[English] 日本語
Yorodumi
- PDB-3otb: Crystal structure of human tRNAHis guanylyltransferase (Thg1) - d... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3otb
TitleCrystal structure of human tRNAHis guanylyltransferase (Thg1) - dGTP complex
ComponentstRNA(His) guanylyltransferase
KeywordsTRANSFERASE / guanylyltransferase / polymerase-like palm domain / catalytic carboxylates
Function / homology
Function and homology information


stress-induced mitochondrial fusion / tRNAHis guanylyltransferase / tRNA guanylyltransferase activity / transferase complex / tRNA modification in the nucleus and cytosol / tRNA modification / tRNA processing / mitochondrial fusion / nucleotidyltransferase activity / guanyl-nucleotide exchange factor activity ...stress-induced mitochondrial fusion / tRNAHis guanylyltransferase / tRNA guanylyltransferase activity / transferase complex / tRNA modification in the nucleus and cytosol / tRNA modification / tRNA processing / mitochondrial fusion / nucleotidyltransferase activity / guanyl-nucleotide exchange factor activity / protein homotetramerization / mitochondrial outer membrane / response to oxidative stress / tRNA binding / GTP binding / magnesium ion binding / mitochondrion / ATP binding / identical protein binding / cytosol
Similarity search - Function
Thg1 C-terminal domain / Thg1 C terminal domain / tRNAHis guanylyltransferase Thg1 / tRNAHis guanylyltransferase catalytic domain / tRNAHis guanylyltransferase Thg1 superfamily / tRNAHis guanylyltransferase / tRNA(His) guanylyltransferase (Thg1) / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
TRIPHOSPHATE / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / Probable tRNA(His) guanylyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.95 Å
AuthorsHyde, S.J. / Eckenroth, B.E. / Doublie, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: tRNAHis guanylyltransferase (THG1), a unique 3'-5' nucleotidyl transferase, shares unexpected structural homology with canonical 5'-3' DNA polymerases.
Authors: Hyde, S.J. / Eckenroth, B.E. / Smith, B.A. / Eberley, W.A. / Heintz, N.H. / Jackman, J.E. / Doublie, S.
History
DepositionSep 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 9, 2014Group: Source and taxonomy
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_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: tRNA(His) guanylyltransferase
B: tRNA(His) guanylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,93412
Polymers63,2582
Non-polymers1,67610
Water00
1
A: tRNA(His) guanylyltransferase
B: tRNA(His) guanylyltransferase
hetero molecules

A: tRNA(His) guanylyltransferase
B: tRNA(His) guanylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,86824
Polymers126,5164
Non-polymers3,35220
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area16070 Å2
ΔGint-191 kcal/mol
Surface area40950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.912, 140.912, 81.227
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain: (Details: chain A,B, using restrain)
DetailsThe biological unit is a tetramer generated from the dimer in the asymetric unit by the operation: -Y, -X, -Z+1/2

-
Components

#1: Protein tRNA(His) guanylyltransferase / tRNA-histidine guanylyltransferase / Interphase cytoplasmic foci protein 45


Mass: 31628.938 Da / Num. of mol.: 2 / Fragment: UNP residues 30-298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: KATO III / Gene: ICF45, THG1L / Plasmid: pME182-FL / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS
References: UniProt: Q9NWX6, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-3PO / TRIPHOSPHATE


Mass: 257.955 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H5O10P3

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.19 Å3/Da / Density % sol: 61.41 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 7 / Details: Na Formate, pH 7, hanging drop, temperature 298K

-
Data collection

DiffractionMean temperature: 104 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Details: Adjustable focusing mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.95→30 Å / Num. obs: 17903 / % possible obs: 99.7 % / Redundancy: 14 % / Rmerge(I) obs: 0.086 / Χ2: 1.249 / Net I/σ(I): 15.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.95-3.0612.10.95717431.218199.9
3.06-3.1813.90.80917691.2911100
3.18-3.3214.60.4717571.3391100
3.32-3.514.60.27317571.3281100
3.5-3.7214.60.18217911.3621100
3.72-414.60.12117681.1381100
4-4.414.60.09917901.2961100
4.4-5.0414.40.07818001.2281100
5.04-6.3414.20.06118321.1931100
6.34-30130.04218961.08197.3

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.31 Å19.92 Å
Translation3.31 Å19.92 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→30 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7285 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.3014 1770 10 %
Rwork0.2544 --
obs-17681 99.7 %
Solvent computationBsol: 70.7052 Å2
Displacement parametersBiso max: 168.34 Å2 / Biso mean: 100.9726 Å2 / Biso min: 33.58 Å2
Baniso -1Baniso -2Baniso -3
1--6.066 Å20 Å20 Å2
2---6.066 Å20 Å2
3---12.133 Å2
Refinement stepCycle: LAST / Resolution: 2.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3950 0 94 0 4044
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.232
X-RAY DIFFRACTIONc_mcbond_it4.0241.5
X-RAY DIFFRACTIONc_scbond_it5.6062
X-RAY DIFFRACTIONc_mcangle_it6.2892
X-RAY DIFFRACTIONc_scangle_it7.8052.5
Refine LS restraints NCSRms: 0.025 / Type: restrain / Weight: 300
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.95-3.060.39871830.371215571740
3.06-3.180.41631790.378715381717
3.18-3.320.40871810.344715651746
3.32-3.50.38181750.317215731748
3.5-3.720.34021790.305515781757
3.72-40.29421880.265315591747
4-4.40.2891810.253416011782
4.4-5.040.31031590.243216181777
5.04-6.340.26351590.210816441803
6.34-300.25821860.219116781864
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2x-dna-rna_rep.paramx-dna-rna-test.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4ion.paramion.top

+
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://pdbjlvh1.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