[English] 日本語
Yorodumi
- PDB-3d9k: Snapshots of the RNA processing factor SCAF8 bound to different p... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3d9k
TitleSnapshots of the RNA processing factor SCAF8 bound to different phosphorylated forms of the Carboxy-Terminal Domain of RNA-Polymerase II
Components
  • CTD-PEPTIDE
  • RNA-binding protein 16
KeywordsTRANSCRIPTION / SCAF8 / RNA POLYMERASE II CTD INTERACTING DOMAIN / ARM REPEATS / PHOSPHO-CTD / Phosphoprotein / RNA-binding
Function / homology
Function and homology information


negative regulation of termination of RNA polymerase II transcription, poly(A)-coupled / RNA polymerase core enzyme binding / microfibril binding / RNA polymerase II C-terminal domain phosphoserine binding / mRNA cleavage factor complex / Abortive elongation of HIV-1 transcript in the absence of Tat / positive regulation of DNA-templated transcription, elongation / MicroRNA (miRNA) biogenesis / FGFR2 alternative splicing / Viral Messenger RNA Synthesis ...negative regulation of termination of RNA polymerase II transcription, poly(A)-coupled / RNA polymerase core enzyme binding / microfibril binding / RNA polymerase II C-terminal domain phosphoserine binding / mRNA cleavage factor complex / Abortive elongation of HIV-1 transcript in the absence of Tat / positive regulation of DNA-templated transcription, elongation / 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 / termination of RNA polymerase II transcription / 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 / RNA polymerase II complex binding / 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 / kinase binding / DNA-directed 5'-3' RNA polymerase activity / nuclear matrix / 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 / mRNA binding / 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
SCAF8, RNA recognition motif / CID domain / RPR / CID domain / CID domain profile. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #90 / ENTH/VHS / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 ...SCAF8, RNA recognition motif / CID domain / RPR / CID domain / CID domain profile. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #90 / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Nucleotide-binding alpha-beta plait domain superfamily / Mainly Alpha
Similarity search - Domain/homology
DNA-directed RNA polymerase II subunit RPB1 / SR-related and CTD-associated factor 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsBecker, R. / Loll, B. / Meinhart, A.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Snapshots of the RNA Processing Factor SCAF8 Bound to Different Phosphorylated Forms of the Carboxyl-terminal Domain of RNA Polymerase II.
Authors: Becker, R. / Loll, B. / Meinhart, A.
History
DepositionMay 27, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq / 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.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA-binding protein 16
B: RNA-binding protein 16
Y: CTD-PEPTIDE
Z: CTD-PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,30113
Polymers37,4364
Non-polymers8659
Water1,49583
1
B: RNA-binding protein 16
Z: CTD-PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1026
Polymers18,7182
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-51 kcal/mol
Surface area8370 Å2
MethodPISA
2
A: RNA-binding protein 16
Y: CTD-PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1987
Polymers18,7182
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-58 kcal/mol
Surface area8060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.450, 56.450, 106.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

-
Components

#1: Protein RNA-binding protein 16 / RNA-binding motif protein 16


Mass: 16940.648 Da / Num. of mol.: 2
Fragment: CTD INTERACTING DOMAIN OF SCAF8, UNP residues 1-136
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBM16, KIAA1116 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: Q9UPN6
#2: Protein/peptide CTD-PEPTIDE


Mass: 1777.412 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: PEPTIDE DERIVED FROM THE CONSERVED REPEAT SEQUENCE IN RNA POLYMERASE II CTD
References: UniProt: P24928*PLUS
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 1.2M Li2SO4, 1.6M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 25, 2008
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 16475 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 36.7 Å2 / Rsym value: 0.08 / Net I/σ(I): 18.3
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 5.3 / Num. unique all: 1955 / Rsym value: 0.33 / % possible all: 92.6

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345SOFTWAREdata collection
XDSdata reduction
XSCALEdata scaling
REFMAC5.2.0019phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 3D9J

3d9j


Resolution: 2.2→19.89 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.903 / SU B: 12.634 / SU ML: 0.163 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.283 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25161 847 5 %RANDOM
Rwork0.18976 ---
obs0.19284 16046 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.624 Å2
Baniso -1Baniso -2Baniso -3
1-1.62 Å20 Å20 Å2
2--1.62 Å20 Å2
3----3.25 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2399 0 45 83 2527
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222540
X-RAY DIFFRACTIONr_angle_refined_deg1.1951.9853450
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1035306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.13424.649114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.59615.126476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6481511
X-RAY DIFFRACTIONr_chiral_restr0.0820.2372
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021843
X-RAY DIFFRACTIONr_nbd_refined0.1970.21230
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21741
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2130
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0750.22
X-RAY DIFFRACTIONr_mcbond_it0.5391.51548
X-RAY DIFFRACTIONr_mcangle_it0.8822461
X-RAY DIFFRACTIONr_scbond_it1.39631120
X-RAY DIFFRACTIONr_scangle_it2.1424.5980
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 67 -
Rwork0.211 1205 -
obs-1205 100 %
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)
12.73670.16591.1642.95480.91726.3668-0.0357-0.14740.2311-0.148-0.18650.039-0.2054-0.15850.2221-0.2294-0.034-0.01-0.1717-0.0052-0.168643.91434.310516.4277
22.6073-0.46480.37672.94771.32197.4888-0.12610.0708-0.148-0.00960.1931-0.1109-0.3031-0.1135-0.067-0.2042-0.0486-0.0311-0.21140.0081-0.145923.806514.3726-9.7758
385.6712-35.32159.914944.6655-17.34256.9837-0.47731.7098-0.62920.9722-2.89470.39620.7451.97333.3720.3887-0.2790.05310.44650.05950.406831.18770.938113.5174
416.1062-11.453210.238228.089213.971729.15340.1614-1.5022-1.32811.3461-2.01012.310.4171-2.4131.84870.0597-0.21930.08110.33850.13880.394610.95711.7657-5.4595
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1382 - 138
2X-RAY DIFFRACTION2BB1 - 1411 - 141
3X-RAY DIFFRACTION3YC-1 - 46 - 11
4X-RAY DIFFRACTION4ZD1 - 91 - 9

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more