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- PDB-4h3k: Crystal structure of a ternary complex of human symplekin NTD, hu... -

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Basic information

Entry
Database: PDB / ID: 4h3k
TitleCrystal structure of a ternary complex of human symplekin NTD, human Ssu72 and a RNA polymerase II CTD peptide phosphorylated at Ser-2, Ser-5 and Ser-7
Components
  • HexapeptidePeptide
  • RNA polymerase II subunit A C-terminal domain phosphatase SSU72
  • Symplekin
KeywordsHYDROLASE / Heat repeat / phosphatase / RNA polymerase II
Function / homology
Function and homology information


RNA polymerase II CTD heptapeptide repeat phosphatase activity / nuclear stress granule / Processing of Intronless Pre-mRNAs / mRNA cleavage and polyadenylation specificity factor complex / mRNA 3'-end processing / Transport of Mature mRNA Derived from an Intronless Transcript / RNA Polymerase II Transcription Termination / termination of RNA polymerase II transcription / myosin phosphatase activity / : ...RNA polymerase II CTD heptapeptide repeat phosphatase activity / nuclear stress granule / Processing of Intronless Pre-mRNAs / mRNA cleavage and polyadenylation specificity factor complex / mRNA 3'-end processing / Transport of Mature mRNA Derived from an Intronless Transcript / RNA Polymerase II Transcription Termination / termination of RNA polymerase II transcription / myosin phosphatase activity / : / protein-serine/threonine phosphatase / Processing of Capped Intron-Containing Pre-mRNA / RNA polymerase II transcribes snRNA genes / bicellular tight junction / negative regulation of protein binding / nuclear body / cytoskeleton / cell adhesion / nucleoplasm / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Helix Hairpins - #550 / RNA polymerase II subunit A / Ssu72-like protein / Symplekin/Pta1 / Symplekin C-terminal / Symplekin/Pta1, N-terminal / Symplekin/PTA1 N-terminal / Symplekin tight junction protein C terminal / Leucine-rich Repeat Variant / Helix Hairpins ...Helix Hairpins - #550 / RNA polymerase II subunit A / Ssu72-like protein / Symplekin/Pta1 / Symplekin C-terminal / Symplekin/Pta1, N-terminal / Symplekin/PTA1 N-terminal / Symplekin tight junction protein C terminal / Leucine-rich Repeat Variant / Helix Hairpins / Leucine-rich Repeat Variant / Response regulator / Helix non-globular / Special / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Symplekin / RNA polymerase II subunit A C-terminal domain phosphatase SSU72
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsXiang, K. / Tong, L.
CitationJournal: Genes Dev. / Year: 2012
Title: An unexpected binding mode for a Pol II CTD peptide phosphorylated at Ser7 in the active site of the CTD phosphatase Ssu72.
Authors: Xiang, K. / Manley, J.L. / Tong, L.
History
DepositionSep 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Symplekin
B: RNA polymerase II subunit A C-terminal domain phosphatase SSU72
D: Symplekin
E: RNA polymerase II subunit A C-terminal domain phosphatase SSU72
F: Hexapeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,2216
Polymers130,1275
Non-polymers951
Water2,036113
1
A: Symplekin
B: RNA polymerase II subunit A C-terminal domain phosphatase SSU72
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5013
Polymers64,4062
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-14 kcal/mol
Surface area23710 Å2
MethodPISA
2
D: Symplekin
E: RNA polymerase II subunit A C-terminal domain phosphatase SSU72
F: Hexapeptide


Theoretical massNumber of molelcules
Total (without water)65,7213
Polymers65,7213
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-25 kcal/mol
Surface area22990 Å2
MethodPISA
3
B: RNA polymerase II subunit A C-terminal domain phosphatase SSU72
hetero molecules

A: Symplekin


Theoretical massNumber of molelcules
Total (without water)64,5013
Polymers64,4062
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,y-1/2,-z1
Buried area1970 Å2
ΔGint-21 kcal/mol
Surface area24220 Å2
MethodPISA
4
D: Symplekin

E: RNA polymerase II subunit A C-terminal domain phosphatase SSU72
F: Hexapeptide


Theoretical massNumber of molelcules
Total (without water)65,7213
Polymers65,7213
Non-polymers00
Water362
TypeNameSymmetry operationNumber
crystal symmetry operation2_556-x,y+1/2,-z+11
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-29 kcal/mol
Surface area23500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.583, 97.364, 105.278
Angle α, β, γ (deg.)90.00, 97.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Symplekin


Mass: 39646.957 Da / Num. of mol.: 2 / Fragment: N-terminal domain, UNP residues 30-360
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SYMPK, SPK / Production host: Escherichia coli (E. coli) / References: UniProt: Q92797
#2: Protein RNA polymerase II subunit A C-terminal domain phosphatase SSU72 / / CTD phosphatase SSU72


Mass: 24758.787 Da / Num. of mol.: 2 / Mutation: C12S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SSU72, HSPC182, PNAS-120 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NP77, protein-serine/threonine phosphatase
#3: Protein/peptide Hexapeptide / Peptide


Mass: 1315.022 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O

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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: 2.65 Å3/Da / Density % sol: 53.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.6M ammonium chloride, 27% (w/v) PEG 3350, 10mM Sodium potassium tartrate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 21, 2012
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 91319 / Num. obs: 88854 / % possible obs: 97.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 2→2.108 Å / % possible all: 89

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Processing

Software
NameVersionClassification
CBASSdata collection
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / SU B: 7.617 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23295 4376 5 %RANDOM
Rwork0.19676 ---
all0.19857 86668 --
obs0.19857 83323 96.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.189 Å2
Baniso -1Baniso -2Baniso -3
1-1.7 Å20 Å20.5 Å2
2---1.1 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8129 0 5 113 8247
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0228279
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4611.97511216
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.37651011
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.59524.949396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.4915.0291550
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4971555
X-RAY DIFFRACTIONr_chiral_restr0.1090.21311
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216131
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.8571.55091
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.67928294
X-RAY DIFFRACTIONr_scbond_it2.93633188
X-RAY DIFFRACTIONr_scangle_it4.8514.52922
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.108 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.25 579 -
Rwork0.225 11256 -
obs--88.99 %
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)
10.8519-0.382-0.02230.798-0.06250.31320.02440.00280.08660.00720.0353-0.0253-0.0055-0.0152-0.05970.0108-0.01640.00050.04040.01310.0246-26.010614.1912-11.2862
20.64690.4427-0.22141.80070.62541.083-0.15190.0984-0.0872-0.03130.04770.04640.1221-0.04380.10420.0627-0.02250.03950.0411-0.01280.0275-25.6761-16.7927-12.1075
30.1923-0.15340.13641.7122-0.26970.489-0.03250.00120.0178-0.0225-0.0452-0.13030.00630.02540.07770.0269-0.00110.00110.04990.00920.0182-1.4371-11.661739.9592
41.21210.3919-0.27631.38070.20430.35020.0254-0.06440.1112-0.0574-0.018-0.0685-0.06380.0411-0.00750.0615-0.00460.01190.0325-0.00190.03031.342518.53740.3197
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 340
2X-RAY DIFFRACTION2B6 - 194
3X-RAY DIFFRACTION3D30 - 340
4X-RAY DIFFRACTION4E5 - 194

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