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- PDB-1j2x: Crystal structure of RAP74 C-terminal domain complexed with FCP1 ... -

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Basic information

Entry
Database: PDB / ID: 1j2x
TitleCrystal structure of RAP74 C-terminal domain complexed with FCP1 C-terminal peptide
Components
  • RNA polymerase II CTD phosphatase
  • Transcription initiation factor IIF, alpha subunit
KeywordsTRANSCRIPTION / GENERAL TRANSCRIPTION FACTOR / RAP74 / RAP30 / TFIIF / RNA POLYMERASE II / WINGED-HELIX DOMAIN / FCP1 / CTD / phosphatase
Function / homology
Function and homology information


RNA polymerase II CTD heptapeptide repeat phosphatase activity / negative regulation of cell growth involved in cardiac muscle cell development / phosphatase activator activity / TFIIF-class transcription factor complex binding / transcription factor TFIIF complex / exit from mitosis / Tat protein binding / host-mediated activation of viral transcription / RNA polymerase II general transcription initiation factor binding / Abortive elongation of HIV-1 transcript in the absence of Tat ...RNA polymerase II CTD heptapeptide repeat phosphatase activity / negative regulation of cell growth involved in cardiac muscle cell development / phosphatase activator activity / TFIIF-class transcription factor complex binding / transcription factor TFIIF complex / exit from mitosis / Tat protein binding / host-mediated activation of viral transcription / RNA polymerase II general transcription initiation factor binding / Abortive elongation of HIV-1 transcript in the absence of Tat / FGFR2 alternative splicing / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / protein-serine/threonine phosphatase / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / spindle midzone / 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 / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / phosphoprotein phosphatase activity / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / RNA polymerase II transcribes snRNA genes / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / protein dephosphorylation / Formation of HIV elongation complex in the absence of HIV Tat / negative regulation of protein binding / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / mRNA Splicing - Major Pathway / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / promoter-specific chromatin binding / positive regulation of transcription elongation by RNA polymerase II / response to virus / spindle / spindle pole / cell junction / midbody / protein phosphatase binding / Estrogen-dependent gene expression / transcription by RNA polymerase II / protein domain specific binding / cell division / intracellular membrane-bounded organelle / centrosome / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
FCP1-like phosphatase, C-terminal / FCP1, C-terminal / FCP1-like phosphatase, phosphatase domain / CTD phosphatase Fcp1 / FCP1 homology domain / NLI interacting factor-like phosphatase / FCP1 homology domain profile. / catalytic domain of ctd-like phosphatases / Transcription initiation factor IIF, alpha subunit / Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) ...FCP1-like phosphatase, C-terminal / FCP1, C-terminal / FCP1-like phosphatase, phosphatase domain / CTD phosphatase Fcp1 / FCP1 homology domain / NLI interacting factor-like phosphatase / FCP1 homology domain profile. / catalytic domain of ctd-like phosphatases / Transcription initiation factor IIF, alpha subunit / Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) / Transcription Factor IIF, Rap30/Rap74, interaction / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / HAD superfamily / HAD-like superfamily / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
General transcription factor IIF subunit 1 / RNA polymerase II subunit A C-terminal domain phosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKamada, K. / Roeder, R.G. / Burley, S.K.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Molecular mechanism of recruitment of TFIIF- associating RNA polymerase C-terminal domain phosphatase (FCP1) by transcription factor IIF
Authors: Kamada, K. / Roeder, R.G. / Burley, S.K.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Crystal structure of the C-terminal domain of the RAP74 subunit of human transcription factor IIF
Authors: Kamada, K. / De Angelis, J. / Roeder, R.G. / Burley, S.K.
History
DepositionJan 15, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Transcription initiation factor IIF, alpha subunit
B: RNA polymerase II CTD phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6145
Polymers10,3562
Non-polymers2583
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-54 kcal/mol
Surface area5950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.605, 30.446, 47.379
Angle α, β, γ (deg.)90.00, 106.38, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Transcription initiation factor IIF, alpha subunit / RAP74 Subunit of Transcription Factor IIF / TFIIF


Mass: 8374.801 Da / Num. of mol.: 1 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAP74 / Plasmid: PGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): UT5600 / References: UniProt: P35269
#2: Protein/peptide RNA polymerase II CTD phosphatase / TFIIF-associating CTD phosphatase / FCP1


Mass: 1981.183 Da / Num. of mol.: 1 / Fragment: C-terminal peptide / Source method: obtained synthetically / Details: chemical synthesis / References: UniProt: Q9Y5B0
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 1.9 Å3/Da / Density % sol: 34.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEGMME 550, zinc sulfate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
2100 mMMES1reservoirpH6.5
310 mMzinc sulfate heptahydrate1reservoir
425 %(v/v)PEG5501reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.97899 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 18, 2001 / Details: flat cylindrically bent mirror
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97899 Å / Relative weight: 1
ReflectionResolution: 2→22.73 Å / Num. all: 5657 / Num. obs: 5657 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 11 Å2 / Limit h max: 28 / Limit h min: -29 / Limit k max: 15 / Limit k min: -29 / Limit l max: 23 / Limit l min: 0 / Observed criterion F max: 791649.05 / Observed criterion F min: 4.9 / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 18.1
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.164 / Mean I/σ(I) obs: 5.3 / Num. unique all: 271 / Rsym value: 0.164 / % possible all: 97.8
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 30 Å / Num. measured all: 29692

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Processing

Software
NameVersionClassificationNB
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1I27

1i27


Resolution: 2→22.73 Å / Rfactor Rfree error: 0.013 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 403 7.2 %RANDOM
Rwork0.203 ---
all0.209 5672 --
obs0.207 5603 98.8 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 36.4994 Å2 / ksol: 0.378793 e/Å3
Displacement parametersBiso max: 74.28 Å2 / Biso mean: 25.29 Å2 / Biso min: 7.16 Å2
Baniso -1Baniso -2Baniso -3
1-2.63 Å20 Å21.14 Å2
2---0.11 Å20 Å2
3----2.52 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.09 Å
Luzzati d res high-2
Refinement stepCycle: LAST / Resolution: 2→22.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms707 0 11 56 774
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1
X-RAY DIFFRACTIONx_torsion_deg18.4
X-RAY DIFFRACTIONx_torsion_impr_deg0.66
X-RAY DIFFRACTIONx_mcbond_it2.0342
X-RAY DIFFRACTIONx_mcangle_it3.0612.5
X-RAY DIFFRACTIONx_scbond_it3.2892.5
X-RAY DIFFRACTIONx_scangle_it4.8863
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2-2.090.203466.40.2056440.0371569096.4
2.09-2.20.218497.10.2166340.03169368398.6
2.2-2.340.2154970.2156410.03170169098.4
2.34-2.520.222436.20.2226470.03469669099
2.52-2.770.175598.20.1756540.02372171398.9
2.77-3.170.208436.20.2086450.03269468899.1
3.17-3.990.206608.40.2046480.02771370899.3
3.99-22.730.197547.20.1986870.02774674199.3
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 22.7 Å / % reflection Rfree: 7 % / Rfactor Rfree: 0.255 / Rfactor Rwork: 0.204
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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