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- PDB-3enh: Crystal structure of Cgi121/Bud32/Kae1 complex -

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Basic information

Entry
Database: PDB / ID: 3enh
TitleCrystal structure of Cgi121/Bud32/Kae1 complex
Components
  • Putative O-sialoglycoprotein endopeptidase
  • Uncharacterized protein MJ0187
Keywordshydrolase/unknown function / Hydrolase / Metal-binding / Metalloprotease / Protease / dimerization domain / KEOPS / telomere / transcription / hydrolase-unknown function COMPLEX
Function / homology
Function and homology information


N6-L-threonylcarbamoyladenine synthase / N(6)-L-threonylcarbamoyladenine synthase activity / EKC/KEOPS complex / tRNA threonylcarbamoyladenosine modification / protein serine/threonine/tyrosine kinase activity / metalloendopeptidase activity / non-specific serine/threonine protein kinase / iron ion binding / phosphorylation / protein serine kinase activity ...N6-L-threonylcarbamoyladenine synthase / N(6)-L-threonylcarbamoyladenine synthase activity / EKC/KEOPS complex / tRNA threonylcarbamoyladenosine modification / protein serine/threonine/tyrosine kinase activity / metalloendopeptidase activity / non-specific serine/threonine protein kinase / iron ion binding / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / zinc ion binding / ATP binding / cytoplasm
Similarity search - Function
Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein / PF0523-like / CGI121/TPRKB / tRNA N6-adenosine threonylcarbamoyltransferase Kae1, archaea and eukaryote / Serine/threonine-protein kinase Bud32 / CGI121/TPRKB / CGI121/TPRKB superfamily / Kinase binding protein CGI-121 / Peptidase M22, conserved site / Glycoprotease family signature. ...Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein / PF0523-like / CGI121/TPRKB / tRNA N6-adenosine threonylcarbamoyltransferase Kae1, archaea and eukaryote / Serine/threonine-protein kinase Bud32 / CGI121/TPRKB / CGI121/TPRKB superfamily / Kinase binding protein CGI-121 / Peptidase M22, conserved site / Glycoprotease family signature. / Kae1/TsaD family / Gcp-like domain / tRNA N6-adenosine threonylcarbamoyltransferase / RIO1 family / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
HEXATANTALUM DODECABROMIDE / Regulatory protein Cgi121 / Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsNeculai, D.
CitationJournal: Mol.Cell / Year: 2008
Title: Atomic Structure of the KEOPS Complex: An Ancient Protein Kinase-Containing Molecular Machine
Authors: Mao, D.Y.L. / Neculai, D. / Downey, M. / Orlicky, S. / Haffani, Y.Z. / Ceccarelli, D.F. / Ho, J.S.L. / Szilard, R.K. / Zhang, W. / Ho, C.S. / Wan, L. / Fares, C. / Rumpel, S. / Kurinov, I. / ...Authors: Mao, D.Y.L. / Neculai, D. / Downey, M. / Orlicky, S. / Haffani, Y.Z. / Ceccarelli, D.F. / Ho, J.S.L. / Szilard, R.K. / Zhang, W. / Ho, C.S. / Wan, L. / Fares, C. / Rumpel, S. / Kurinov, I. / Arrowsmith, C.H. / Durocher, D. / Sicheri, F.
History
DepositionSep 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
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: Putative O-sialoglycoprotein endopeptidase
B: Putative O-sialoglycoprotein endopeptidase
C: Uncharacterized protein MJ0187
D: Uncharacterized protein MJ0187
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,79712
Polymers156,4414
Non-polymers16,3568
Water0
1
A: Putative O-sialoglycoprotein endopeptidase
D: Uncharacterized protein MJ0187
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3996
Polymers78,2202
Non-polymers8,1784
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-8 kcal/mol
Surface area28980 Å2
MethodPISA
2
B: Putative O-sialoglycoprotein endopeptidase
C: Uncharacterized protein MJ0187
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3996
Polymers78,2202
Non-polymers8,1784
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-14 kcal/mol
Surface area29380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.990, 106.910, 209.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 31
2111B1 - 31
1211A43 - 200
2211B43 - 200
1311A342 - 474
2311B342 - 474
1411A476 - 532
2411B476 - 532
1121C5 - 150
2121D5 - 150

NCS ensembles :
ID
1
2

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Components

#1: Protein Putative O-sialoglycoprotein endopeptidase / E.C.3.4.24.57 / fusion Kae1/Bud32


Mass: 61128.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: DSM 2661 / Gene: gcp, MJ1130 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q58530, EC: 3.4.24.57
#2: Protein Uncharacterized protein MJ0187 / Cgi121


Mass: 17092.066 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: DSM 2661 / Gene: MJ0187 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q57646
#3: Chemical
ChemComp-TBR / HEXATANTALUM DODECABROMIDE / DODECABROMOHEXATANTALUM


Mass: 2044.535 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Br12Ta6

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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: 2.76 Å3/Da / Density % sol: 55.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES and 10-15% PEG 3000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97922
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 23, 2007 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97922 Å / Relative weight: 1
ReflectionResolution: 3.6→208.84 Å / Num. obs: 20565 / % possible obs: 99.8 % / Observed criterion σ(I): 3.21 / Redundancy: 1.86 % / Rmerge(I) obs: 0.0747 / Rsym value: 0.0747 / Net I/σ(I): 11.96
Reflection shellResolution: 3.6→3.7 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.2171 / Mean I/σ(I) obs: 3.4 / Num. unique all: 1582 / Rsym value: 0.2171

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
REFMAC5.5refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ARCHEAL CGI121 AND ARCHEAL KAE1/BUD32 STRUCTURES

Resolution: 3.6→94.92 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.883 / SU B: 101.685 / SU ML: 0.82 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.852 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.3241 1052 5.1 %RANDOM
Rwork0.27109 ---
obs0.27371 19689 99.97 %-
all-20608 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 103.972 Å2
Baniso -1Baniso -2Baniso -3
1--12.94 Å20 Å20 Å2
2--8.77 Å20 Å2
3---4.17 Å2
Refinement stepCycle: LAST / Resolution: 3.6→94.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9998 0 144 0 10142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0470.02210465
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3692.04514725
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.72651243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.46724.43465
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.91151930
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3811566
X-RAY DIFFRACTIONr_chiral_restr0.0780.21560
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027446
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1511.56211
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.293210018
X-RAY DIFFRACTIONr_scbond_it0.37233942
X-RAY DIFFRACTIONr_scangle_it0.6714.53651
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Rms dev position: 0.02 Å

Ens-IDAuth asym-IDNumberTypeWeight position
1A2871TIGHT POSITIONAL0.05
1A2871TIGHT THERMAL0.5
2C1100TIGHT POSITIONAL0.05
2C1100TIGHT THERMAL0.5
LS refinement shellResolution: 3.6→3.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 83 -
Rwork0.326 1434 -
obs--99.93 %
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)
13.8053-2.96051.06466.0896-1.76374.96530.4974-0.0208-0.3837-0.2651-0.5690.3111-0.71970.23990.07160.2317-0.0411-0.03450.0945-0.00250.2857-13.0925.90840.232
26.3757-1.14451.3475.3794-1.57343.11990.69311.3970.2502-0.7585-1.5698-0.363-0.30770.64220.87670.31610.3639-0.04870.8630.41160.591518.13517.39341.132
31.3695-0.9382-0.99322.28071.40633.5227-0.3442-0.0107-0.11230.33740.6016-0.44120.037-0.2561-0.25730.6967-0.01080.00870.45370.0060.44121.20340.316-2.001
43.84950.0273-0.67823.31610.40963.4982-0.07980.61050.243-0.44160.0979-0.1147-0.1237-0.4856-0.01811.11730.2280.0160.6991-0.23260.7278-10.03670.7741.436
54.3881-0.4594-0.90755.14332.464.75980.24630.25530.2103-0.3209-0.2332-0.2782-0.3537-0.1709-0.01310.8750.16220.02350.4105-0.08710.4547-12.03596.75724.864
610.1057-1.57390.13093.21840.34086.2526-0.21910.0840.04630.4775-0.1237-0.4040.4490.35620.34280.09640.0051-0.03560.0660.13090.295741.2952.79362.321
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 324
2X-RAY DIFFRACTION2A342 - 530
3X-RAY DIFFRACTION3B1 - 324
4X-RAY DIFFRACTION4B342 - 527
5X-RAY DIFFRACTION5C4 - 147
6X-RAY DIFFRACTION6D4 - 147

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