[English] 日本語
Yorodumi
- PDB-6now: Human Mitochondrial Alanyl-tRNA Synthetase C-Ala domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6now
TitleHuman Mitochondrial Alanyl-tRNA Synthetase C-Ala domain
ComponentsAlanine--tRNA ligase, mitochondrial
KeywordsLIGASE / Alanyl-tRNA synthetase / mitochondria / C-terminal domain / alpha-beta domain
Function / homology
Function and homology information


mitochondrial alanyl-tRNA aminoacylation / peptide lactyltransferase (ATP-dependent) activity / Ligases / alanine-tRNA ligase / alanine-tRNA ligase activity / alanyl-tRNA aminoacylation / Mitochondrial tRNA aminoacylation / aminoacyl-tRNA deacylase activity / negative regulation of cGAS/STING signaling pathway / tRNA binding ...mitochondrial alanyl-tRNA aminoacylation / peptide lactyltransferase (ATP-dependent) activity / Ligases / alanine-tRNA ligase / alanine-tRNA ligase activity / alanyl-tRNA aminoacylation / Mitochondrial tRNA aminoacylation / aminoacyl-tRNA deacylase activity / negative regulation of cGAS/STING signaling pathway / tRNA binding / mitochondrion / zinc ion binding / ATP binding
Similarity search - Function
Alanine-tRNA ligase, eukaryota/bacteria / Alanine-tRNA ligase, class IIc / Alanine-tRNA ligase, class IIc, anti-codon-binding domain superfamily / : / Alanyl-tRNA synthetase, class IIc, N-terminal / Alanyl-tRNA synthetase, class IIc, core domain / tRNA synthetases class II (A) / Alanyl-transfer RNA synthetases family profile. / Threonyl and Alanyl tRNA synthetase second additional domain / Threonyl/alanyl tRNA synthetase, SAD ...Alanine-tRNA ligase, eukaryota/bacteria / Alanine-tRNA ligase, class IIc / Alanine-tRNA ligase, class IIc, anti-codon-binding domain superfamily / : / Alanyl-tRNA synthetase, class IIc, N-terminal / Alanyl-tRNA synthetase, class IIc, core domain / tRNA synthetases class II (A) / Alanyl-transfer RNA synthetases family profile. / Threonyl and Alanyl tRNA synthetase second additional domain / Threonyl/alanyl tRNA synthetase, SAD / Threonyl and Alanyl tRNA synthetase second additional domain / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Translation protein, beta-barrel domain superfamily
Similarity search - Domain/homology
Alanine--tRNA ligase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.099 Å
AuthorsKuhle, B. / Schimmel, P.
CitationJournal: Nat Commun / Year: 2020
Title: Relaxed sequence constraints favor mutational freedom in idiosyncratic metazoan mitochondrial tRNAs.
Authors: Kuhle, B. / Chihade, J. / Schimmel, P.
History
DepositionJan 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _struct.title
Revision 1.2Oct 11, 2023Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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: Alanine--tRNA ligase, mitochondrial
B: Alanine--tRNA ligase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)44,0332
Polymers44,0332
Non-polymers00
Water00
1
A: Alanine--tRNA ligase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)22,0161
Polymers22,0161
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alanine--tRNA ligase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)22,0161
Polymers22,0161
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.420, 104.420, 164.270
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 793 or (resid 794 and (name...
21(chain B and (resseq 793:797 or resseq 799:810 or resseq...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYGLYGLY(chain A and (resseq 793 or (resid 794 and (name...AA79311
12GLNGLNGLNGLN(chain A and (resseq 793 or (resid 794 and (name...AA79412
13ALAALALEULEU(chain A and (resseq 793 or (resid 794 and (name...AA786 - 9864 - 204
14ALAALALEULEU(chain A and (resseq 793 or (resid 794 and (name...AA786 - 9864 - 204
15ALAALALEULEU(chain A and (resseq 793 or (resid 794 and (name...AA786 - 9864 - 204
16ALAALALEULEU(chain A and (resseq 793 or (resid 794 and (name...AA786 - 9864 - 204
17ALAALALEULEU(chain A and (resseq 793 or (resid 794 and (name...AA786 - 9864 - 204
21GLYGLYALAALA(chain B and (resseq 793:797 or resseq 799:810 or resseq...BB793 - 79711 - 15
22GLUGLUGLYGLY(chain B and (resseq 793:797 or resseq 799:810 or resseq...BB799 - 81017 - 28
23ARGARGALAALA(chain B and (resseq 793:797 or resseq 799:810 or resseq...BB812 - 81530 - 33
24ARGARGGLYGLY(chain B and (resseq 793:797 or resseq 799:810 or resseq...BB817 - 82535 - 43
25ARGARGARGARG(chain B and (resseq 793:797 or resseq 799:810 or resseq...BB82644
26GLUGLULEULEU(chain B and (resseq 793:797 or resseq 799:810 or resseq...BB791 - 9869 - 204
27GLUGLULEULEU(chain B and (resseq 793:797 or resseq 799:810 or resseq...BB791 - 9869 - 204
28GLUGLULEULEU(chain B and (resseq 793:797 or resseq 799:810 or resseq...BB791 - 9869 - 204
29GLUGLULEULEU(chain B and (resseq 793:797 or resseq 799:810 or resseq...BB791 - 9869 - 204

-
Components

#1: Protein Alanine--tRNA ligase, mitochondrial / Alanyl-tRNA synthetase / AlaRS


Mass: 22016.475 Da / Num. of mol.: 2 / Fragment: C-terminal domain (UNP residues 783-985)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AARS2, AARSL, KIAA1270 / Plasmid: pET21 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5JTZ9, alanine-tRNA ligase

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.08 Å3/Da / Density % sol: 75.81 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7 / Details: 0.1 M imidazole, 2 M sodium chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97938 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 24, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97938 Å / Relative weight: 1
ReflectionResolution: 4.1→35.89 Å / Num. obs: 6904 / % possible obs: 99.7 % / Redundancy: 7.568 % / Biso Wilson estimate: 205.59 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rrim(I) all: 0.059 / Χ2: 1.012 / Net I/σ(I): 17.45 / Num. measured all: 52247
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
4.1-4.217.0280.6842.7435425065040.8730.73899.6
4.21-4.328.0020.4094.6238734844840.9830.438100
4.32-4.457.9440.3056.1938614864860.9790.326100
4.45-4.587.8780.2397.4237424764750.9890.25699.8
4.58-4.737.8640.2188.3935944574570.990.233100
4.73-4.97.60.2228.431924224200.9830.23899.5
4.9-5.087.2410.18310.231284324320.9860.197100
5.08-5.297.5150.18110.4431944254250.990.194100
5.29-5.538.0080.15612.2830993873870.9940.167100
5.53-5.87.9640.15712.7230583843840.9890.168100
5.8-6.117.7490.11216.9427203513510.9950.12100
6.11-6.487.5880.0822.7326183463450.9960.08699.7
6.48-6.936.8980.05727.8721733163150.9980.06299.7
6.93-7.487.9050.04933.3223322952950.9990.052100
7.48-8.27.6870.03941.2420602682680.9990.041100
8.2-9.177.2330.03544.618592572570.9990.038100
9.17-10.586.7040.02847.0114482182160.9990.0399.1
10.58-12.967.3910.03149.5513601841840.9990.033100
12.96-18.336.8950.0348.85104815215210.033100
18.33-35.895.1640.0442.7934678670.9980.04485.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.1 Å35.89 Å
Translation4.1 Å35.89 Å

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASER2.7.17phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6NLY

6nly


Resolution: 4.099→35.89 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 40.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.282 345 5.01 %
Rwork0.2332 6539 -
obs0.2358 6884 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 527.07 Å2 / Biso mean: 259.1622 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 4.099→35.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2909 0 0 0 2909
Num. residues----397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032949
X-RAY DIFFRACTIONf_angle_d0.6533993
X-RAY DIFFRACTIONf_chiral_restr0.038498
X-RAY DIFFRACTIONf_plane_restr0.003502
X-RAY DIFFRACTIONf_dihedral_angle_d19.2721835
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1742X-RAY DIFFRACTION3.415TORSIONAL
12B1742X-RAY DIFFRACTION3.415TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.0995-5.16250.34761710.26963246341799
5.1625-35.8910.26341740.222432933467100
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)
10.4245-0.25-0.13244.07322.73871.13482.27123.3852.5523-2.1003-0.08090.23822.06141.2055-0.05534.0553-0.21161.06483.60370.04612.40251.6285-47.1482-55.5778
28.2434-4.1274-3.95091.1788-0.02325.54231.3971-1.88641.3632-1.2633-1.8441-0.42621.0822-0.8202-0.49821.8787-0.3797-0.26742.22770.32881.9326-8.66-44.6529-43.7987
39.37780.15011.51350.5239-2.90089.2649-0.72330.67420.25250.28180.07911.8072-0.55830.14330.79651.6781-0.23680.36251.8888-0.07472.3683-22.7827-48.4274-17.2004
40.061-0.13280.0050.17970.10241.1657-1.44540.61171.39421.00880.93035.33150.1735-1.3278-1.42752.5946-0.1557-0.44564.95040.35183.84-9.711-54.39099.9096
52.24173.53489.79368.58643.18327.7452-0.25352.4134-1.52634.72441.40941.79581.67195.31921.74242.8198-0.1510.49962.68820.04041.4939-11.9576-55.55730.5226
60.663-3.2912-2.31646.5501-2.31599.15710.1161-0.71090.67360.8889-0.681-0.6433-1.76221.80610.93861.4088-0.626-0.46392.30870.41191.8438-7.6536-37.7243-19.6512
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 786 through 809 )A786 - 809
2X-RAY DIFFRACTION2chain 'A' and (resid 810 through 875 )A810 - 875
3X-RAY DIFFRACTION3chain 'A' and (resid 876 through 986 )A876 - 986
4X-RAY DIFFRACTION4chain 'B' and (resid 791 through 809 )B791 - 809
5X-RAY DIFFRACTION5chain 'B' and (resid 810 through 837 )B810 - 837
6X-RAY DIFFRACTION6chain 'B' and (resid 838 through 986 )B838 - 986

+
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