[English] 日本語
Yorodumi
- PDB-4jnt: Crystal structure of the ectodomain of Bovine viral diarrhea viru... -

+
Open data


ID or keywords:

Loading...

-
Basic information

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


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 ...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 / 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 / ribonucleoprotein complex / 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 / DNA binding / RNA binding / ATP binding / membrane / identical protein binding
Similarity search - Function
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. ...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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesBovine viral diarrhea virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.09 Å
AuthorsLi, Y. / Wang, J. / Modis, Y.
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
DepositionMar 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 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_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_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_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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Envelope glycoprotein E2
B: Envelope glycoprotein E2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,45710
Polymers77,0622
Non-polymers3,3958
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint26 kcal/mol
Surface area39220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.632, 67.885, 139.406
Angle α, β, γ (deg.)90.00, 121.89, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 0 / Auth seq-ID: 694 - 1023 / Label seq-ID: 2 - 331

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Envelope glycoprotein E2 / gp55


Mass: 38531.094 Da / Num. of mol.: 2 / Fragment: Ectodomain (UNP residues 693-1030)
Source method: isolated from a genetically manipulated source
Details: N-terminal 8XHis-tag / Source: (gene. exp.) Bovine viral diarrhea virus 1 / 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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.06 Å3/Da / Density % sol: 69.68 %
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, SITTING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 195 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 4.09→50 Å / Num. obs: 18935 / % possible obs: 98.1 % / Observed criterion σ(I): 1.34 / Rsym value: 0.151 / Net I/σ(I): 4.78
Reflection shellResolution: 4.09→4.34 Å / Redundancy: 2.12 % / Rmerge(I) obs: 1.002 / Mean I/σ(I) obs: 1.34 / Rsym value: 1.37 / % possible all: 98.1

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.7.0029refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ILD

4ild


Resolution: 4.09→48.57 Å / Cor.coef. Fo:Fc: 0.809 / Cor.coef. Fo:Fc free: 0.725 / SU B: 124.886 / SU ML: 0.811 / Cross valid method: THROUGHOUT / ESU R Free: 0.816
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.376 780 5 %RANDOM
Rwork0.321 ---
obs0.323 14725 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 112.78 Å2
Baniso -1Baniso -2Baniso -3
1-3.4 Å2-0 Å20.88 Å2
2---14.35 Å20 Å2
3---5.86 Å2
Refinement stepCycle: LAST / Resolution: 4.09→48.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5156 0 224 0 5380
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.025534
X-RAY DIFFRACTIONr_bond_other_d0.0020.025146
X-RAY DIFFRACTIONr_angle_refined_deg1.8942.0127510
X-RAY DIFFRACTIONr_angle_other_deg0.9183.00511808
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.9745644
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.26223.966232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.37815934
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8281530
X-RAY DIFFRACTIONr_chiral_restr0.0930.2840
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216000
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021206
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 1598 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.23 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.5→3.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.524 51 -
Rwork0.5 886 -
obs--80.15 %
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)
15.0086-0.7534-2.74934.0320.03913.35550.37160.43260.11470.2902-0.19640.1397-0.3532-0.1808-0.17530.08820.04580.11630.98220.04150.3591-75.82710.9599.176
24.4756-1.61551.21692.9264-3.27893.77460.21810.2682-0.07970.00760.01190.2162-0.0328-0.0306-0.230.08530.05870.12341.0735-0.03590.2308-61.7711.76772.601
31.93550.0818-1.7270.9147-1.89055.18850.08230.1583-0.12140.34910.06290.091-0.7705-0.2719-0.14510.15530.17860.04321.1924-0.00820.212-48.51219.01144.832
41.9016-0.7832-1.16941.1454-0.51893.45960.3469-0.0901-0.12020.2958-0.30310.0208-0.5467-0.1526-0.04380.3991-0.09-0.03651.21360.05410.0468-27.99525.88318.353
51.0642-0.5294-1.88762.03991.00834.89790.0573-0.22050.0962-0.1347-0.1217-0.40070.59530.11650.06450.3672-0.08480.02270.86620.1070.4302-26.10335.302-107.658
60.4716-0.2748-0.91820.18380.52185.89240.05610.0086-0.0162-0.0159-0.06080.09580.42510.05540.00460.1072-0.1280.05951.0819-0.04180.369-34.09826.796-76.812
70.5876-0.58930.75421.6539-3.972810.7354-0.00680.03040.0254-0.0582-0.0857-0.03720.12480.06950.09240.38340.09320.04240.74720.040.4107-23.24623.649-42.982
81.5909-0.80630.99366.53432.56022.3265-0.38780.1422-0.07440.03690.1670.2355-0.23450.39320.22080.1911-0.05740.10861.27090.21250.1752-23.43531.085-9.51
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A694 - 780
2X-RAY DIFFRACTION2A781 - 856
3X-RAY DIFFRACTION2A2401 - 2402
4X-RAY DIFFRACTION3A857 - 936
5X-RAY DIFFRACTION3A2403 - 2406
6X-RAY DIFFRACTION4A937 - 1023
7X-RAY DIFFRACTION4A2407 - 2408
8X-RAY DIFFRACTION5B694 - 780
9X-RAY DIFFRACTION6B781 - 856
10X-RAY DIFFRACTION6B2401 - 2402
11X-RAY DIFFRACTION7B857 - 936
12X-RAY DIFFRACTION7B2403 - 2406
13X-RAY DIFFRACTION8B937 - 1023
14X-RAY DIFFRACTION8B2407 - 2408

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more