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- PDB-2ght: CTD-specific phosphatase Scp1 in complex with peptide from C-term... -

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Basic information

Entry
Database: PDB / ID: 2ght
TitleCTD-specific phosphatase Scp1 in complex with peptide from C-terminal domain of RNA polymerase II
Components
  • Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1
  • DNA-directed RNA polymerase II largest subunit
KeywordsHYDROLASE / protein-peptide complex / HAD superfamily
Function / homology
Function and homology information


RNA polymerase II CTD heptapeptide repeat phosphatase activity / microfibril binding / Abortive elongation of HIV-1 transcript in the absence of Tat / FGFR2 alternative splicing / MicroRNA (miRNA) biogenesis / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM / myosin phosphatase activity / negative regulation of G1/S transition of mitotic cell cycle / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection ...RNA polymerase II CTD heptapeptide repeat phosphatase activity / microfibril binding / Abortive elongation of HIV-1 transcript in the absence of Tat / FGFR2 alternative splicing / MicroRNA (miRNA) biogenesis / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM / myosin phosphatase activity / negative regulation of G1/S transition of mitotic cell cycle / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / protein-serine/threonine phosphatase / mRNA Splicing - Minor Pathway / PIWI-interacting RNA (piRNA) biogenesis / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / Processing of Capped Intron-Containing Pre-mRNA / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / RNA polymerase II activity / RNA polymerase II transcribes snRNA genes / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / negative regulation of neuron differentiation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / RNA polymerase II, core complex / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / Inhibition of DNA recombination at telomere / mRNA Splicing - Major Pathway / protein dephosphorylation / positive regulation of RNA splicing / negative regulation of protein phosphorylation / promoter-specific chromatin binding / DNA-templated transcription termination / TP53 Regulates Transcription of DNA Repair Genes / Transcriptional regulation by small RNAs / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / kinase binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / negative regulation of neurogenesis / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / chromosome / Estrogen-dependent gene expression / transcription by RNA polymerase II / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / ubiquitin protein ligase binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular exosome / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Dullard phosphatase domain, eukaryotic / CTD small RNA polymerase II polypeptide A phosphatase-like / FCP1 homology domain / NLI interacting factor-like phosphatase / FCP1 homology domain profile. / catalytic domain of ctd-like phosphatases / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1 C-terminal repeat ...Dullard phosphatase domain, eukaryotic / CTD small RNA polymerase II polypeptide A phosphatase-like / FCP1 homology domain / NLI interacting factor-like phosphatase / FCP1 homology domain profile. / catalytic domain of ctd-like phosphatases / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1 C-terminal repeat / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 5 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA-directed RNA polymerase II subunit RPB1 / Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsZhang, Y. / Noel, J.P.
CitationJournal: Mol.Cell / Year: 2006
Title: Determinants for dephosphorylation of the RNA polymerase II C-terminal domain by Scp1.
Authors: Zhang, Y. / Kim, Y. / Genoud, N. / Gao, J. / Kelly, J.W. / Pfaff, S.L. / Gill, G.N. / Dixon, J.E. / Noel, J.P.
History
DepositionMar 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1
B: Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1
C: DNA-directed RNA polymerase II largest subunit
D: DNA-directed RNA polymerase II largest subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6126
Polymers43,5634
Non-polymers492
Water4,414245
1
A: Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1
C: DNA-directed RNA polymerase II largest subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8063
Polymers21,7822
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-21 kcal/mol
Surface area9160 Å2
MethodPISA
2
B: Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1
D: DNA-directed RNA polymerase II largest subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8063
Polymers21,7822
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-21 kcal/mol
Surface area9050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.916, 78.787, 62.948
Angle α, β, γ (deg.)90.00, 112.08, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1 / Nuclear LIM interactor-interacting factor 3 / NLI-interacting factor 3 / NLI-IF


Mass: 20876.754 Da / Num. of mol.: 2 / Mutation: D96N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTDSP1 / Plasmid: pet28 derivative / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9GZU7, protein-serine/threonine phosphatase
#2: Protein/peptide DNA-directed RNA polymerase II largest subunit / RPB1


Mass: 904.813 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P24928, DNA-directed RNA polymerase
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 3.25 Å3/Da / Density % sol: 62.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: (1) 0.5M Ammonium sulfate, 0.2M Lithium sulfate, 100mM HEPES 7.5 (2) 2M sodium tartrate, 100mM Tris pH 8.5, pH 7.5 - 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 3, 2005 / Details: mirror
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→39.2 Å / Num. obs: 50244 / % possible obs: 90.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Rsym value: 0.04 / Net I/σ(I): 14.5
Reflection shellResolution: 1.8→1.9 Å / Mean I/σ(I) obs: 3 / Num. unique all: 7853 / Rsym value: 0.311 / % possible all: 77.4

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Processing

Software
NameVersionClassification
ADSCdata collection
XDSdata reduction
AMoREphasing
CNS1.1refinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GHQ

2ghq


Resolution: 1.8→39.2 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.232 2513 -random
Rwork0.216 ---
all0.243 52830 --
obs0.242 50243 95.1 %-
Displacement parametersBiso mean: 0.105 Å2
Baniso -1Baniso -2Baniso -3
1-3.344 Å20 Å2-5.27 Å2
2---4.047 Å20 Å2
3---0.704 Å2
Refinement stepCycle: LAST / Resolution: 1.8→39.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3027 0 2 245 3274
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0108
X-RAY DIFFRACTIONc_angle_deg1.4
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.018
RfactorNum. reflection% reflection
Rfree0.359 397 -
Rwork0.327 --
obs-7938 90.6 %

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