[English] 日本語
Yorodumi
- PDB-7nz7: Crystal structure of mouse ADAT2/ADAT3 tRNA deamination complex 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7nz7
TitleCrystal structure of mouse ADAT2/ADAT3 tRNA deamination complex 1
Components
  • Probable inactive tRNA-specific adenosine deaminase-like protein 3
  • tRNA-specific adenosine deaminase 2
KeywordsHYDROLASE / tRNA modification / wobble adenine / inosine / ADAT / intellectual disability / neurological disorders
Function / homology
Function and homology information


tRNA(adenine34) deaminase / tRNA wobble adenosine to inosine editing / tRNA-specific adenosine-34 deaminase activity / tRNA processing / catalytic activity / zinc ion binding / metal ion binding
Similarity search - Function
tRNA-specific adenosine deaminase / MafB19-like deaminase / Cytidine and deoxycytidylate deaminase zinc-binding region / APOBEC/CMP deaminase, zinc-binding / Cytidine and deoxycytidylate deaminases zinc-binding region signature. / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. / Cytidine deaminase-like
Similarity search - Domain/homology
tRNA-specific adenosine deaminase 2 / Probable inactive tRNA-specific adenosine deaminase-like protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.96 Å
AuthorsRamos Morales, E. / Romier, C.
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: The structure of the mouse ADAT2/ADAT3 complex reveals the molecular basis for mammalian tRNA wobble adenosine-to-inosine deamination.
Authors: Ramos-Morales, E. / Bayam, E. / Del-Pozo-Rodriguez, J. / Salinas-Giege, T. / Marek, M. / Tilly, P. / Wolff, P. / Troesch, E. / Ennifar, E. / Drouard, L. / Godin, J.D. / Romier, C.
History
DepositionMar 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 2.0Jun 9, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / citation_author / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id ..._atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id
Revision 2.1Jun 30, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: tRNA-specific adenosine deaminase 2
B: Probable inactive tRNA-specific adenosine deaminase-like protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6884
Polymers55,5572
Non-polymers1312
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-65 kcal/mol
Surface area20910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.471, 105.471, 187.076
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

-
Components

#1: Protein tRNA-specific adenosine deaminase 2 / Deaminase domain-containing protein 1 / tRNA-specific adenosine-34 deaminase subunit ADAT2


Mass: 21333.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Adat2, Deadc1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6P6J0, tRNA(adenine34) deaminase
#2: Protein Probable inactive tRNA-specific adenosine deaminase-like protein 3 / tRNA-specific adenosine-34 deaminase subunit ADAT3


Mass: 34223.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Adat3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6PAT0
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.1 Å3/Da / Density % sol: 75.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 7% (W/V) PEG8000, 0.1 M HEPES pH 7.0, 8% ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.96→50 Å / Num. obs: 25887 / % possible obs: 99.9 % / Redundancy: 19.7 % / Biso Wilson estimate: 113.11 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.092 / Net I/σ(I): 26.48
Reflection shellResolution: 2.96→3.13 Å / Redundancy: 19.7 % / Rmerge(I) obs: 3.82 / Mean I/σ(I) obs: 1.02 / Num. unique obs: 4112 / CC1/2: 0.55 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX1.19rc4_4035refinement
PHENIX1.19rc4_4035refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DH1

3dh1


Resolution: 2.96→45.94 Å / SU ML: 0.3567 / Cross valid method: FREE R-VALUE / σ(F): 0.45 / Phase error: 31.4172
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2332 2432 4.99 %
Rwork0.1948 46286 -
obs0.1967 25868 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 122.5 Å2
Refinement stepCycle: LAST / Resolution: 2.96→45.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3438 0 2 1 3441
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093524
X-RAY DIFFRACTIONf_angle_d1.06524799
X-RAY DIFFRACTIONf_chiral_restr0.0533538
X-RAY DIFFRACTIONf_plane_restr0.0105640
X-RAY DIFFRACTIONf_dihedral_angle_d16.18131319
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.96-3.020.42011340.38432776X-RAY DIFFRACTION99.42
3.02-3.080.34581160.35842729X-RAY DIFFRACTION99.93
3.08-3.150.39781380.33952714X-RAY DIFFRACTION99.93
3.15-3.230.29271160.33842743X-RAY DIFFRACTION99.9
3.23-3.320.41541280.34692732X-RAY DIFFRACTION99.86
3.32-3.420.38361340.30352733X-RAY DIFFRACTION99.72
3.42-3.530.34561540.28332768X-RAY DIFFRACTION99.73
3.53-3.650.33941720.26482651X-RAY DIFFRACTION99.82
3.65-3.80.24211240.2462731X-RAY DIFFRACTION99.9
3.8-3.970.3191580.21022710X-RAY DIFFRACTION99.76
3.97-4.180.27111300.22582714X-RAY DIFFRACTION100
4.18-4.440.21291480.1842715X-RAY DIFFRACTION100
4.44-4.790.18581740.15452735X-RAY DIFFRACTION99.97
4.79-5.270.22731660.16872694X-RAY DIFFRACTION100
5.27-6.030.22531500.19162693X-RAY DIFFRACTION100
6.03-7.590.19711540.15882723X-RAY DIFFRACTION100
7.59-45.940.1581360.13532725X-RAY DIFFRACTION99.55
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)
10.8467689437230.1809234147930.7918542293632.61372579974-0.7470979800962.08213226076-0.2316712663710.000424963560577-0.06299249370750.351868687290.428034211053-0.123550046262-0.309314297830.0490597407443-0.0002977756977581.01946557460.2413002070930.05847361368030.927171973377-0.1206490770880.99881939981254.13934751129.23967889767-41.2948213792
21.286089384460.5829374580130.03754822717870.6403939803490.4638566892231.479013620240.0144935720504-0.03249709150760.07258189159030.2207320147210.1259803439950.02012127124920.292533798481-0.110305744334-0.0001168706060461.33067687694-0.175665445515-0.1150241250530.871072709584-0.01913602904950.92270664735739.5571030176-30.5926420453-77.1569230125
31.804074704820.4930307199740.4141995646222.28459554519-0.6152847354553.35568495129-0.198371965549-0.0593243344841-0.264684625696-0.305462297190.338437164006-0.0357469788970.459414823307-0.2258486188538.70408201541E-51.124384863510.156831435240.01291957662160.844786983651-0.01065263846181.0162862203247.4912073994-15.7192573138-45.0193726895
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain AAA - B11 - 2001
22chain B and resid 25:151BC25 - 1511 - 127
33chain B and resid 162:400BC - D162 - 400128

+
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