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- PDB-4wxa: Crystal structure of binary complex Gon7-Pcc1 -

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Basic information

Entry
Database: PDB / ID: 4wxa
TitleCrystal structure of binary complex Gon7-Pcc1
Components
  • EKC/KEOPS complex subunit GON7
  • EKC/KEOPS complex subunit PCC1
KeywordsTRANSCRIPTION / KEOPS / binary complex / Gon7-Pcc1 / tRNA t6A
Function / homology
Function and homology information


cellular response to pheromone / tRNA threonylcarbamoyladenosine metabolic process / EKC/KEOPS complex / tRNA threonylcarbamoyladenosine modification / cell wall mannoprotein biosynthetic process / telomere maintenance via recombination / telomere maintenance / maintenance of translational fidelity / chromatin DNA binding / molecular adaptor activity ...cellular response to pheromone / tRNA threonylcarbamoyladenosine metabolic process / EKC/KEOPS complex / tRNA threonylcarbamoyladenosine modification / cell wall mannoprotein biosynthetic process / telomere maintenance via recombination / telomere maintenance / maintenance of translational fidelity / chromatin DNA binding / molecular adaptor activity / chromosome, telomeric region / chromatin / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
EKC/KEOPS complex, subunit Gon7 / Gon7 family / CTAG/Pcc1 family / Transcription factor Pcc1 / Alpha-D-phosphohexomutase, C-terminal domain / TATA-Binding Protein / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / EKC/KEOPS complex subunit GON7 / EKC/KEOPS complex subunit PCC1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.44 Å
AuthorsZhang, W. / van Tilbeurgh, H.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Crystal structures of the Gon7/Pcc1 and Bud32/Cgi121 complexes provide a model for the complete yeast KEOPS complex.
Authors: Zhang, W. / Collinet, B. / Graille, M. / Daugeron, M.C. / Lazar, N. / Libri, D. / Durand, D. / van Tilbeurgh, H.
History
DepositionNov 13, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Feb 19, 2025Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_struct_assembly_gen / pdbx_struct_oper_list

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EKC/KEOPS complex subunit PCC1
B: EKC/KEOPS complex subunit PCC1
C: EKC/KEOPS complex subunit PCC1
D: EKC/KEOPS complex subunit GON7
E: EKC/KEOPS complex subunit GON7
F: EKC/KEOPS complex subunit GON7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5238
Polymers73,3726
Non-polymers1512
Water25214
1
A: EKC/KEOPS complex subunit PCC1
hetero molecules

D: EKC/KEOPS complex subunit GON7


Theoretical massNumber of molelcules
Total (without water)24,6094
Polymers24,4572
Non-polymers1512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_859-x+3,y,-z+41
2
D: EKC/KEOPS complex subunit GON7


Theoretical massNumber of molelcules
Total (without water)13,6231
Polymers13,6231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: EKC/KEOPS complex subunit PCC1
E: EKC/KEOPS complex subunit GON7


Theoretical massNumber of molelcules
Total (without water)24,4572
Polymers24,4572
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: EKC/KEOPS complex subunit PCC1
F: EKC/KEOPS complex subunit GON7


Theoretical massNumber of molelcules
Total (without water)24,4572
Polymers24,4572
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.730, 104.390, 89.890
Angle α, β, γ (deg.)90.00, 111.55, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
12D
22E

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 88
2114B1 - 88
3114C1 - 88
1124D1 - 112
2124E1 - 112

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.163583, 0.875802, 0.454106), (-0.87712, -0.339808, 0.339397), (0.451554, -0.342786, 0.82377)-11.33127, -1.39042, 22.14339
3given(-0.528365, -0.59694, 0.603733), (0.589496, -0.769683, -0.245118), (0.611004, 0.226387, 0.758567)-1.96337, 17.53037, 36.45188

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Components

#1: Protein EKC/KEOPS complex subunit PCC1 / Polarized growth chromatin-associated controller 1


Mass: 10834.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: PCC1, YKR095W-A
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q3E833
#2: Protein EKC/KEOPS complex subunit GON7 / Low-dye-binding protein 6 / Polarized growth chromatin-associated controller 2


Mass: 13623.011 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: GON7, LDB6, PCC2, YJL184W, J0420
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P46984
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Sodium Acetate pH 6.5, 20% PEG1500, 20% Glycerol, 3% Methanol
PH range: 6.0 - 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.44→44.28 Å / Num. all: 94329 / Num. obs: 25516 / % possible obs: 99.11 % / Redundancy: 3.69 % / Net I/σ(I): 14.69
Reflection shellResolution: 2.443→2.53 Å / % possible all: 94.59

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
XDSdata reduction
XSCALEdata scaling
RefinementResolution: 2.44→44.28 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.924 / SU B: 21.586 / SU ML: 0.226 / Cross valid method: THROUGHOUT / ESU R: 0.296 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26991 1276 5 %RANDOM
Rwork0.22452 ---
obs0.22677 24239 99.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.221 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å2-1.4 Å2
2--2.28 Å2-0 Å2
3----0.79 Å2
Refinement stepCycle: 1 / Resolution: 2.44→44.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3180 0 10 14 3204
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193231
X-RAY DIFFRACTIONr_bond_other_d0.0020.023066
X-RAY DIFFRACTIONr_angle_refined_deg1.7111.9834389
X-RAY DIFFRACTIONr_angle_other_deg0.86537049
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.25423
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.37926.228114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.28915530
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.14158
X-RAY DIFFRACTIONr_chiral_restr0.0860.2549
X-RAY DIFFRACTIONr_gen_planes_refined0.020.0213607
X-RAY DIFFRACTIONr_gen_planes_other0.0170.02629
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_it3.4993.7971720
X-RAY DIFFRACTIONr_mcbond_other3.4553.7871718
X-RAY DIFFRACTIONr_mcangle_it5.1826.3622133
X-RAY DIFFRACTIONr_mcangle_other5.1816.372134
X-RAY DIFFRACTIONr_scbond_it4.4094.1391511
X-RAY DIFFRACTIONr_scbond_other4.4094.141512
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.276.8222257
X-RAY DIFFRACTIONr_long_range_B_refined7.9138.4553444
X-RAY DIFFRACTIONr_long_range_B_other7.9148.4573445
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1075medium positional0.320.5
11B1075medium positional0.350.5
11C1075medium positional0.320.5
22E932medium positional0.30.5
11A1075medium thermal6.215
11B1075medium thermal3.95
11C1075medium thermal7.475
22E932medium thermal4.185
LS refinement shellResolution: 2.443→2.506 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.513 87 -
Rwork0.436 1649 -
obs--92.64 %
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)
11.59020.06970.80463.35872.36056.2559-0.11990.02630.2406-0.0246-0.00720.193-0.1797-0.47360.12710.21710.02220.13030.05580.02590.154243.29717.716167.521
22.18570.5453-0.26622.5515-2.39475.2217-0.23650.22-0.132-0.42140.14540.12830.5511-0.65540.09120.4695-0.15990.13910.1533-0.06290.140640.098-8.568151.416
36.90680.69761.54252.91430.34614.8045-0.35450.83230.0823-0.51770.2127-0.03210.4028-0.09020.14170.6397-0.14570.20790.31140.01140.08657.1472.243127.977
40.3560.58230.59382.8829-0.59223.9298-0.16220.18020.0041-0.6736-0.0452-0.50790.35930.99180.20740.56820.10640.23680.40730.03110.250671.52416.866152.73
52.73380.98410.84641.3521-0.31560.688-0.0471-0.2062-0.3644-0.4949-0.184-0.54680.39890.00310.23110.87030.02390.38610.09590.01650.469347.408-18.051161.335
66.6166-1.02473.59542.4897-0.81148.42-0.26880.32030.8578-0.38860.04340.03750.0134-0.04280.22540.5055-0.090.09050.0980.05050.198260.42212.116133.936
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 90
2X-RAY DIFFRACTION2B7 - 90
3X-RAY DIFFRACTION3C8 - 85
4X-RAY DIFFRACTION4D2 - 112
5X-RAY DIFFRACTION5E2 - 113
6X-RAY DIFFRACTION6F2 - 93

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