941-0.64930.23430.3147-0.1152-0.03510.0550.4513-0.07890.16970.0571-0.08490.4453-0.15050.1088.858626.722470.5967
50.4435-0.752-1.70631.44623.31037.6977-0.2096-0.1933-0.00360.18090.1291-0.00010.46730.15860.08050.40250.25040.02110.4222-0.08970.094815.15699.791841.2229
62.07581.47670.78091.07890.75387.5385-0.07370.068-0.1966-0.06010.0191-0.1873-0.2802-0.74670.05450.19240.07720.0770.3906-0.08250.170813.54274.53876.9588
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A783 - 856
2X-RAY DIFFRACTION1A2401 - 2402
3X-RAY DIFFRACTION2A857 - 936
4X-RAY DIFFRACTION2A2403 - 2406
5X-RAY DIFFRACTION3A937 - 1023
6X-RAY DIFFRACTION3A2407 - 2408
7X-RAY DIFFRACTION4B783 - 856
8X-RAY DIFFRACTION4B2401 - 2402
9X-RAY DIFFRACTION5B857 - 936
10X-RAY DIFFRACTION5B2403 - 2406
11X-RAY DIFFRACTION6B937 - 1023
12X-RAY DIFFRACTION6B2407 - 2408

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