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- PDB-6xkb: Crystal structure of SR-related and CTD-associated factor 4(SCAF4... -

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Entry
Database: PDB / ID: 6xkb
TitleCrystal structure of SR-related and CTD-associated factor 4(SCAF4-CID)with peptide S2,S5p-CTD
Components
  • S2,S5p-CTD peptide
  • SR-related and CTD-associated factor 4
KeywordsPEPTIDE BINDING PROTEIN / SCAF4-CID / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


negative regulation of termination of RNA polymerase II transcription, poly(A)-coupled / microfibril binding / RNA polymerase II C-terminal domain phosphoserine binding / : / 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 ...negative regulation of termination of RNA polymerase II transcription, poly(A)-coupled / microfibril binding / RNA polymerase II C-terminal domain phosphoserine binding / : / 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 / 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 / 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 / RNA polymerase II activity / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / Inhibition of DNA recombination at telomere / mRNA Splicing - Major Pathway / positive regulation of RNA splicing / promoter-specific chromatin binding / TP53 Regulates Transcription of DNA Repair Genes / DNA-templated transcription termination / Transcriptional regulation by small RNAs / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / mRNA processing / kinase binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / 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 / chromosome / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / Estrogen-dependent gene expression / transcription by RNA polymerase II / hydrolase activity / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / ubiquitin protein ligase binding / regulation of DNA-templated transcription / magnesium ion binding / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
SCAF4, RNA recognition motif / CID domain / RPR / CID domain / CID domain profile. / ENTH/VHS / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1 C-terminal repeat ...SCAF4, RNA recognition motif / CID domain / RPR / CID domain / CID domain profile. / ENTH/VHS / 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 / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / 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 / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
SR-related and CTD-associated factor 4 / DNA-directed RNA polymerase II subunit RPB1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsZhou, M.Q. / Dong, A. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Febs Lett. / Year: 2022
Title: Structural basis for the recognition of the S2, S5-phosphorylated RNA polymerase II CTD by the mRNA anti-terminator protein hSCAF4.
Authors: Zhou, M. / Ehsan, F. / Gan, L. / Dong, A. / Li, Y. / Liu, K. / Min, J.
History
DepositionJun 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 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

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Assembly

Deposited unit
A: SR-related and CTD-associated factor 4
B: SR-related and CTD-associated factor 4
C: SR-related and CTD-associated factor 4
D: SR-related and CTD-associated factor 4
E: SR-related and CTD-associated factor 4
F: S2,S5p-CTD peptide
G: S2,S5p-CTD peptide
I: S2,S5p-CTD peptide
J: S2,S5p-CTD peptide
K: S2,S5p-CTD peptide


Theoretical massNumber of molelcules
Total (without water)92,72622
Polymers92,72610
Non-polymers012
Water11,890660
1
A: SR-related and CTD-associated factor 4
G: S2,S5p-CTD peptide


Theoretical massNumber of molelcules
Total (without water)18,5453
Polymers18,5452
Non-polymers01
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-7 kcal/mol
Surface area7770 Å2
MethodPISA
2
B: SR-related and CTD-associated factor 4
F: S2,S5p-CTD peptide


Theoretical massNumber of molelcules
Total (without water)18,5454
Polymers18,5452
Non-polymers02
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-8 kcal/mol
Surface area7880 Å2
MethodPISA
3
C: SR-related and CTD-associated factor 4
I: S2,S5p-CTD peptide


Theoretical massNumber of molelcules
Total (without water)18,5455
Polymers18,5452
Non-polymers03
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-9 kcal/mol
Surface area8160 Å2
MethodPISA
4
D: SR-related and CTD-associated factor 4
J: S2,S5p-CTD peptide


Theoretical massNumber of molelcules
Total (without water)18,5454
Polymers18,5452
Non-polymers02
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-5 kcal/mol
Surface area7560 Å2
MethodPISA
5
E: SR-related and CTD-associated factor 4
K: S2,S5p-CTD peptide


Theoretical massNumber of molelcules
Total (without water)18,5456
Polymers18,5452
Non-polymers04
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-7 kcal/mol
Surface area8020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.718, 46.923, 139.250
Angle α, β, γ (deg.)90.000, 92.300, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
SR-related and CTD-associated factor 4 / CTD-binding SR-like protein RA4 / Splicing factor / arginine/serine-rich 15


Mass: 16020.017 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SCAF4, KIAA1172, SFRS15 / Plasmid: pET28-MHL / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): -V2R-pRARE2 / References: UniProt: O95104
#2: Protein/peptide
S2,S5p-CTD peptide


Mass: 2525.230 Da / Num. of mol.: 5 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P24928*PLUS
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 12 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 660 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.52 Å3/Da / Density % sol: 51.22 % / Mosaicity: 0.313 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 25% PEG 3350, 0.2 M NH4OAc, 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 114559 / % possible obs: 94.5 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.025 / Rrim(I) all: 0.064 / Χ2: 0.814 / Net I/σ(I): 7.6 / Num. measured all: 715061
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.635.80.75656780.8130.3340.8290.41994.8
1.63-1.666.10.71856980.8390.310.7840.42994.4
1.66-1.696.20.61956810.8540.2660.6760.4394.4
1.69-1.726.10.51356390.9010.2220.5610.44793.7
1.72-1.7660.42854530.9240.1870.4680.46790.6
1.76-1.86.10.33448860.9460.1450.3650.47880.7
1.8-1.856.40.30256390.9680.1280.3290.49593.9
1.85-1.96.60.26257730.9760.1090.2840.49596.2
1.9-1.956.60.2158320.9840.0870.2270.52296.5
1.95-2.026.50.16658580.9880.070.1810.57696.7
2.02-2.096.40.12658050.9930.0540.1380.61296.9
2.09-2.176.30.10458510.9950.0450.1130.66196.6
2.17-2.276.20.08858440.9950.0380.0960.75796.6
2.27-2.3960.0757510.9970.030.0770.85395.2
2.39-2.545.70.0653460.9960.0270.0660.9887.9
2.54-2.746.40.05558990.9970.0240.061.04596.6
2.74-3.016.70.05159520.9980.0210.0551.2798.3
3.01-3.456.50.04460000.9980.0190.0481.6198.2
3.45-4.346.10.03759850.9990.0160.0411.79997.1
4.34-5060.03459890.9990.0150.0371.7294.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-3000data reduction
HKL-3000data scaling
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D9I

3d9i


Resolution: 1.6→44.5 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.802 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2104 2347 2 %RANDOM
Rwork0.1834 ---
obs0.184 112199 94.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.54 Å2 / Biso mean: 23.828 Å2 / Biso min: 11.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å2-0.79 Å2
2--1.45 Å2-0 Å2
3----1.16 Å2
Refinement stepCycle: final / Resolution: 1.6→44.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5965 0 12 666 6643
Biso mean--26.43 34.42 -
Num. residues----757
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0136191
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175789
X-RAY DIFFRACTIONr_angle_refined_deg1.4521.6548430
X-RAY DIFFRACTIONr_angle_other_deg1.4111.57613438
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2625765
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.93522.369249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.626151035
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3981525
X-RAY DIFFRACTIONr_chiral_restr0.0810.2843
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026680
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021231
LS refinement shellResolution: 1.6→1.64 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.294 149 -
Rwork0.265 8180 -
obs--93.67 %

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