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- PDB-7cv1: Structure of human tRNAHis guanylyltransferase (Thg1) in the pres... -

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Basic information

Entry
Database: PDB / ID: 7cv1
TitleStructure of human tRNAHis guanylyltransferase (Thg1) in the presence of human mitochondrial tRNAHis
ComponentsProbable tRNA(His) guanylyltransferase
KeywordsTRANSFERASE / tRNA modification
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 / mitochondrial fusion / tRNA processing / 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 / mitochondrial fusion / tRNA processing / nucleotidyltransferase activity / guanyl-nucleotide exchange factor activity / protein homotetramerization / response to oxidative stress / mitochondrial outer membrane / 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
Similarity search - Domain/homology
Probable tRNA(His) guanylyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsNakamura, A. / Wang, D. / Komatsu, Y.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)16K18511 Japan
Japan Society for the Promotion of Science (JSPS)19K06519 Japan
CitationJournal: Rna / Year: 2021
Title: Analysis of GTP addition in the reverse (3'-5') direction by human tRNA His guanylyltransferase.
Authors: Nakamura, A. / Wang, D. / Komatsu, Y.
History
DepositionAug 25, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 2, 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 1.2Nov 29, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable tRNA(His) guanylyltransferase
B: Probable tRNA(His) guanylyltransferase
C: Probable tRNA(His) guanylyltransferase
D: Probable tRNA(His) guanylyltransferase


Theoretical massNumber of molelcules
Total (without water)130,5844
Polymers130,5844
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9920 Å2
ΔGint-70 kcal/mol
Surface area46970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.878, 155.878, 201.500
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 4 through 217 or resid 241 through 267))
21chain B
31(chain C and (resid 4 through 217 or resid 241 through 267))
41(chain D and (resid 4 through 217 or resid 241 through 267))

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
11SERSERVALVAL(chain A and (resid 4 through 217 or resid 241 through 267))AA4 - 21712 - 225
12THRTHRGLUGLU(chain A and (resid 4 through 217 or resid 241 through 267))AA241 - 267249 - 275
21SERSERGLUGLUchain BBB4 - 26712 - 275
31SERSERVALVAL(chain C and (resid 4 through 217 or resid 241 through 267))CC4 - 21712 - 225
32THRTHRGLUGLU(chain C and (resid 4 through 217 or resid 241 through 267))CC241 - 267249 - 275
41SERSERVALVAL(chain D and (resid 4 through 217 or resid 241 through 267))DD4 - 21712 - 225
42THRTHRGLUGLU(chain D and (resid 4 through 217 or resid 241 through 267))DD241 - 267249 - 275

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Components

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


Mass: 32646.066 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: THG1L, ICF45 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NWX6, tRNAHis guanylyltransferase

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 5.41 Å3/Da / Density % sol: 77.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris-HCl pH 7.0, 10% (w/v) PEG6000, 5% (w/v) Tacsimate pH7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 4→49.462 Å / Num. obs: 24468 / % possible obs: 100 % / Redundancy: 20.4 % / CC1/2: 0.989 / Rmerge(I) obs: 1.011 / Rpim(I) all: 0.226 / Rrim(I) all: 1.036 / Net I/σ(I): 5.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
4-4.2821.37.8939300543630.5471.7428.0851.2100
11.31-49.4619.40.0962271411730.9970.0220.09921.598.9

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OTE

3ote


Resolution: 4→49.462 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2554 2431 9.96 %
Rwork0.2423 21972 -
obs0.2436 24403 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 241.29 Å2 / Biso mean: 138.8651 Å2 / Biso min: 94.68 Å2
Refinement stepCycle: final / Resolution: 4→49.462 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8211 0 0 0 8211
Num. residues----986
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2924X-RAY DIFFRACTION2.862TORSIONAL
12B2924X-RAY DIFFRACTION2.862TORSIONAL
13C2924X-RAY DIFFRACTION2.862TORSIONAL
14D2924X-RAY DIFFRACTION2.862TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
4.0001-4.08180.3491410.33731251
4.0818-4.17050.331440.3411293
4.1705-4.26740.32631400.31041272
4.2674-4.37410.30451410.29331278
4.3741-4.49230.25591430.27681271
4.4923-4.62440.26641390.26741265
4.6244-4.77350.31161420.26571260
4.7735-4.9440.25011440.23321286
4.944-5.14170.23431370.23431291
5.1417-5.37550.25561460.23491294
5.3755-5.65850.25961450.25351282
5.6585-6.01240.2751420.25111292
6.0124-6.47570.23491420.23751297
6.4757-7.12570.26181400.24051306
7.1257-8.15280.19271460.20671305
8.1528-10.25660.17351490.15841327
10.2566-49.4620.27711500.23751402
Refinement TLS params.Method: refined / Origin x: 89.052 Å / Origin y: -38.5717 Å / Origin z: 11.6573 Å
111213212223313233
T0.9055 Å20.0896 Å20.0878 Å2-1.0222 Å20.0295 Å2--0.9775 Å2
L0.8368 °2-0.0094 °20.3255 °2-1.5404 °20.0367 °2--1.6965 °2
S0.0566 Å °0.2231 Å °0.1604 Å °-0.36 Å °-0.1421 Å °-0.186 Å °0.0338 Å °0.3926 Å °0.0964 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 267
2X-RAY DIFFRACTION1allB4 - 267
3X-RAY DIFFRACTION1allC4 - 267
4X-RAY DIFFRACTION1allD4 - 267

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