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- PDB-4wx8: Crystal structure of binary complex Gon7-Pcc1 -

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Basic information

Entry
Database: PDB / ID: 4wx8
TitleCrystal structure of binary complex Gon7-Pcc1
Components
  • EKC/KEOPS complex subunit GON7
  • EKC/KEOPS complex subunit PCC1
KeywordsCELL CYCLE / KEOPS / 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: 2.99 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 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)74,2757
Polymers74,2166
Non-polymers591
Water25214
1
D: EKC/KEOPS complex subunit GON7

A: EKC/KEOPS complex subunit PCC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7983
Polymers24,7392
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area2390 Å2
ΔGint-19 kcal/mol
Surface area8430 Å2
MethodPISA
2
B: EKC/KEOPS complex subunit PCC1
E: EKC/KEOPS complex subunit GON7


Theoretical massNumber of molelcules
Total (without water)24,7392
Polymers24,7392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-18 kcal/mol
Surface area8390 Å2
MethodPISA
3
C: EKC/KEOPS complex subunit PCC1
F: EKC/KEOPS complex subunit GON7


Theoretical massNumber of molelcules
Total (without water)24,7392
Polymers24,7392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-16 kcal/mol
Surface area6830 Å2
MethodPISA
4
A: EKC/KEOPS complex subunit PCC1
hetero molecules

D: EKC/KEOPS complex subunit GON7


Theoretical massNumber of molelcules
Total (without water)24,7983
Polymers24,7392
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area2390 Å2
ΔGint-19 kcal/mol
Surface area8430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.100, 102.500, 88.800
Angle α, β, γ (deg.)90.00, 111.80, 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
1114A7 - 90
2114B7 - 90
3114C7 - 90
1124D2 - 113
2124E2 - 113

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.162983, 0.881485, 0.443194), (-0.882217, -0.331321, 0.334544), (0.441735, -0.336468, 0.831661)-73.66135, 53.51404, 45.65115
3given(-0.54824, -0.590229, 0.592505), (0.584933, -0.776969, -0.232751), (0.597734, 0.218972, 0.77121)6.01756, 115.58437, 33.65894
4given(1), (1), (1)
5given(0.150449, -0.878948, -0.452565), (-0.880888, -0.326988, 0.34222), (-0.448777, 0.347173, -0.82345)87.29021, 52.82147, 118.23556

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Components

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


Mass: 10975.087 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: 13763.696 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-ACT / ACETATE ION


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


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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46 %
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 1 / Wavelength: 0.97895 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 2.99→43.53 Å / Num. obs: 13327 / % possible obs: 99.54 % / Redundancy: 3.83 % / Net I/σ(I): 8.08
Reflection shellResolution: 2.992→3.099 Å / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
XDSdata reduction
SHELXDEphasing
RefinementResolution: 2.99→43.53 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.883 / SU B: 42.091 / SU ML: 0.399 / Cross valid method: THROUGHOUT / ESU R: 2.274 / ESU R Free: 0.463 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30816 667 5 %RANDOM
Rwork0.25079 ---
obs0.25377 12660 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.138 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å2-0 Å2-1.51 Å2
2---0.44 Å20 Å2
3---1.57 Å2
Refinement stepCycle: 1 / Resolution: 2.99→43.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3060 0 4 14 3078
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193103
X-RAY DIFFRACTIONr_bond_other_d0.0020.022839
X-RAY DIFFRACTIONr_angle_refined_deg1.4811.9874226
X-RAY DIFFRACTIONr_angle_other_deg0.67836499
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8595412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.63425.965114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.27115443
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.714159
X-RAY DIFFRACTIONr_chiral_restr0.0690.2528
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.0213520
X-RAY DIFFRACTIONr_gen_planes_other0.0160.02614
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_it2.5813.6451682
X-RAY DIFFRACTIONr_mcbond_other2.5663.6421680
X-RAY DIFFRACTIONr_mcangle_it4.1346.1062082
X-RAY DIFFRACTIONr_mcangle_other4.1336.1082083
X-RAY DIFFRACTIONr_scbond_it3.4823.8141421
X-RAY DIFFRACTIONr_scbond_other3.483.8151422
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7466.3332145
X-RAY DIFFRACTIONr_long_range_B_refined5.6088.1193608
X-RAY DIFFRACTIONr_long_range_B_other5.6088.1193608
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
11A979medium positional0.560.5
11B979medium positional0.480.5
11B979medium positional0.530.5
22D804medium positional0.40.5
11A979medium thermal4.275
11B979medium thermal3.485
11C979medium thermal4.25
22D804medium thermal3.495
LS refinement shellResolution: 2.992→3.069 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.473 49 -
Rwork0.4 936 -
obs--96.66 %
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)
12.28930.70050.97362.41551.97243.0657-0.2970.0470.1092-0.1716-0.0240.2458-0.2925-0.32710.3210.35840.06480.13730.42660.0220.128-4.82868.63382.598
21.3993-0.1592-0.832.41240.05212.3232-0.11950.2002-0.158-0.27410.11280.02590.2101-0.67870.00660.386-0.13680.12040.5307-0.03260.0621-8.20843.18866.451
33.92831.2029-0.01822.9877-0.02153.3914-0.00960.6157-0.0175-0.54880.07810.16640.45140.0058-0.06850.588-0.05280.17330.571-0.01870.12928.32553.60442.669
41.4496-1.88262.11032.7631-2.62983.2752-0.15370.31770.3731-0.0564-0.3464-0.7174-0.16420.74290.50010.46210.01570.22890.67740.04580.29722.84468.21168.278
50.41440.13130.16710.05190.00630.3028-0.07330.0713-0.2339-0.12140.0357-0.10130.4580.00740.03761.0349-0.10440.32350.5978-0.03310.2165-0.54834.88175.061
63.9911-2.70182.29733.8519-1.75754.04440.1190.63370.7643-0.2912-0.1369-0.274-0.02550.58210.01780.515-0.07130.18210.46630.07990.294115.23562.17749.324
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 90
2X-RAY DIFFRACTION2B8 - 90
3X-RAY DIFFRACTION3C9 - 88
4X-RAY DIFFRACTION4D3 - 111
5X-RAY DIFFRACTION5E3 - 109
6X-RAY DIFFRACTION6F3 - 94

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