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- PDB-3kfu: Crystal structure of the transamidosome -

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Basic information

Entry
Database: PDB / ID: 3kfu
TitleCrystal structure of the transamidosome
Components
  • (Glutamyl-tRNA(Gln) amidotransferase subunit ...) x 2
  • Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
  • Non-discriminating and archaeal-type aspartyl-tRNA synthetase
  • tRNA-Asn
KeywordsLIGASE/RNA / AspRS / GatCAB / ATP-binding / Aminoacyl-tRNA synthetase / Ligase / Nucleotide-binding / Protein biosynthesis / LIGASE-RNA complex
Function / homology
Function and homology information


aspartate-tRNAAsn ligase / aspartate-tRNA(Asn) ligase activity / glutaminyl-tRNA synthase (glutamine-hydrolysing) / glutamyl-tRNA(Gln) amidotransferase complex / Ligases; Forming carbon-nitrogen bonds; Carbon-nitrogen ligases with glutamine as amido-N-donor / glutaminyl-tRNA synthase (glutamine-hydrolyzing) activity / aspartyl-tRNA aminoacylation / aspartate-tRNA ligase activity / regulation of translational fidelity / nucleic acid binding ...aspartate-tRNAAsn ligase / aspartate-tRNA(Asn) ligase activity / glutaminyl-tRNA synthase (glutamine-hydrolysing) / glutamyl-tRNA(Gln) amidotransferase complex / Ligases; Forming carbon-nitrogen bonds; Carbon-nitrogen ligases with glutamine as amido-N-donor / glutaminyl-tRNA synthase (glutamine-hydrolyzing) activity / aspartyl-tRNA aminoacylation / aspartate-tRNA ligase activity / regulation of translational fidelity / nucleic acid binding / hydrolase activity / translation / ATP binding / cytoplasm
Similarity search - Function
Helicase, Ruva Protein; domain 3 - #990 / Glu-tRNAGln amidotransferase C subunit / Glu-tRNAGln amidotransferase superfamily, subunit C / Glu-tRNAGln amidotransferase C subunit / Glu-tRNAGln amidotransferase C subunit, N-terminal domain / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit / Glutamyl-tRNA(Gln) amidotransferase A subunit / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C-terminal, domain 1 / Aspartate-tRNA synthetase, type 2 / Aspartyl/Glutamyl-tRNA(Gln) amidotransferase, subunit B/E, catalytic ...Helicase, Ruva Protein; domain 3 - #990 / Glu-tRNAGln amidotransferase C subunit / Glu-tRNAGln amidotransferase superfamily, subunit C / Glu-tRNAGln amidotransferase C subunit / Glu-tRNAGln amidotransferase C subunit, N-terminal domain / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit / Glutamyl-tRNA(Gln) amidotransferase A subunit / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C-terminal, domain 1 / Aspartate-tRNA synthetase, type 2 / Aspartyl/Glutamyl-tRNA(Gln) amidotransferase, subunit B/E, catalytic / Glutamyl-tRNA(Gln) amidotransferase, subunit B, conserved site / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, subunit B /E / GatB/GatE catalytic domain / Glutamyl-tRNA(Gln) amidotransferase subunit B signature. / Asn/Gln amidotransferase / GatB domain / GatB domain / Aspartyl/glutamyl-tRNA amidotransferase subunit B-like / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C-terminal, domain 2 / Amidase / Amidase, conserved site / Amidases signature. / Aspartyl/Asparaginyl-tRNA synthetase, class IIb / Amidase signature (AS) enzymes / Amidase signature (AS) domain / Amidase signature domain / Amidase signature (AS) superfamily / Amidase / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / Glutamine synthetase/guanido kinase, catalytic domain / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Histone, subunit A / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Helicase, Ruva Protein; domain 3 / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Alpha-Beta Complex / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Aspartate--tRNA(Asp/Asn) ligase / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B / Glutamyl-tRNA(Gln) amidotransferase subunit A / Glutamyl-tRNA(Gln) amidotransferase subunit C
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBlaise, M. / Bailly, M. / Frechin, M. / Thirup, S. / Becker, H.D. / Kern, D.
CitationJournal: Embo J. / Year: 2010
Title: Crystal structure of a transfer-ribonucleoprotein particle that promotes asparagine formation.
Authors: Blaise, M. / Bailly, M. / Frechin, M. / Behrens, M.A. / Fischer, F. / Oliveira, C.L. / Becker, H.D. / Pedersen, J.S. / Thirup, S. / Kern, D.
History
DepositionOct 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_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_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Non-discriminating and archaeal-type aspartyl-tRNA synthetase
B: Non-discriminating and archaeal-type aspartyl-tRNA synthetase
C: Non-discriminating and archaeal-type aspartyl-tRNA synthetase
D: Non-discriminating and archaeal-type aspartyl-tRNA synthetase
E: Glutamyl-tRNA(Gln) amidotransferase subunit A
F: Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
G: Glutamyl-tRNA(Gln) amidotransferase subunit C
H: Glutamyl-tRNA(Gln) amidotransferase subunit A
I: Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
J: Glutamyl-tRNA(Gln) amidotransferase subunit C
K: tRNA-Asn
L: tRNA-Asn
M: tRNA-Asn
N: tRNA-Asn
hetero molecules


Theoretical massNumber of molelcules
Total (without water)514,21018
Polymers514,03114
Non-polymers1794
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area59360 Å2
ΔGint-357 kcal/mol
Surface area172900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.920, 214.000, 127.840
Angle α, β, γ (deg.)90.00, 93.36, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24
15
25
16
26
17
27

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain H and (resseq 2:393 )
211chain E and (resseq 2:393 )
112chain B and (resseq 1:150 or resseq 180:200 or resseq 211:415 )
212chain D and (resseq 1:150 or resseq 180:200 or resseq 211:415 )
113chain A and (resseq 1:150 or resseq 180:200 or resseq 211:415 )
213chain C and (resseq 1:150 or resseq 180:200 or resseq 211:415 )
114chain J and (resseq 3:47 or resseq 51:88 )
214chain G and (resseq 3:47 or resseq 51:88 )
115chain I and (resseq 2:194 or resseq 200:253 or resseq 260:391 )
215chain F and (resseq 2:194 or resseq 200:253 or resseq 260:391 )
116chain K
216chain L
117chain N
217chain M

NCS ensembles :
ID
1
2
3
4
5
6
7

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Components

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Protein , 2 types, 6 molecules ABCDFI

#1: Protein
Non-discriminating and archaeal-type aspartyl-tRNA synthetase


Mass: 48397.262 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA1452 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SIC2
#3: Protein Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B / Asp/Glu-ADT subunit B


Mass: 50545.543 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / Gene: gatB, TTHA0366 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9LCX2, Ligases; Forming carbon-nitrogen bonds; Carbon-nitrogen ligases with glutamine as amido-N-donor

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Glutamyl-tRNA(Gln) amidotransferase subunit ... , 2 types, 4 molecules EHGJ

#2: Protein Glutamyl-tRNA(Gln) amidotransferase subunit A / Glu-ADT subunit A


Mass: 50280.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / Gene: gatA, TTHA0573 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9LCX3, Ligases; Forming carbon-nitrogen bonds; Carbon-nitrogen ligases with glutamine as amido-N-donor
#4: Protein Glutamyl-tRNA(Gln) amidotransferase subunit C / Glu-ADT subunit C


Mass: 10253.733 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / Gene: gatC, TTHA0876 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9LCX4, Ligases; Forming carbon-nitrogen bonds; Carbon-nitrogen ligases with glutamine as amido-N-donor

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RNA chain , 1 types, 4 molecules KLMN

#5: RNA chain
tRNA-Asn


Mass: 24570.650 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Production host: Escherichia coli (E. coli)

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Non-polymers , 3 types, 10 molecules

#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE AUTHORS STATE THAT THE C-TERMINAL RESIDUES FOR CHAINS F AND I HAVE ONLY WEAK ELECTRON DENSITY ...THE AUTHORS STATE THAT THE C-TERMINAL RESIDUES FOR CHAINS F AND I HAVE ONLY WEAK ELECTRON DENSITY SO IT WAS NOT POSSIBLE TO ACCURATELY ASSIGN THE SIDE CHAINS. THE C-TERMINI WERE MODELED AS ALA, BUT THE SEQUENCE ALIGNMENT IS UNKNOWN, AND WERE THEREFORE CHANGED TO UNK IN THIS ENTRY. THE UNK CORRESPOND TO RESIDUES WITHIN THE SEQUENCE LVRERGLKVVADEGALKALVAEAIAAMPEAAESVRQGKVKALDALVGQVMRK TRGQARPDLVRRLLLEALGVG BUT CANNOT BE NUMBERED FOR CERTAINTY SINCE THEY ARE NOT SURE OF THE FRAME.

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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: 3.08 Å3/Da / Density % sol: 60.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES pH 6.5 10% peg4000 0.2 M MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9807 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 14, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9807 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 123945

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.5_2) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N9W and 2F2A

1n9w

2f2a


Resolution: 3→39.189 Å / SU ML: 0.38 / σ(F): 1.38 / Phase error: 25.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2517 2487 2.01 %
Rwork0.1993 --
obs0.2004 123923 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.365 Å2 / ksol: 0.313 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.4704 Å20 Å24.5113 Å2
2--1.4741 Å2-0 Å2
3----3.9445 Å2
Refinement stepCycle: LAST / Resolution: 3→39.189 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27198 6224 4 6 33432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00734742
X-RAY DIFFRACTIONf_angle_d0.73448537
X-RAY DIFFRACTIONf_dihedral_angle_d15.79314024
X-RAY DIFFRACTIONf_chiral_restr0.0625625
X-RAY DIFFRACTIONf_plane_restr0.0045250
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11H2945X-RAY DIFFRACTIONPOSITIONAL
12E2945X-RAY DIFFRACTIONPOSITIONAL0.057
21B3003X-RAY DIFFRACTIONPOSITIONAL
22D3003X-RAY DIFFRACTIONPOSITIONAL0.017
31A3019X-RAY DIFFRACTIONPOSITIONAL
32C3019X-RAY DIFFRACTIONPOSITIONAL0.026
41J662X-RAY DIFFRACTIONPOSITIONAL
42G662X-RAY DIFFRACTIONPOSITIONAL0.036
51I3000X-RAY DIFFRACTIONPOSITIONAL
52F3000X-RAY DIFFRACTIONPOSITIONAL0.03
61K1579X-RAY DIFFRACTIONPOSITIONAL
62L1579X-RAY DIFFRACTIONPOSITIONAL0.012
71N1525X-RAY DIFFRACTIONPOSITIONAL
72M1525X-RAY DIFFRACTIONPOSITIONAL0.082
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.05770.36421430.34676764X-RAY DIFFRACTION100
3.0577-3.12010.391320.3186750X-RAY DIFFRACTION100
3.1201-3.18790.32041400.28726688X-RAY DIFFRACTION100
3.1879-3.2620.26281310.24636713X-RAY DIFFRACTION100
3.262-3.34350.32921410.23486745X-RAY DIFFRACTION100
3.3435-3.43390.29831410.22796750X-RAY DIFFRACTION100
3.4339-3.53490.28761550.21286677X-RAY DIFFRACTION100
3.5349-3.64890.26041490.2026749X-RAY DIFFRACTION100
3.6489-3.77920.28851220.19876738X-RAY DIFFRACTION100
3.7792-3.93040.27531340.17966738X-RAY DIFFRACTION100
3.9304-4.10910.22861350.17586774X-RAY DIFFRACTION100
4.1091-4.32550.21171280.16286712X-RAY DIFFRACTION100
4.3255-4.59610.19331200.15656787X-RAY DIFFRACTION100
4.5961-4.95030.17941230.16116765X-RAY DIFFRACTION100
4.9503-5.44730.26591380.17866756X-RAY DIFFRACTION100
5.4473-6.23280.23891550.19326746X-RAY DIFFRACTION100
6.2328-7.84240.23371540.18656780X-RAY DIFFRACTION100
7.8424-39.19280.22821460.19856804X-RAY DIFFRACTION99

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