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- PDB-2vwb: Structure of the archaeal Kae1-Bud32 fusion protein MJ1130: a mod... -

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Basic information

Entry
Database: PDB / ID: 2vwb
TitleStructure of the archaeal Kae1-Bud32 fusion protein MJ1130: a model for the eukaryotic EKC-KEOPS subcomplex involved in transcription and telomere homeostasis.
ComponentsPUTATIVE O-SIALOGLYCOPROTEIN ENDOPEPTIDASE
KeywordsHYDROLASE / EKC / KAE1 / BUD32 / KEOPS / MJ1130 / PROTEASE / TELOMERE / METALLOPROTEASE
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 / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 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 / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / iron ion binding / protein serine kinase activity / zinc ion binding / ATP binding / cytoplasm
Similarity search - Function
Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein / tRNA N6-adenosine threonylcarbamoyltransferase Kae1, archaea and eukaryote / Serine/threonine-protein kinase Bud32 / Peptidase M22, conserved site / Glycoprotease family signature. / Kae1/TsaD family / Gcp-like domain / tRNA N6-adenosine threonylcarbamoyltransferase / : / RIO domain ...Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein / tRNA N6-adenosine threonylcarbamoyltransferase Kae1, archaea and eukaryote / Serine/threonine-protein kinase Bud32 / Peptidase M22, conserved site / Glycoprotease family signature. / Kae1/TsaD family / Gcp-like domain / tRNA N6-adenosine threonylcarbamoyltransferase / : / RIO domain / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein
Similarity search - Component
Biological speciesMETHANOCALDOCOCCUS JANNASCHII (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.05 Å
AuthorsHecker, A. / Lopreiato, R. / Graille, M. / Collinet, B. / Forterre, P. / Domenico, L. / van Tilbeurgh, H.
CitationJournal: Embo J. / Year: 2008
Title: Structure of the Archaeal Kae1/Bud32 Fusion Protein Mj1130: A Model for the Eukaryotic Ekc/Keops Subcomplex
Authors: Hecker, A. / Lopreiato, R. / Graille, M. / Collinet, B. / Forterre, P. / Libri, D. / Van Tilbeurgh, H.
History
DepositionJun 20, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: PUTATIVE O-SIALOGLYCOPROTEIN ENDOPEPTIDASE
B: PUTATIVE O-SIALOGLYCOPROTEIN ENDOPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,3264
Polymers121,3142
Non-polymers1,0122
Water00
1
A: PUTATIVE O-SIALOGLYCOPROTEIN ENDOPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1632
Polymers60,6571
Non-polymers5061
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PUTATIVE O-SIALOGLYCOPROTEIN ENDOPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1632
Polymers60,6571
Non-polymers5061
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)147.418, 148.948, 65.118
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein PUTATIVE O-SIALOGLYCOPROTEIN ENDOPEPTIDASE / GLYCOPROTEASE / MJ1130


Mass: 60656.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHANOCALDOCOCCUS JANNASCHII (archaea)
Strain: DSM 2661 / Plasmid: PET-9A / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): ROSETTA PLYSS / References: UniProt: Q58530, EC: 3.4.24.57
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM

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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: 2.8 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growpH: 5.6
Details: 0.1 M SODIUM CITRATE, 5-10% ISOPROPANOL, 0.1 M SODIUM CITRATE PH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9799
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 20, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9799 Å / Relative weight: 1
ReflectionResolution: 3.05→20 Å / Num. obs: 26424 / % possible obs: 94.7 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.4
Reflection shellResolution: 3.05→3.21 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.8 / % possible all: 96.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD
Starting model: PDB ENTRY 1IVN

1ivn


Resolution: 3.05→19.95 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.859 / SU B: 23.424 / SU ML: 0.425 / Cross valid method: THROUGHOUT / ESU R Free: 0.544 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FINAL MODEL CONTAINS RESIDUES 1-31 AND 43-530 FROM MONOMER A AND RESIDUES 1-31, 43-325 AND 340-532 FROM MONOMER B
RfactorNum. reflection% reflectionSelection details
Rfree0.301 1319 5 %RANDOM
Rwork0.22 ---
obs0.224 25085 94.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.94 Å2
Baniso -1Baniso -2Baniso -3
1--1.54 Å20 Å20 Å2
2---0.92 Å20 Å2
3---2.46 Å2
Refinement stepCycle: LAST / Resolution: 3.05→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8148 0 62 0 8210
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0228359
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4781.98111284
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.81851021
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.36724.297377
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.373151545
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.041552
X-RAY DIFFRACTIONr_chiral_restr0.1020.21263
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026162
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2410.24136
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.25623
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2280
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.246
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1150.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.541.55216
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.9528181
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.10433564
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.8694.53103
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.05→3.13 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.369 91
Rwork0.264 1811

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