[English] 日本語
Yorodumi
- PDB-4ije: Crystal structure of the Zaire ebolavirus VP35 interferon inhibit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ije
TitleCrystal structure of the Zaire ebolavirus VP35 interferon inhibitory domain R312A/K319A/R322A mutant
ComponentsPolymerase cofactor VP35
KeywordsVIRAL PROTEIN / IFN inhibition / polymerase cofactor / RNA binding protein / interferon antagonism / virus
Function / homology
Function and homology information


suppression by virus of host cytokine production / symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / negative regulation of miRNA-mediated gene silencing / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / suppression by virus of host type I interferon production / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / molecular sequestering activity / positive regulation of protein sumoylation ...suppression by virus of host cytokine production / symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / negative regulation of miRNA-mediated gene silencing / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / suppression by virus of host type I interferon production / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / molecular sequestering activity / positive regulation of protein sumoylation / : / viral transcription / viral genome replication / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / viral nucleocapsid / host cell cytoplasm / negative regulation of gene expression / RNA binding
Similarity search - Function
Filoviridae VP35, C-terminal inhibitory domain, beta-sheet subdomain / Filoviridae VP35, C-terminal inhibitory domain, helical subdomain / Filoviruses VP35 interferon inhibitory domain, beta-sheet subdomain / Filoviridae VP35 protein / Filoviruses VP35 interferon inhibitory domain / Filoviruses VP35 interferon inhibitory domain, helical subdomain / Filoviridae VP35 / Filoviruses VP35 interferon inhibitory domain profile. / Seminal Fluid Protein PDC-109 (Domain B) / Helicase, Ruva Protein; domain 3 ...Filoviridae VP35, C-terminal inhibitory domain, beta-sheet subdomain / Filoviridae VP35, C-terminal inhibitory domain, helical subdomain / Filoviruses VP35 interferon inhibitory domain, beta-sheet subdomain / Filoviridae VP35 protein / Filoviruses VP35 interferon inhibitory domain / Filoviruses VP35 interferon inhibitory domain, helical subdomain / Filoviridae VP35 / Filoviruses VP35 interferon inhibitory domain profile. / Seminal Fluid Protein PDC-109 (Domain B) / Helicase, Ruva Protein; domain 3 / Ribbon / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / PHOSPHATE ION / Polymerase cofactor VP35
Similarity search - Component
Biological speciesZaire ebolavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.899 Å
AuthorsBinning, J.B. / Wang, T. / Leung, D.W. / Xu, W. / Borek, D. / Amarasinghe, G.K.
CitationJournal: Biochemistry / Year: 2013
Title: Development of RNA Aptamers Targeting Ebola Virus VP35.
Authors: Binning, J.M. / Wang, T. / Luthra, P. / Shabman, R.S. / Borek, D.M. / Liu, G. / Xu, W. / Leung, D.W. / Basler, C.F. / Amarasinghe, G.K.
History
DepositionDec 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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 / _struct_conn.pdbx_dist_value / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Polymerase cofactor VP35
B: Polymerase cofactor VP35
C: Polymerase cofactor VP35
D: Polymerase cofactor VP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,36013
Polymers55,9214
Non-polymers4399
Water6,323351
1
A: Polymerase cofactor VP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0423
Polymers13,9801
Non-polymers622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polymerase cofactor VP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1214
Polymers13,9801
Non-polymers1413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Polymerase cofactor VP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0752
Polymers13,9801
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Polymerase cofactor VP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1214
Polymers13,9801
Non-polymers1413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.012, 81.012, 344.410
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein
Polymerase cofactor VP35


Mass: 13980.188 Da / Num. of mol.: 4
Fragment: interferon inhibitory domain (UNP residues 218-340)
Mutation: R312A, K319A, R322A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zaire ebolavirus / Strain: Mayinga-76 / Gene: VP35 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q05127
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 351 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.83 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 2.2 M sodium potassium phosphate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.15K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 21, 2012
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792075 Å / Relative weight: 1
ReflectionResolution: 1.899→50 Å / Num. obs: 54187 / % possible obs: 99.8 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.13 / Χ2: 1.047 / Net I/σ(I): 9.3
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2Diffraction-ID% possible allRmerge(I) obs
1.899-1.935.726480.915199.5
1.93-1.976.426250.98199.7
1.97-2.017.126420.946199.70.852
2.01-2.057.726250.974199.80.705
2.05-2.098.426631.016199.90.639
2.09-2.14926561.008199.80.577
2.14-2.199.526701.004199.90.53
2.19-2.259.726741.05911000.456
2.25-2.329.826460.99811000.395
2.32-2.399.826601.031199.80.303
2.39-2.489.926671.02111000.26
2.48-2.589.926911.029199.90.215
2.58-2.71027101.068199.90.179
2.7-2.841026871.0611000.144
2.84-3.021027261.12211000.124
3.02-3.251027511.24811000.11
3.25-3.581027371.37211000.101
3.58-4.099.927921.23411000.086
4.09-5.169.728451.02911000.074
5.16-509.330720.663198.80.058

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FKE

3fke


Resolution: 1.899→33.096 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8677 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2283 2559 5.07 %RANDOM
Rwork0.1933 ---
obs0.195 50452 93.21 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.96 Å2 / Biso mean: 29.037 Å2 / Biso min: -0 Å2
Refinement stepCycle: LAST / Resolution: 1.899→33.096 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3784 0 21 351 4156
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0194057
X-RAY DIFFRACTIONf_angle_d0.885545
X-RAY DIFFRACTIONf_chiral_restr0.06617
X-RAY DIFFRACTIONf_plane_restr0.004730
X-RAY DIFFRACTIONf_dihedral_angle_d12.6521526
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.899-1.9360.3106750.23361430150551
1.936-1.97550.2798920.23831733182562
1.9755-2.01850.26761110.23182220233179
2.0185-2.06540.2361390.22052541268091
2.0654-2.11710.25051400.22092694283496
2.1171-2.17430.25791490.20932726287598
2.1743-2.23830.25251620.20462740290298
2.2383-2.31050.26651490.19832805295499
2.3105-2.3930.23981320.193628352967100
2.393-2.48880.24491650.199127982963100
2.4888-2.60210.25491450.196128593004100
2.6021-2.73920.24381550.201828252980100
2.7392-2.91070.22251420.200228693011100
2.9107-3.13530.22381670.198128533020100
3.1353-3.45050.22771550.189728823037100
3.4505-3.94910.22541590.180629213080100
3.9491-4.97270.18221740.158129583132100
4.9727-33.10060.19751480.18953204335299
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)
11.61-0.5070.40241.81730.30130.8674-0.0203-0.0282-0.3984-0.08670.0101-0.08090.23190.0717-0.06240.25540.04420.03610.03470.02550.1593-16.690313.075119.9157
22.18970.62940.31371.80591.01841.2745-0.04220.0059-0.1682-0.30670.03650.05150.15310.1063-0.07050.29130.02440.02580.04830.02480.1473-18.900517.52814.2661
32.5032-0.4789-0.73263.18660.7564.2596-0.03640.2543-0.2377-0.36510.05980.2097-0.0389-0.1245-0.0350.31320.0076-0.05860.085-0.03430.1687-32.1316.5489.4481
41.1905-0.95250.00582.89690.81992.48310.0059-0.01480.2052-0.08890.0073-0.4957-0.20270.2854-0.12630.24670.05170.10520.11810.01820.20677.176235.86119.7241
50.8896-0.3408-0.15261.99290.02060.9269-0.04750.0626-0.0178-0.2358-0.0118-0.1682-0.10650.0487-0.11880.3083-0.00010.08740.07970.01960.16551.579644.361314.9434
60.5019-0.1848-0.38260.48030.26290.89120.14920.16480.0099-0.3224-0.08820.0435-0.2567-0.12580.03910.34790.07460.10260.0808-0.01620.1137-1.81935.722111.1871
71.65262.8149-2.01964.8141-3.22434.8333-0.1267-0.5195-0.574-0.0051-0.1121-0.55550.57750.80090.26610.31990.15130.13250.28710.07340.359812.926717.473415.0439
86.1509-1.924.77045.30451.45455.5412-0.4368-0.6851-0.73191.3950.29970.20960.4908-0.21760.110.45630.11880.09560.18880.03990.26125.17519.160423.1553
90.3257-0.0886-0.32470.59890.03971.0489-0.1238-0.0443-0.11-0.03170.0216-0.02310.07450.0062-0.08360.37050.0970.15590.13480.02110.18882.006920.926610.9391
103.75682.08871.90672.40410.66093.35740.05050.2193-0.49420.06320.087-0.41990.39560.3936-0.13890.38780.09160.14650.13970.0110.2416.972115.75112.0129
112.00150.6079-0.00743.2941-0.7163.3331-0.0478-0.10750.16440.0757-0.06660.5196-0.1318-0.1578-0.03390.1927-0.04490.06120.1026-0.01180.15980.565933.2467-17.5075
1211.2421-0.20152.8798-0.88670.70960.074-0.08270.12230.284-0.02040.2285-0.1313-0.0292-0.00830.2549-0.08360.08470.0574-0.00820.13646.288941.9983-14.4556
130.1587-0.30280.060.5755-0.11750.07210.0732-0.15450.08490.5163-0.0399-0.0869-0.27150.1479-0.060.3365-0.05560.05230.0946-0.00660.141710.964134.2753-10.8865
141.4952-0.413-0.02632.5833-0.263.5995-0.15620.1268-0.3036-0.00490.10330.3760.2677-0.19680.04750.3059-0.04790.1590.0977-0.02250.23262.455918.0463-9.6904
152.9595-1.55531.13982.2016-0.14613.03870.1299-0.2197-0.560.02010.05090.40710.4492-0.4385-0.2050.3373-0.11060.1180.1394-0.01350.28561.536514.2428-7.5584
160.4385-0.0892-0.2091.48060.09290.3788-0.0877-0.00060.1745-0.14010.0250.2391-0.2136-0.08350.05180.31250.0543-0.08540.0198-0.04480.1853-15.851359.716616.8046
172.33330.24790.14740.7036-0.3421.0193-0.20590.14470.2205-0.34860.16410.0552-0.1281-0.043-0.00420.3364-0.0034-0.07610.0654-0.00590.1382-13.029654.742111.8804
181.4632-0.51690.79562.942-0.08061.9122-0.13680.15210.0997-0.32430.1542-0.3695-0.00030.05390.01570.4307-0.08030.07420.1009-0.0150.15650.452154.90678.2122
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 217 through 252 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 253 through 307 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 308 through 340 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 217 through 252 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 253 through 269 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 270 through 292 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 293 through 302 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 303 through 307 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 308 through 329 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 330 through 340 )B0
11X-RAY DIFFRACTION11chain 'C' and (resid 217 through 252 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 253 through 268 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 269 through 292 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 293 through 329 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 330 through 340 )C0
16X-RAY DIFFRACTION16chain 'D' and (resid 217 through 252 )D0
17X-RAY DIFFRACTION17chain 'D' and (resid 253 through 307 )D0
18X-RAY DIFFRACTION18chain 'D' and (resid 308 through 340 )D0

+
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