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- PDB-4n0i: Crystal structure of S. cerevisiae mitochondrial GatFAB in comple... -

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Basic information

Entry
Database: PDB / ID: 4n0i
TitleCrystal structure of S. cerevisiae mitochondrial GatFAB in complex with glutamine
Components(Glutamyl-tRNA(Gln) amidotransferase subunit ...) x 3
KeywordsLIGASE / amidotransferase
Function / homology
Function and homology information


glutaminyl-tRNAGln biosynthesis via transamidation / 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 / endoplasmic reticulum organization / mitochondrial translation / mitochondrial inner membrane / mitochondrion / ATP binding
Similarity search - Function
Glutamyl-tRNA(Gln) amidotransferase subunit F, mitochondrial / Glutamyl-tRNA(Gln) amidotransferase subunit F / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit / Glutamyl-tRNA(Gln) amidotransferase A subunit / 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 ...Glutamyl-tRNA(Gln) amidotransferase subunit F, mitochondrial / Glutamyl-tRNA(Gln) amidotransferase subunit F / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit / Glutamyl-tRNA(Gln) amidotransferase A subunit / 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. / Amidase signature (AS) enzymes / Amidase signature (AS) domain / Amidase signature domain / Amidase signature (AS) superfamily / Amidase / Glutamine synthetase/guanido kinase, catalytic domain / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
GLUTAMINE / NITRATE ION / Glutamyl-tRNA(Gln) amidotransferase subunit B, mitochondrial / Glutamyl-tRNA(Gln) amidotransferase subunit F, mitochondrial / Glutamyl-tRNA(Gln) amidotransferase subunit A, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 Å
AuthorsAraiso, Y. / Ishitani, R. / Nureki, O.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Crystal structure of Saccharomyces cerevisiae mitochondrial GatFAB reveals a novel subunit assembly in tRNA-dependent amidotransferases
Authors: Araiso, Y. / Huot, J.L. / Sekiguchi, T. / Frechin, M. / Fischer, F. / Enkler, L. / Senger, B. / Ishitani, R. / Becker, H.D. / Nureki, O.
History
DepositionOct 2, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamyl-tRNA(Gln) amidotransferase subunit A, mitochondrial
B: Glutamyl-tRNA(Gln) amidotransferase subunit B, mitochondrial
F: Glutamyl-tRNA(Gln) amidotransferase subunit F, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,0155
Polymers105,8063
Non-polymers2082
Water5,891327
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12560 Å2
ΔGint-86 kcal/mol
Surface area32310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.438, 85.426, 194.784
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Glutamyl-tRNA(Gln) amidotransferase subunit ... , 3 types, 3 molecules ABF

#1: Protein Glutamyl-tRNA(Gln) amidotransferase subunit A, mitochondrial / Glu-AdT subunit A / HMG2-induced ER-remodeling protein 2 / Loss of respiratory capacity protein 6


Mass: 50981.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: GatA, GEP6, HER2, LRC6, YMR293C / Plasmid: pCGFP-BC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Star2 CodonPlus
References: UniProt: Q03557, Ligases; Forming carbon-nitrogen bonds; Carbon-nitrogen ligases with glutamine as amido-N-donor
#2: Protein Glutamyl-tRNA(Gln) amidotransferase subunit B, mitochondrial / Glu-AdT subunit B / Cytochrome c oxidase assembly factor PET112


Mass: 36704.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: GatB, PET112, YBL0724, YBL080C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Star2 CodonPlus
References: UniProt: P33893, Ligases; Forming carbon-nitrogen bonds; Carbon-nitrogen ligases with glutamine as amido-N-donor
#3: Protein Glutamyl-tRNA(Gln) amidotransferase subunit F, mitochondrial / Glu-AdT subunit F


Mass: 18120.826 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: GatF, GTF1, YGR102C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Star2 CodonPlus
References: UniProt: P53260, Ligases; Forming carbon-nitrogen bonds; Carbon-nitrogen ligases with glutamine as amido-N-donor

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Non-polymers , 3 types, 329 molecules

#4: Chemical ChemComp-GLN / GLUTAMINE / Glutamine


Type: L-peptide linking / Mass: 146.144 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10N2O3
#5: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O

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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: 2.45 Å3/Da / Density % sol: 49.89 % / Mosaicity: 0.71 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 50mM Sodium malonate, 200mM Mg(NO3)2, 10% PEG3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 68988 / % possible obs: 96.9 % / Redundancy: 5.3 % / Biso Wilson estimate: 30.69 Å2 / Rmerge(I) obs: 0.071 / Χ2: 2.257 / Net I/σ(I): 15.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.034.20.33234501.435197.5
2.03-2.074.40.30834501.54198.3
2.07-2.114.50.27334121.508198
2.11-2.154.40.24334351.465197.3
2.15-2.24.40.20833921.459196.9
2.2-2.254.40.18633761.461196.1
2.25-2.314.40.16634181.486196.4
2.31-2.374.50.14633351.547195.4
2.37-2.444.70.13433531.683195.4
2.44-2.524.80.12534191.783196.2
2.52-2.614.90.11333701.798195.5
2.61-2.715.20.10134201.965196.4
2.71-2.845.40.09234272.115196.2
2.84-2.995.70.08334302.364197.7
2.99-3.176.10.07735182.587198.3
3.17-3.426.70.0735532.799199.1
3.42-3.766.90.06435553.116199.6
3.76-4.316.70.05835703.302198.7
4.31-5.436.60.05436233.347199
5.43-5060.0534823.218190.2

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.7.2_869refinement
PDB_EXTRACT3.11data extraction
uguisdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Yeast GatFAB, free form

Resolution: 2.001→26.458 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.5 / σ(F): 1.49 / Phase error: 19.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2192 3447 5 %RANDOM
Rwork0.189 ---
obs0.1906 68955 96.93 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.306 Å2 / ksol: 0.338 e/Å3
Displacement parametersBiso max: 190.49 Å2 / Biso mean: 50.9464 Å2 / Biso min: 16.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.861 Å2-0 Å20 Å2
2---3.4658 Å20 Å2
3---2.6049 Å2
Refinement stepCycle: LAST / Resolution: 2.001→26.458 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6565 0 13 327 6905
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066742
X-RAY DIFFRACTIONf_angle_d1.069150
X-RAY DIFFRACTIONf_chiral_restr0.0681060
X-RAY DIFFRACTIONf_plane_restr0.0051176
X-RAY DIFFRACTIONf_dihedral_angle_d13.8832473
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.001-2.02860.3031340.27352551268596
2.0286-2.05760.27331370.24932595273298
2.0576-2.08830.27341400.24042664280498
2.0883-2.12090.25361360.22242576271298
2.1209-2.15570.24031370.22012612274997
2.1557-2.19280.23571370.20072594273197
2.1928-2.23270.25711350.19692569270496
2.2327-2.27560.21621340.19052549268396
2.2756-2.3220.24641360.18822580271696
2.322-2.37250.18061330.1812560269396
2.3725-2.42760.22311340.18342533266795
2.4276-2.48830.2421370.19132611274896
2.4883-2.55550.23561350.19932559269497
2.5555-2.63070.23771360.19982574271095
2.6307-2.71550.26741370.20332613275096
2.7155-2.81240.25521340.2052560269496
2.8124-2.92490.25941390.19932634277397
2.9249-3.05780.20921400.19172653279398
3.0578-3.21880.22911410.18812671281298
3.2188-3.42010.21271430.18952714285799
3.4201-3.68350.19081420.180827112853100
3.6835-4.0530.19091430.16722717286099
4.053-4.63680.17241430.15372711285499
4.6368-5.83150.18221460.16762769291599
5.8315-26.46030.25131380.20992628276690
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)
10.65210.1872-0.70851.479-0.07571.3072-0.2497-0.4477-0.37350.65370.0283-0.22660.77870.44890.31640.81130.24140.22720.39960.17290.336523.0019-15.58971.4721
20.6437-0.3416-0.43671.23370.85951.6369-0.3119-0.2267-0.43720.32350.08240.09650.86680.12560.22220.54280.22930.25340.20180.01380.285423.9967-14.621-15.1839
31.1655-0.2465-0.79310.420.44291.7349-0.2815-0.252-0.44140.4935-0.07030.3580.6767-0.25690.37490.62360.03050.27620.30220.03850.458611.8018-12.5304-4.6143
41.0187-0.2709-0.82941.13920.34131.7531-0.2891-0.3191-0.15390.36720.08090.05560.63350.21180.2170.31090.09850.09270.2920.00440.225418.9082-1.6778-7.3172
50.592-0.1139-0.65541.31350.98671.614-0.0355-0.15030.1411-0.11990.1493-0.2392-0.03030.2945-0.0590.165-0.0040.01660.2995-0.06540.253124.679913.3849-14.8463
60.7616-0.4242-0.53310.99350.54491.1088-0.3174-0.1232-0.32080.1431-0.06860.28630.3976-0.2810.18890.2339-0.08720.16270.1889-0.16020.33627.5452-0.8938-14.9473
71.07890.85080.14312.44410.9351.2194-0.28710.2876-0.2196-0.1301-0.180.53350.0598-0.34060.11630.1847-0.02710.0480.3777-0.1870.37724.34433.8843-25.953
81.5377-0.2101-0.72141.5670.27042.1795-0.2238-0.2183-0.15290.21710.0010.21730.2288-0.06960.1330.17090.03150.05580.2443-0.08650.238311.71768.6694-7.3968
90.60540.2755-0.53142.52310.54471.4244-0.13080.2208-0.2899-0.5676-0.07380.14090.32050.1435-0.02160.53140.07080.30170.2419-0.11830.215326.3762-12.0452-45.5111
101.04140.2596-0.69782.06360.13631.3422-0.19570.10270.0219-0.452-0.0250.16770.0204-0.22150.12510.3527-0.00770.09870.2322-0.06540.264320.6479-2.6579-40.3915
110.9153-0.71930.10221.0773-0.44061.7953-0.02440.4558-0.1276-1.288-0.24210.170.0732-0.33850.19951.12940.0613-0.04850.4655-0.08140.334619.6204-3.4665-58.774
121.4555-0.2404-0.01062.11330.19971.2367-0.1560.6006-0.1163-1.1217-0.23930.53840.0407-0.1608-0.05140.8862-0.0003-0.00160.3753-0.17290.329220.9517-8.2618-55.7519
134.30611.4648-0.20965.5440.96942.7223-0.07520.2172-0.1253-1.0598-0.17630.56090.1083-0.11610.26350.84130.00450.0130.2841-0.05350.425123.7538-9.227-56.3653
140.0758-0.06730.15480.0582-0.13340.309-0.11890.22170.0951-0.91-0.03910.9622-0.3464-0.46010.38921.1335-0.0737-0.73460.7644-0.24081.64034.4776-10.8381-64.0764
150.0587-0.0893-0.12141.21272.28354.3373-0.04390.5437-0.5608-1.1134-0.08150.25930.1152-0.13050.14860.8404-0.0889-0.06380.6264-0.37650.66276.2795-12.3652-50.2164
161.09130.4319-1.04430.9835-0.42392.6099-0.1560.0475-0.0553-0.6487-0.1267-0.2227-0.33520.0972-0.0190.6014-0.04490.18860.23790.0340.31929.2547.6652-45.5853
171.03740.0636-1.11681.0861-0.50633.14470.0258-0.0640.1078-0.0508-0.09380.1703-0.176-0.2250.20360.24570.0274-0.0050.2808-0.13180.34394.985225.70260.2352
185.155-3.7196-2.42425.80350.32361.7915-0.07920.4452-0.2168-0.3156-0.29290.489-0.0955-0.40470.25190.12720.0967-0.02470.49-0.20870.3894-6.021619.244-5.3587
190.2621-0.3485-0.29830.47890.45460.5538-0.03330.0407-0.21150.0797-0.28470.38590.1489-0.40910.53020.2605-0.03320.08610.6534-0.38550.5308-7.89375.2243-16.4184
201.08290.1869-0.19960.32380.29850.6294-0.14050.0287-0.13970.0873-0.18310.37370.2838-0.3881-0.02320.4487-0.29170.21430.5887-0.42920.7273-4.0553-15.6625-31.1253
211.256-0.1662-0.32360.19430.1770.3469-0.19270.17460.0381-0.2056-0.070.49710.1304-0.44960.14860.2313-0.103-0.00590.4989-0.31490.5926-0.43983.0371-26.0082
220.16980.175-0.09194.1395-2.43941.4458-0.0966-0.34350.29880.2596-0.261-0.3763-0.10450.34810.45550.3279-0.05690.06790.29640.03530.431437.4673-0.1851-35
230.03130.1848-0.00311.15710.26640.8927-0.14130.1405-0.39910.1274-0.15760.11980.663-0.10530.13210.58210.03670.2890.2239-0.09180.430224.7257-25.0428-32.225
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 6:52)A6 - 52
2X-RAY DIFFRACTION2chain 'A' and (resseq 53:87)A53 - 87
3X-RAY DIFFRACTION3chain 'A' and (resseq 88:123)A88 - 123
4X-RAY DIFFRACTION4chain 'A' and (resseq 124:206)A124 - 206
5X-RAY DIFFRACTION5chain 'A' and (resseq 207:243)A207 - 243
6X-RAY DIFFRACTION6chain 'A' and (resseq 244:328)A244 - 328
7X-RAY DIFFRACTION7chain 'A' and (resseq 329:368)A329 - 368
8X-RAY DIFFRACTION8chain 'A' and (resseq 369:464)A369 - 464
9X-RAY DIFFRACTION9chain 'B' and (resseq 27:66)B27 - 66
10X-RAY DIFFRACTION10chain 'B' and (resseq 67:126)B67 - 126
11X-RAY DIFFRACTION11chain 'B' and (resseq 127:171)B127 - 171
12X-RAY DIFFRACTION12chain 'B' and (resseq 172:211)B172 - 211
13X-RAY DIFFRACTION13chain 'B' and (resseq 212:231)B212 - 231
14X-RAY DIFFRACTION14chain 'B' and (resseq 232:276)B232 - 276
15X-RAY DIFFRACTION15chain 'B' and (resseq 277:302)B277 - 302
16X-RAY DIFFRACTION16chain 'B' and (resseq 303:327)B303 - 327
17X-RAY DIFFRACTION17chain 'F' and (resseq 29:46)F29 - 46
18X-RAY DIFFRACTION18chain 'F' and (resseq 47:52)F47 - 52
19X-RAY DIFFRACTION19chain 'F' and (resseq 53:70)F53 - 70
20X-RAY DIFFRACTION20chain 'F' and (resseq 71:89)F71 - 89
21X-RAY DIFFRACTION21chain 'F' and (resseq 90:134)F90 - 134
22X-RAY DIFFRACTION22chain 'F' and (resseq 135:151)F135 - 151
23X-RAY DIFFRACTION23chain 'F' and (resseq 152:176)F152 - 176

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