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- PDB-6wqx: Human PRPK-TPRKB complex -

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Basic information

Entry
Database: PDB / ID: 6wqx
TitleHuman PRPK-TPRKB complex
Components
  • EKC/KEOPS complex subunit TP53RK
  • EKC/KEOPS complex subunit TPRKB
KeywordsPROTEIN BINDING/TRANSFERASE / tRNA modification / kinase / protein binding / PROTEIN BINDING-TRANSFERASE complex
Function / homology
Function and homology information


tRNA threonylcarbamoyladenosine metabolic process / EKC/KEOPS complex / tRNA threonylcarbamoyladenosine modification / Hydrolases; Acting on acid anhydrides / tRNA modification in the nucleus and cytosol / tRNA processing / regulation of signal transduction by p53 class mediator / p53 binding / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase ...tRNA threonylcarbamoyladenosine metabolic process / EKC/KEOPS complex / tRNA threonylcarbamoyladenosine modification / Hydrolases; Acting on acid anhydrides / tRNA modification in the nucleus and cytosol / tRNA processing / regulation of signal transduction by p53 class mediator / p53 binding / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase / hydrolase activity / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Lipopolysaccharide kinase (Kdo/WaaP) family / Serine/threonine-protein kinase Bud32 / CGI121/TPRKB / CGI121/TPRKB superfamily / Kinase binding protein CGI-121 / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / EKC/KEOPS complex subunit TP53RK / EKC/KEOPS complex subunit TPRKB
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsLi, J. / Ma, X.L. / Banerjee, S. / Dong, Z.G.
CitationJournal: Commun Biol / Year: 2021
Title: Crystal structure of the human PRPK-TPRKB complex.
Authors: Li, J. / Ma, X. / Banerjee, S. / Chen, H. / Ma, W. / Bode, A.M. / Dong, Z.
History
DepositionApr 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: EKC/KEOPS complex subunit TPRKB
C: EKC/KEOPS complex subunit TP53RK
A: EKC/KEOPS complex subunit TPRKB
D: EKC/KEOPS complex subunit TP53RK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,8569
Polymers99,7714
Non-polymers1,0855
Water1,17165
1
B: EKC/KEOPS complex subunit TPRKB
C: EKC/KEOPS complex subunit TP53RK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4405
Polymers49,8862
Non-polymers5553
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-45 kcal/mol
Surface area18950 Å2
MethodPISA
2
A: EKC/KEOPS complex subunit TPRKB
D: EKC/KEOPS complex subunit TP53RK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4164
Polymers49,8862
Non-polymers5312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-32 kcal/mol
Surface area19080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.856, 77.540, 100.413
Angle α, β, γ (deg.)90.000, 106.814, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein EKC/KEOPS complex subunit TPRKB / PRPK-binding protein / TP53RK-binding protein


Mass: 20130.455 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TPRKB, CGI-121, My019 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y3C4
#2: Protein EKC/KEOPS complex subunit TP53RK / Atypical serine/threonine protein kinase TP53RK / Nori-2 / TP53-regulating kinase / p53-related protein kinase


Mass: 29755.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP53RK, C20orf64, PRPK / Production host: Escherichia coli (E. coli)
References: UniProt: Q96S44, Hydrolases; Acting on acid anhydrides, non-specific serine/threonine protein kinase
#3: 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
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.6 Å3/Da / Density % sol: 52.72 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M KCl, 0.1 M HEPES pH 7.5, 15% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.53→49.36 Å / Num. obs: 32683 / % possible obs: 99.1 % / Redundancy: 5.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.107 / Net I/σ(I): 11.1
Reflection shellResolution: 2.53→2.64 Å / Rmerge(I) obs: 1.017 / Mean I/σ(I) obs: 2 / Num. unique obs: 3987 / CC1/2: 0.806

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ENP, 3EN9

3enp

3en9


Resolution: 2.53→49.358 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.265 1560 4.78 %
Rwork0.2113 --
obs0.2139 32629 98.83 %
Refinement stepCycle: LAST / Resolution: 2.53→49.358 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6401 0 65 65 6531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00826560
X-RAY DIFFRACTIONf_angle_d0.99178853
X-RAY DIFFRACTIONf_chiral_restr0.05291035
X-RAY DIFFRACTIONf_plane_restr0.00511121
X-RAY DIFFRACTIONf_dihedral_angle_d22.91072518
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.53-2.610.37611480.32782782X-RAY DIFFRACTION98.95
2.61-2.710.37331420.31292816X-RAY DIFFRACTION98.63
2.71-2.810.32691470.2682770X-RAY DIFFRACTION98.08
2.81-2.940.31831490.25362834X-RAY DIFFRACTION99.4
2.94-3.10.29371530.24232814X-RAY DIFFRACTION99.4
3.1-3.290.30521300.24922824X-RAY DIFFRACTION99.26
3.29-3.540.32091340.2322831X-RAY DIFFRACTION98.9
3.54-3.90.26421230.21032824X-RAY DIFFRACTION98.2
3.9-4.460.21531330.17162873X-RAY DIFFRACTION99.5
4.46-5.620.23071460.17712811X-RAY DIFFRACTION98.24
5.62-49.370.21581550.17452890X-RAY DIFFRACTION98.58

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