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- PDB-4h3h: Crystal structure of a ternary complex of human symplekin NTD, hu... -

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Basic information

Entry
Database: PDB / ID: 4h3h
TitleCrystal structure of a ternary complex of human symplekin NTD, human Ssu72 and a RNA poymerase II CTD peptide phosphorylated at SER-7
Components
  • Pol II CTD peptide
  • 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 / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / Processing of Intronless Pre-mRNAs / mRNA cleavage and polyadenylation specificity factor complex / nuclear stress granule / mRNA 3'-end processing / Transport of Mature mRNA Derived from an Intronless Transcript / RNA Polymerase II Transcription Termination / termination of RNA polymerase II transcription / histone H2AXS140 phosphatase activity ...RNA polymerase II CTD heptapeptide repeat phosphatase activity / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / Processing of Intronless Pre-mRNAs / mRNA cleavage and polyadenylation specificity factor complex / nuclear stress granule / mRNA 3'-end processing / Transport of Mature mRNA Derived from an Intronless Transcript / RNA Polymerase II Transcription Termination / termination of RNA polymerase II transcription / histone H2AXS140 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MAP kinase serine/threonine phosphatase activity / calmodulin-dependent protein phosphatase activity / 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 / mRNA processing / cytoskeleton / cell adhesion / nuclear body / 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 / Helix Hairpins / Leucine-rich Repeat Variant ...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 / Helix Hairpins / Leucine-rich Repeat Variant / 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: 2.2 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
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: Pol II CTD peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,0066
Polymers129,9115
Non-polymers951
Water1,13563
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 area2420 Å2
ΔGint-14 kcal/mol
Surface area23890 Å2
MethodPISA
2
D: Symplekin
E: RNA polymerase II subunit A C-terminal domain phosphatase SSU72
F: Pol II CTD peptide


Theoretical massNumber of molelcules
Total (without water)65,5053
Polymers65,5053
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-19 kcal/mol
Surface area23250 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 area1920 Å2
ΔGint-22 kcal/mol
Surface area24380 Å2
MethodPISA
4
D: Symplekin

E: RNA polymerase II subunit A C-terminal domain phosphatase SSU72
F: Pol II CTD peptide


Theoretical massNumber of molelcules
Total (without water)65,5053
Polymers65,5053
Non-polymers00
Water362
TypeNameSymmetry operationNumber
crystal symmetry operation2_556-x,y+1/2,-z+11
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-25 kcal/mol
Surface area23690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.819, 97.742, 104.603
Angle α, β, γ (deg.)90.00, 98.63, 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 Pol II CTD peptide


Mass: 1099.042 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 63 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.78 %
Crystal growTemperature: 293 K / pH: 8.5
Details: 1.6M ammonium chloride, 27% (w/v) PEG 3350, 10mM Sodium potassium tartrate,, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 24, 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: 2.2→50 Å / Num. obs: 67207 / % possible obs: 99.9 % / Observed criterion σ(I): -3
Reflection shellResolution: 2.2→2.32 Å / % possible all: 99

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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: 2.2→50 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.934 / SU B: 10.941 / SU ML: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.228 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.227 3400 5.1 %RANDOM
Rwork0.198 ---
obs0.199 63783 99.7 %-
all-63949 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.43 Å2
Baniso -1Baniso -2Baniso -3
1-1.56 Å20 Å20.89 Å2
2---1.28 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8140 0 5 63 8208
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0228279
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5781.97311213
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.70751012
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.64224.924394
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.28515.011548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3131555
X-RAY DIFFRACTIONr_chiral_restr0.1140.21312
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216135
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_it0.7941.55097
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.55728304
X-RAY DIFFRACTIONr_scbond_it2.95333182
X-RAY DIFFRACTIONr_scangle_it4.8754.52909
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.32 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.274 439 -
Rwork0.227 9226 -
obs--99.06 %
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)
12.3849-0.45120.28050.8935-0.3210.58350.06070.06820.1696-0.0376-0.0123-0.0074-0.0521-0.0262-0.04840.0269-0.0110.01440.0395-0.00510.0312-25.836514.3005-11.476
21.56090.8931-0.20054.07870.68451.8075-0.12790.099-0.2246-0.2310.05150.12250.2631-0.10660.07630.0672-0.02490.00560.06230.00290.0558-25.5547-16.8207-12.2172
30.8577-0.36490.17142.3383-0.1141.4616-0.0776-0.02690.0586-0.01950.0038-0.19-0.01550.22220.07390.0432-0.02990.00970.0673-0.00120.0244-1.6694-11.770639.9043
42.86491.364-0.08613.3787-0.21791.0881-0.0162-0.03290.240.0299-0.0674-0.1048-0.11140.09730.08350.09490.01-0.00590.04040.0040.04470.999518.68540.1714
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 DIFFRACTION4E3 - 194

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