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- PDB-7szb: Crystal Structure Analysis of human PRPK complex with a compound -

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Basic information

Entry
Database: PDB / ID: 7szb
TitleCrystal Structure Analysis of human PRPK complex with a compound
Components
  • EKC/KEOPS complex subunit TP53RK
  • EKC/KEOPS complex subunit TPRKB
KeywordsTRANSFERASE / protein kinase / p53 / immunomodulatory drugs / IMiDs
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 / cytosol / cytoplasm
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
Chem-DQ4 / CITRATE ANION / EKC/KEOPS complex subunit TP53RK / EKC/KEOPS complex subunit TPRKB
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsSeo, H.-S. / Dhe-Paganon, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Biorxiv / Year: 2021
Title: Development of PRPK Directed Phthalimides
Authors: Seo, H.-S. / Mizutani, T. / Hideshima, T. / Vangos, N.E. / Zhang, T. / Anderson, K.C. / Gray, N.S. / Dhe-Paganon, S.
History
DepositionNov 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Feb 7, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)97,5948
Polymers96,6704
Non-polymers9254
Water8,881493
1
A: EKC/KEOPS complex subunit TP53RK
B: EKC/KEOPS complex subunit TPRKB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7974
Polymers48,3352
Non-polymers4622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-17 kcal/mol
Surface area18940 Å2
MethodPISA
2
C: EKC/KEOPS complex subunit TP53RK
D: EKC/KEOPS complex subunit TPRKB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7974
Polymers48,3352
Non-polymers4622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-15 kcal/mol
Surface area17930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)295.770, 47.630, 62.140
Angle α, β, γ (deg.)90.000, 96.770, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein EKC/KEOPS complex subunit TP53RK / Atypical serine/threonine protein kinase TP53RK / Nori-2 / TP53-regulating kinase / p53-related protein kinase


Mass: 28358.646 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 BL21(DE3) (bacteria)
References: UniProt: Q96S44, Hydrolases; Acting on acid anhydrides, non-specific serine/threonine protein kinase
#2: Protein EKC/KEOPS complex subunit TPRKB / PRPK-binding protein / TP53RK-binding protein


Mass: 19976.223 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 BL21(DE3) (bacteria) / References: UniProt: Q9Y3C4
#3: Chemical ChemComp-DQ4 / 5-amino-2-[(3R)-2,6-dioxopiperidin-3-yl]-1H-isoindole-1,3(2H)-dione


Mass: 273.244 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H11N3O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 493 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.25 Å3/Da / Density % sol: 45.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 100mM Sodium citrate pH 5.2, 12.8% PEG8000, 10mM MgCl2, 10mM TCEP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.02→61.71 Å / Num. obs: 56764 / % possible obs: 99.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 27.293 Å2 / Rpim(I) all: 0.047 / Rrim(I) all: 0.091 / Net I/σ(I): 14.3 / Num. measured all: 208593
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
2.02-2.053.71.61056828410.5621.094100
5.48-61.743.540.51031329600.0150.02898.4

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ENP, 4WW5

3enp

4ww5


Resolution: 2.02→61.707 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.209 2890 5.09 %
Rwork0.1698 53864 -
obs0.1718 56754 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.18 Å2 / Biso mean: 37.3591 Å2 / Biso min: 17.01 Å2
Refinement stepCycle: final / Resolution: 2.02→61.707 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6222 0 76 493 6791
Biso mean--32.96 43.43 -
Num. residues----813
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0146386
X-RAY DIFFRACTIONf_angle_d1.3288649
X-RAY DIFFRACTIONf_dihedral_angle_d6.1013907
X-RAY DIFFRACTIONf_chiral_restr0.0671027
X-RAY DIFFRACTIONf_plane_restr0.0071104
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.02-2.05320.31461130.27972599100
2.0532-2.08860.2981320.24682520100
2.0886-2.12650.27171460.22052520100
2.1265-2.16750.261240.21042610100
2.1675-2.21170.23651390.20272509100
2.2117-2.25980.27081460.21122557100
2.2598-2.31240.26171240.19422579100
2.3124-2.37020.23341320.17872571100
2.3702-2.43430.20591440.18012501100
2.4343-2.50590.2541350.17932601100
2.5059-2.58680.23971250.17032552100
2.5868-2.67920.21141320.17182556100
2.6792-2.78650.22341420.18112571100
2.7865-2.91330.24511670.18092515100
2.9133-3.06690.25191310.17792575100
3.0669-3.25910.2441480.17362588100
3.2591-3.51070.20041240.1585255299
3.5107-3.86390.19331440.1476257099
3.8639-4.42290.14681370.1352258299
4.4229-5.57180.16931480.1449258699
5.5718-61.7070.17641570.1678265098
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)
10.6596-0.02240.09780.55020.7190.9366-0.0630.1551-0.4344-0.3852-0.0637-0.3101-0.2956-0.003-0.00730.32170.04320.04750.33890.00470.26671.2714-13.6278-5.6625
20.8643-0.0002-0.17231.2573-0.59090.59160.1445-0.0695-0.3034-0.00520.0174-0.36460.17590.2253-0.00050.23970.0101-0.00150.26540.05120.268659.2475-27.62631.5117
30.8282-0.1610.20350.79440.52840.33170.07370.00250.0592-0.14190.1334-0.1089-0.52810.39080.0010.2216-0.03640.03910.2942-0.010.217659.3799-22.1917-4.2477
40.98190.5013-0.36531.28320.07560.15270.05670.15480.1549-0.07510.00980.0944-0.3101-0.23080.00220.2165-0.0004-0.02120.2391-0.00040.250450.2565-13.9178-3.5977
50.84880.48970.40641.2575-0.16750.4320.1122-0.2372-0.0820.1621-0.05330.02370.09650.068600.2121-0.00520.01380.2741-0.00450.191854.2429-19.48915.8911
62.71570.03670.69010.799-0.20212.08370.054-0.1501-0.33740.32860.01140.17820.407-0.2265-0.00280.3559-0.05340.02030.2990.00880.231335.5377-33.33348.0723
71.06120.24480.5880.53990.59711.0159-0.053-0.11960.16650.14490.02920.02740.0515-0.12140.00020.2323-0.00320.03440.23490.02320.228841.5562-23.34734.0549
80.3878-0.47710.06972.5794-0.35140.59290.08610.3805-0.0294-1.010.13730.14520.1665-0.060.02330.2368-0.0084-0.02810.3165-0.01970.323233.554-27.228-5.2134
91.43480.1870.57660.438-0.34830.742-0.1623-0.1763-0.4154-0.21090.21880.49940.2628-0.29280.00040.3197-0.1070.03150.40910.00260.359728.5172-31.83393.6367
100.7639-0.08570.40421.2593-0.3180.617-0.21430.1383-0.1735-0.4107-0.14290.9715-0.3766-0.6667-0.00650.3613-0.0688-0.05460.44320.02630.424624.8251-21.9016-5.5679
110.4124-0.05460.1770.2323-0.13470.4644-0.2182-0.1947-0.33750.43310.13560.03220.06511.389-0.01260.4288-0.0495-0.02530.4632-0.00740.39474.126-11.003524.067
121.37350.03450.70911.82670.10161.220.01710.0465-0.08070.1816-0.0860.1005-0.2467-0.0703-0.00080.2664-0.01080.01960.2164-0.02270.188770.22870.450519.6844
130.55430.50740.23221.11380.71251.343-0.01550.11080.0804-0.04560.0610.0932-0.1868-0.07880.00040.210.0070.0260.2427-0.01530.2265.1469-2.01511.1957
141.57441.44170.31911.5216-0.26391.30940.0553-0.07650.23430.0464-0.09770.244-0.2708-0.1179-0.00090.26220.06180.03070.2297-0.0380.229262.57822.741516.2397
150.668-0.0091-0.59610.65680.57161.8196-0.06460.1532-0.1799-0.2420.5253-0.58810.43250.61320.11570.2775-0.0190.04450.4266-0.05940.30280.7532-0.49519.577
160.548-0.15010.28920.49-0.48910.50420.2123-0.55110.12970.6355-0.16580.248-0.2135-0.27450.00490.3755-0.03370.05180.30320.00160.193264.4498-3.2430.3081
170.44090.65370.3121.03640.73130.6501-0.0059-0.58450.0652-0.0185-0.32870.5179-0.1023-0.8003-0.02960.2875-0.01850.08040.5094-0.03930.384345.7862-7.017918.9169
180.23140.1638-0.00490.67780.48680.43150.2239-0.12110.10960.2075-0.07080.24620.1057-0.08620.00230.2419-0.0030.04430.304-0.04410.246452.2849-8.18969.7892
190.15410.29670.88711.22572.09175.7440.5186-1.0302-0.77670.7362-0.65230.1499-0.1671-0.7142-0.71420.5056-0.2971-0.05290.57370.17880.45237.9826-2.734347.1508
200.84551.79220.73183.85461.72941.40130.4489-0.465-0.66031.2965-0.1495-1.15660.7961-0.17430.54130.484-0.2693-0.18410.08060.28270.381424.5485-2.189847.4986
211.70520.87070.57061.4826-0.36631.18370.4153-0.3028-0.14010.6102-0.57520.24990.2269-0.5903-0.0050.3376-0.13220.00980.34030.01560.304918.63223.144547.8262
221.40510.68930.29910.77880.41790.55080.257-0.10680.5104-0.1840.00410.043-0.3054-0.250.00170.3346-0.0486-0.00270.28780.01360.281719.4810.936138.1976
231.17540.95010.77370.970.18371.10940.26230.1448-0.24030.1545-0.0714-0.29790.2406-0.0575-0.00020.2901-0.0399-0.06110.2210.03060.344923.83830.04637.7917
242.46340.9417-0.62632.78660.47091.3276-0.00230.2036-0.64080.0004-0.0035-0.40020.1380.41420.00270.2563-0.00040.030.26830.00280.361344.78917.206738.3886
252.60770.8535-0.10822.8620.25791.9034-0.0133-0.0034-0.313-0.10960.0638-0.15480.03740.1164-0.00020.2154-0.0168-0.00070.21270.01410.235138.795312.881539.1321
260.3769-0.1541-0.04120.5635-0.0540.2819-0.14680.00630.3404-0.1516-0.0749-0.0354-0.488-0.2054-0.00520.2979-0.0294-0.03330.26680.05910.261640.549126.683336.8719
270.3408-0.23510.07580.4876-0.50850.678-0.04390.0735-0.63830.5006-0.110.0020.6757-0.22390.00990.4619-0.0779-0.08940.33930.03810.659811.4959-17.697832.9319
280.6080.05830.37720.47780.1910.27710.04320.3001-0.9472-0.30190.1172-0.02580.6253-0.1198-0.26960.5108-0.1015-0.11640.416-0.160.54768.1824-18.413419.6058
290.0726-0.24470.18421.1794-0.31960.8024-0.84620.10070.5857-0.19380.40010.6288-1.1611-1.11560.04170.60350.1294-0.23230.5983-0.20060.5664-2.1016-11.240813.4535
300.1853-0.05070.12380.41170.23850.3097-0.4176-0.2693-0.2593-0.19630.04930.258-0.1347-0.43840.00010.367-0.0278-0.02290.471-0.11550.40888.5547-11.100719.1924
310.74160.3762-0.65551.39560.09111.1980.02430.1649-0.095-0.379-0.04740.2987-0.0545-0.25140.00010.3145-0.0213-0.09970.2735-0.00640.3476.9036-3.818829.4256
320.24820.0952-0.01780.20250.10650.16-0.04330.63990.0912-0.76010.39970.3558-0.34720.04780.00220.564-0.0392-0.12440.38380.05750.33489.18021.904518.2631
331.0621-0.22330.19710.4812-0.26440.16770.37390.4524-0.39-0.46130.06650.4154-0.2878-0.86320.00230.6057-0.0241-0.03860.4879-0.06810.48846.3151-13.476119.3881
340.2148-0.0337-0.09860.2641-0.10950.19250.01470.0446-0.842-0.26530.20040.3427-0.7108-0.39880.0090.47080.0165-0.06750.4725-0.11170.8078-1.0033-21.413125.3944
351.3405-0.72740.23940.5940.14661.3294-0.20270.7173-0.6253-0.92920.2628-0.5619-0.07780.4706-0.01710.5638-0.05140.1180.4822-0.14850.430621.2126-9.237116.8648
360.30550.29970.0550.33070.1290.34770.09880.34620.296-0.46220.1139-0.1299-0.0488-0.07840.0010.3811-0.0445-0.02210.30880.01520.323119.34231.381326.8568
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 14 through 33 )A14 - 33
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 52 )A34 - 52
3X-RAY DIFFRACTION3chain 'A' and (resid 53 through 69 )A53 - 69
4X-RAY DIFFRACTION4chain 'A' and (resid 70 through 94 )A70 - 94
5X-RAY DIFFRACTION5chain 'A' and (resid 95 through 121 )A95 - 121
6X-RAY DIFFRACTION6chain 'A' and (resid 122 through 155 )A122 - 155
7X-RAY DIFFRACTION7chain 'A' and (resid 156 through 192 )A156 - 192
8X-RAY DIFFRACTION8chain 'A' and (resid 193 through 210 )A193 - 210
9X-RAY DIFFRACTION9chain 'A' and (resid 211 through 228 )A211 - 228
10X-RAY DIFFRACTION10chain 'A' and (resid 229 through 245 )A229 - 245
11X-RAY DIFFRACTION11chain 'B' and (resid -2 through 6 )B-2 - 6
12X-RAY DIFFRACTION12chain 'B' and (resid 7 through 34 )B7 - 34
13X-RAY DIFFRACTION13chain 'B' and (resid 35 through 83 )B35 - 83
14X-RAY DIFFRACTION14chain 'B' and (resid 84 through 112 )B84 - 112
15X-RAY DIFFRACTION15chain 'B' and (resid 113 through 125 )B113 - 125
16X-RAY DIFFRACTION16chain 'B' and (resid 126 through 141 )B126 - 141
17X-RAY DIFFRACTION17chain 'B' and (resid 142 through 160 )B142 - 160
18X-RAY DIFFRACTION18chain 'B' and (resid 161 through 175 )B161 - 175
19X-RAY DIFFRACTION19chain 'C' and (resid 18 through 35 )C18 - 35
20X-RAY DIFFRACTION20chain 'C' and (resid 36 through 52 )C36 - 52
21X-RAY DIFFRACTION21chain 'C' and (resid 53 through 69 )C53 - 69
22X-RAY DIFFRACTION22chain 'C' and (resid 70 through 94 )C70 - 94
23X-RAY DIFFRACTION23chain 'C' and (resid 95 through 121 )C95 - 121
24X-RAY DIFFRACTION24chain 'C' and (resid 122 through 156 )C122 - 156
25X-RAY DIFFRACTION25chain 'C' and (resid 157 through 228 )C157 - 228
26X-RAY DIFFRACTION26chain 'C' and (resid 229 through 245 )C229 - 245
27X-RAY DIFFRACTION27chain 'D' and (resid -1 through 12 )D-1 - 12
28X-RAY DIFFRACTION28chain 'D' and (resid 13 through 25 )D13 - 25
29X-RAY DIFFRACTION29chain 'D' and (resid 26 through 35 )D26 - 35
30X-RAY DIFFRACTION30chain 'D' and (resid 36 through 50 )D36 - 50
31X-RAY DIFFRACTION31chain 'D' and (resid 51 through 83 )D51 - 83
32X-RAY DIFFRACTION32chain 'D' and (resid 84 through 96 )D84 - 96
33X-RAY DIFFRACTION33chain 'D' and (resid 97 through 112 )D97 - 112
34X-RAY DIFFRACTION34chain 'D' and (resid 113 through 125 )D113 - 125
35X-RAY DIFFRACTION35chain 'D' and (resid 126 through 160 )D126 - 160
36X-RAY DIFFRACTION36chain 'D' and (resid 161 through 175 )D161 - 175

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