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- PDB-2c35: Subunits Rpb4 and Rpb7 of human RNA polymerase II -

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Basic information

Entry
Database: PDB / ID: 2c35
TitleSubunits Rpb4 and Rpb7 of human RNA polymerase II
Components
  • DNA-DIRECTED RNA POLYMERASE II 16 KDA POLYPEPTIDE
  • DNA-DIRECTED RNA POLYMERASE II 19 KDA POLYPEPTIDE
KeywordsTRANSFERASE / TRANSCRIPTION / RNA POLYMERASE II / POLYMERASE / NUCLEOTIDYLTRANSFERASE
Function / homology
Function and homology information


Abortive elongation of HIV-1 transcript in the absence of Tat / MicroRNA (miRNA) biogenesis / FGFR2 alternative splicing / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM / 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 ...Abortive elongation of HIV-1 transcript in the absence of Tat / MicroRNA (miRNA) biogenesis / FGFR2 alternative splicing / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM / 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 / 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 / mRNA Splicing - Minor Pathway / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / Processing of Capped Intron-Containing Pre-mRNA / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RNA polymerase II transcribes snRNA genes / Tat-mediated elongation of the HIV-1 transcript / positive regulation of translational initiation / 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 / translation initiation factor binding / RNA Polymerase II Pre-transcription Events / Inhibition of DNA recombination at telomere / mRNA Splicing - Major Pathway / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / Transcriptional regulation by small RNAs / P-body / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / single-stranded DNA binding / Estrogen-dependent gene expression / transcription by RNA polymerase II / single-stranded RNA binding / nuclear speck / nucleotide binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
RNA Polymerase II, Rpb4 subunit / RNA polymerase Rpb7-like, N-terminal domain / Growth Hormone; Chain: A; / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / Rpb4/RPC9 superfamily / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / RNA polymerase subunit Rpb7-like ...RNA Polymerase II, Rpb4 subunit / RNA polymerase Rpb7-like, N-terminal domain / Growth Hormone; Chain: A; / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / Rpb4/RPC9 superfamily / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / RNA polymerase subunit Rpb7-like / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / HRDC-like superfamily / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / Nucleic acid-binding proteins / Dna Ligase; domain 1 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Up-down Bundle / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerase II subunit RPB7
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMeka, H. / Werner, F. / Cordell, S.C. / Onesti, S. / Brick, P.
CitationJournal: Nucleic Acids Res. / Year: 2005
Title: Crystal Structure and RNA Binding of the Rpb4/Rpb7 Subunits of Human RNA Polymerase II.
Authors: Meka, H. / Werner, F. / Cordell, S.C. / Onesti, S. / Brick, P.
History
DepositionOct 4, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2005Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2013Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Refinement description / Version format compliance
Revision 1.2Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.temp
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA", "DA", "FA", "HA" IN EACH CHAIN ON ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA", "DA", "FA", "HA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-DIRECTED RNA POLYMERASE II 16 KDA POLYPEPTIDE
B: DNA-DIRECTED RNA POLYMERASE II 19 KDA POLYPEPTIDE
C: DNA-DIRECTED RNA POLYMERASE II 16 KDA POLYPEPTIDE
D: DNA-DIRECTED RNA POLYMERASE II 19 KDA POLYPEPTIDE
E: DNA-DIRECTED RNA POLYMERASE II 16 KDA POLYPEPTIDE
F: DNA-DIRECTED RNA POLYMERASE II 19 KDA POLYPEPTIDE
G: DNA-DIRECTED RNA POLYMERASE II 16 KDA POLYPEPTIDE
H: DNA-DIRECTED RNA POLYMERASE II 19 KDA POLYPEPTIDE


Theoretical massNumber of molelcules
Total (without water)146,5348
Polymers146,5348
Non-polymers00
Water97354
1
A: DNA-DIRECTED RNA POLYMERASE II 16 KDA POLYPEPTIDE
B: DNA-DIRECTED RNA POLYMERASE II 19 KDA POLYPEPTIDE


Theoretical massNumber of molelcules
Total (without water)36,6342
Polymers36,6342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-20.9 kcal/mol
Surface area14720 Å2
MethodPISA
2
C: DNA-DIRECTED RNA POLYMERASE II 16 KDA POLYPEPTIDE
D: DNA-DIRECTED RNA POLYMERASE II 19 KDA POLYPEPTIDE


Theoretical massNumber of molelcules
Total (without water)36,6342
Polymers36,6342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-20.8 kcal/mol
Surface area14750 Å2
MethodPISA
3
E: DNA-DIRECTED RNA POLYMERASE II 16 KDA POLYPEPTIDE
F: DNA-DIRECTED RNA POLYMERASE II 19 KDA POLYPEPTIDE


Theoretical massNumber of molelcules
Total (without water)36,6342
Polymers36,6342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-18.8 kcal/mol
Surface area14570 Å2
MethodPISA
4
G: DNA-DIRECTED RNA POLYMERASE II 16 KDA POLYPEPTIDE
H: DNA-DIRECTED RNA POLYMERASE II 19 KDA POLYPEPTIDE


Theoretical massNumber of molelcules
Total (without water)36,6342
Polymers36,6342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-18.8 kcal/mol
Surface area14560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.690, 83.190, 99.310
Angle α, β, γ (deg.)85.53, 81.80, 81.77
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
DNA-DIRECTED RNA POLYMERASE II 16 KDA POLYPEPTIDE / HUMAN RPB4


Mass: 17319.320 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-2TK (AMERSHAM) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O15514, DNA-directed RNA polymerase
#2: Protein
DNA-DIRECTED RNA POLYMERASE II 19 KDA POLYPEPTIDE / HUMAN RPB7


Mass: 19314.283 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-2TK / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62487
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.59 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.4
Details: VAPOUR DIFFUSION AT 18C USING EQUAL VOLUMES OF PROTEIN AT 15MG/ML IN 20MM PIPES PH 6.8, 100MM NACL, 15% GLYCEROL, PRECIPITANT CONTAINING 100MM PIPES PH 7.4, 25% PEG (MW4000), 15% GLYCEROL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 3, 2003 / Details: OSMIC
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→43.3 Å / Num. obs: 37416 / % possible obs: 95.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 38.6 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.5
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.4 / % possible all: 93.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Y14

1y14


Resolution: 2.7→43.26 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 981491.52 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: GROUP 1 CHAINS A,B,S RESTRAINED TO CHAINS C,D,T GROUP 2 CHAINS E,F,U RESTRAINED TO CHAINS G,H,V THE INITIAL 10 RESIDUES OF CHAINS A, C, E, G ARE DERIVED FROM THE EXPRESSION VECTOR. THEY ARE ...Details: GROUP 1 CHAINS A,B,S RESTRAINED TO CHAINS C,D,T GROUP 2 CHAINS E,F,U RESTRAINED TO CHAINS G,H,V THE INITIAL 10 RESIDUES OF CHAINS A, C, E, G ARE DERIVED FROM THE EXPRESSION VECTOR. THEY ARE DISORDERED IN THE CRYSTAL STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1860 5 %RANDOM
Rwork0.23 ---
obs0.23 37414 95.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.8003 Å2 / ksol: 0.359069 e/Å3
Displacement parametersBiso mean: 46 Å2
Baniso -1Baniso -2Baniso -3
1-19.25 Å214.24 Å2-7.84 Å2
2---6.86 Å2-7.75 Å2
3----12.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.61 Å0.56 Å
Refinement stepCycle: LAST / Resolution: 2.7→43.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9236 0 0 54 9290
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.231.5
X-RAY DIFFRACTIONc_mcangle_it2.152
X-RAY DIFFRACTIONc_scbond_it8.72
X-RAY DIFFRACTIONc_scangle_it10.982.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.368 296 4.8 %
Rwork0.342 5890 -
obs--93.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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