[English] 日本語
Yorodumi
- PDB-7c0i: Crystal structure of chimeric mutant of E3L in complex with Z-DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7c0i
TitleCrystal structure of chimeric mutant of E3L in complex with Z-DNA
Components
  • DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3')
  • Double-stranded RNA-binding protein,Double-stranded RNA-specific adenosine deaminase
KeywordsDNA BINDING PROTEIN / E3L / Protein-DNA complex / protein engineering / Z-DNA binding protein
Function / homology
Function and homology information


somatic diversification of immune receptors via somatic mutation / negative regulation of post-transcriptional gene silencing by regulatory ncRNA / C6 deamination of adenosine / Formation of editosomes by ADAR proteins / supraspliceosomal complex / double-stranded RNA adenine deaminase / tRNA-specific adenosine deaminase activity / adenosine to inosine editing / negative regulation of protein kinase activity by regulation of protein phosphorylation / double-stranded RNA adenosine deaminase activity ...somatic diversification of immune receptors via somatic mutation / negative regulation of post-transcriptional gene silencing by regulatory ncRNA / C6 deamination of adenosine / Formation of editosomes by ADAR proteins / supraspliceosomal complex / double-stranded RNA adenine deaminase / tRNA-specific adenosine deaminase activity / adenosine to inosine editing / negative regulation of protein kinase activity by regulation of protein phosphorylation / double-stranded RNA adenosine deaminase activity / base conversion or substitution editing / symbiont-mediated perturbation of host apoptosis / response to interferon-alpha / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / hematopoietic stem cell homeostasis / symbiont-mediated suppression of host PKR/eIFalpha signaling / symbiont-mediated suppression of host apoptosis / negative regulation of hepatocyte apoptotic process / symbiont-mediated evasion of host immune response / RISC complex assembly / pre-miRNA processing / definitive hemopoiesis / negative regulation of type I interferon-mediated signaling pathway / hepatocyte apoptotic process / protein serine/threonine kinase inhibitor activity / hematopoietic progenitor cell differentiation / RNA processing / positive regulation of viral genome replication / protein sequestering activity / protein export from nucleus / erythrocyte differentiation / PKR-mediated signaling / cellular response to virus / response to virus / mRNA processing / protein import into nucleus / osteoblast differentiation / Interferon alpha/beta signaling / double-stranded RNA binding / symbiont-mediated suppression of host ISG15-protein conjugation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / defense response to virus / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / innate immune response / nucleolus / mitochondrion / DNA binding / RNA binding / nucleoplasm / metal ion binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Protein E3 / ADAR1, first double-stranded RNA binding domain / ADAR1, third double-stranded RNA binding domain / Z-DNA-binding domain in adenosine deaminases. / Z-binding domain / Adenosine deaminase z-alpha domain / Z-binding domain profile. / Adenosine deaminase/editase / Adenosine-deaminase (editase) domain / Adenosine to inosine editase domain profile. ...Protein E3 / ADAR1, first double-stranded RNA binding domain / ADAR1, third double-stranded RNA binding domain / Z-DNA-binding domain in adenosine deaminases. / Z-binding domain / Adenosine deaminase z-alpha domain / Z-binding domain profile. / Adenosine deaminase/editase / Adenosine-deaminase (editase) domain / Adenosine to inosine editase domain profile. / tRNA-specific and double-stranded RNA adenosine deaminase (RNA-specific editase) / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / RNA-binding protein OPG065 / Double-stranded RNA-specific adenosine deaminase / RNA-binding protein OPG065
Similarity search - Component
Biological speciesVaccinia virus
Homo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsChoi, H.J. / Park, C.H. / Kim, J.S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2019M3E5D6063903 Korea, Republic Of
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Dual conformational recognition by Z-DNA binding protein is important for the B-Z transition process.
Authors: Park, C. / Zheng, X. / Park, C.Y. / Kim, J. / Lee, S.K. / Won, H. / Choi, J. / Kim, Y.G. / Choi, H.J.
History
DepositionMay 1, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Nov 2, 2022Group: Database references / Polymer sequence / Structure summary
Category: database_2 / entity / entity_poly
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity_poly.type
Revision 2.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Double-stranded RNA-binding protein,Double-stranded RNA-specific adenosine deaminase
B: Double-stranded RNA-binding protein,Double-stranded RNA-specific adenosine deaminase
C: Double-stranded RNA-binding protein,Double-stranded RNA-specific adenosine deaminase
D: DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3')
E: DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3')
F: DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8817
Polymers33,7856
Non-polymers961
Water55831
1
A: Double-stranded RNA-binding protein,Double-stranded RNA-specific adenosine deaminase
B: Double-stranded RNA-binding protein,Double-stranded RNA-specific adenosine deaminase
D: DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3')
E: DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6195
Polymers22,5234
Non-polymers961
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-35 kcal/mol
Surface area11260 Å2
MethodPISA
2
C: Double-stranded RNA-binding protein,Double-stranded RNA-specific adenosine deaminase
F: DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3')

C: Double-stranded RNA-binding protein,Double-stranded RNA-specific adenosine deaminase
F: DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)22,5234
Polymers22,5234
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-y,-x,-z+1/31
Buried area3110 Å2
ΔGint-22 kcal/mol
Surface area12440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.759, 72.759, 123.876
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number153
Space group name H-MP3212

-
Components

#1: Protein Double-stranded RNA-binding protein,Double-stranded RNA-specific adenosine deaminase


Mass: 9147.314 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus, (gene. exp.) Homo sapiens (human)
Gene: E3L, ADAR1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q86638, UniProt: P55265, UniProt: P21605*PLUS
#2: DNA chain DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3')


Mass: 2114.398 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.1 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4
Details: Sodium citrate pH 4.0, Ammonium sulfate, ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 14894 / % possible obs: 99.4 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.026 / Rrim(I) all: 0.055 / Χ2: 0.949 / Net I/σ(I): 9.9 / Num. measured all: 66340
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.444.40.4697290.8620.2470.5310.45198.1
2.44-2.494.70.3837440.9090.1940.430.43499.1
2.49-2.534.60.3427140.9340.1760.3850.45999.3
2.53-2.594.60.2777400.9540.1440.3140.4699.3
2.59-2.644.50.2397310.9630.1250.270.48799.2
2.64-2.74.50.1977420.9710.1030.2230.50799.5
2.7-2.774.30.1467320.9810.0790.1660.55899.5
2.77-2.854.20.1137350.9860.0620.130.61999.3
2.85-2.934.60.0967540.9890.050.1080.66899.6
2.93-3.024.60.0877350.9910.0450.0990.75199.3
3.02-3.134.60.0737310.9930.0380.0830.87399.6
3.13-3.264.50.0677430.9930.0350.0760.99299.6
3.26-3.414.30.0657480.9920.0350.0741.24199.6
3.41-3.584.30.0577410.9940.0310.0651.44299.6
3.58-3.814.70.0567540.9950.0280.0631.53499.7
3.81-4.14.50.0517530.9950.0270.0581.52199.7
4.1-4.524.30.0457500.9970.0240.0521.52299.6
4.52-5.174.50.0457580.9970.0240.0511.48799.6
5.17-6.514.40.0447640.9970.0230.051.36799.9
6.51-504.10.0377960.9970.0210.0431.63898.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.16-3549refinement
HKL-2000720data reduction
HKL-2000720data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QBJ

1qbj


Resolution: 2.4→34.905 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2273 759 5.1 %
Rwork0.2016 14118 -
obs0.2028 14877 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 194.24 Å2 / Biso mean: 92.0576 Å2 / Biso min: 46.65 Å2
Refinement stepCycle: final / Resolution: 2.4→34.905 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1527 389 5 31 1952
Biso mean--157.07 67.65 -
Num. residues----212
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4002-2.58540.3811900.2975273699
2.5854-2.84550.29371260.2774281699
2.8455-3.2570.27451500.2482809100
3.257-4.10240.22451490.20212845100
4.1024-34.9050.19131440.1742912100
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)
17.13770.79833.75620.48-0.71165.32111.2340.9258-2.5329-2.1018-0.92020.83592.3995-0.5737-2.04341.28970.1429-0.48461.3618-0.75831.5796-23.98-24.621-31.97
25.1741-3.48862.29442.7381-1.0893.45420.91910.3355-2.9413-0.79690.27070.5722-0.0095-1.9067-0.8210.7714-0.1868-0.23841.3671-0.21721.5014-30.772-20.953-25.582
39.028-3.5402-6.30218.87912.31174.4365-0.37571.2936-0.6094-0.1653-0.30850.45240.8002-0.19060.49650.45230.0375-0.06030.9525-0.21060.6846-19.657-15.156-26.551
42.88890.7424-2.97594.52812.00614.83471.60693.0507-1.3874-2.6389-1.55370.83291.25491.0520.08751.26220.405-0.27762.0611-0.65550.9928-14.599-19.879-35.151
56.59081.5059-3.44247.3003-0.54054.06660.15680.29450.15460.2589-0.59030.0111-0.3578-0.29720.42710.68190.0233-0.13570.6912-0.12160.5376-23.4177.1174.772
64.4016-4.3734-2.10414.53772.77932.944-0.24290.7980.51260.1792-0.48130.0352-1.1137-1.59570.67380.90360.2286-0.15230.9954-0.19330.7796-29.5147.33-13.255
75.1282-5.1095-5.6945.04595.66496.33510.8017-0.01371.2696-0.8250.7084-0.8837-1.8592-0.2332-1.29931.1341-0.119-0.06820.81870.13080.8202-22.06213.288-17.454
83.57555.4074-1.45668.1868-2.57156.42760.49130.23131.07921.1707-0.14090.2229-1.4566-1.7884-0.3680.96740.2734-0.14731.0239-0.1890.7285-31.1967.201-3.165
98.511-2.40442.14572.68381.74463.1542-0.42510.22480.85350.13920.2796-0.5645-0.66480.87050.3710.7955-0.2251-0.08760.7761-0.0880.8564-18.1959.507-5.851
103.4737-2.989-2.51524.2682-0.6156.33850.2350.2702-0.07490.2286-0.05560.50490.2181-0.6311-0.18180.5908-0.1277-0.01730.5763-0.13490.555-18.0278.80213.115
112.6267-1.6362-4.47715.95921.6389.5562-0.27741.1786-0.0218-0.6101-0.16090.2255-0.8179-0.32370.26740.4243-0.0306-0.04410.9004-0.15680.5332-23.707-6.087-23.926
125.5435-3.7738-4.19358.1875-2.14818.3939-0.64791.093-0.4125-0.55660.6190.7734-0.1811-0.4340.04380.5122-0.084-0.09530.9702-0.13110.547-24.966-0.888-20.234
136.99425.51575.51699.38684.52664.26190.1158-0.8807-0.60450.592-0.0151-1.0285-0.06230.0801-0.24190.6862-0.0879-0.04510.6043-0.1280.7071-8.6093.98318.49
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 9:28 )A9 - 28
2X-RAY DIFFRACTION2( CHAIN A AND RESID 29:39 )A29 - 39
3X-RAY DIFFRACTION3( CHAIN A AND RESID 1169:1182 )A1169 - 1182
4X-RAY DIFFRACTION4( CHAIN A AND RESID 1183:1184 OR 56:70 )A1183 - 70
5X-RAY DIFFRACTION5( CHAIN B AND RESID 3:39 )B3 - 39
6X-RAY DIFFRACTION6( CHAIN B AND RESID 1169:1184 OR 56:58 )B1169 - 58
7X-RAY DIFFRACTION7( CHAIN B AND RESID 59:69 )B59 - 69
8X-RAY DIFFRACTION8( CHAIN C AND RESID 6:19 )C6 - 19
9X-RAY DIFFRACTION9( CHAIN C AND RESID 20:39 )C20 - 39
10X-RAY DIFFRACTION10( CHAIN C AND RESID 1169:1184 OR 56:70 )C1169 - 70
11X-RAY DIFFRACTION11( CHAIN D AND RESID 1:6 )D1 - 6
12X-RAY DIFFRACTION12( CHAIN E AND RESID 1:6 )E1 - 6
13X-RAY DIFFRACTION13( CHAIN F AND RESID 0:6 )F0 - 6

+
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