[English] 日本語
Yorodumi
- PDB-9b9l: RPRD1B C-terminal interacting domain bound to a pThr4 CTD peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9b9l
TitleRPRD1B C-terminal interacting domain bound to a pThr4 CTD peptide
Components
  • Regulation of nuclear pre-mRNA domain-containing protein 1B
  • SER-PRO-THR-SER-PRO-SER-TYR-SER-PRO-TPO-SER-PRO-SER-TYR-SER
KeywordsTRANSCRIPTION / complex / CTD / Pol II / Thr4
Function / homology
Function and homology information


microfibril binding / regulation of cell cycle process / RNA polymerase II promoter clearance / mRNA 3'-end processing / Abortive elongation of HIV-1 transcript in the absence of Tat / transcription preinitiation complex / MicroRNA (miRNA) biogenesis / FGFR2 alternative splicing / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM ...microfibril binding / regulation of cell cycle process / RNA polymerase II promoter clearance / mRNA 3'-end processing / Abortive elongation of HIV-1 transcript in the absence of Tat / transcription preinitiation complex / 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 / 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 C-terminal domain binding / RNA polymerase II transcribes snRNA genes / RNA polymerase II activity / 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 / positive regulation of RNA splicing / TP53 Regulates Transcription of DNA Repair Genes / promoter-specific chromatin binding / Transcriptional regulation by small RNAs / DNA-templated transcription termination / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / kinase binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / 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 / positive regulation of cell population proliferation / regulation of DNA-templated transcription / magnesium ion binding / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
: / Regulation of nuclear pre-mRNA domain-containing protein 1A/B / Cell-cycle alteration and expression-elevated protein in tumour / CID domain / RPR / CID domain / CID domain profile. / ENTH/VHS / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 6 ...: / Regulation of nuclear pre-mRNA domain-containing protein 1A/B / Cell-cycle alteration and expression-elevated protein in tumour / 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 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 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus
Similarity search - Domain/homology
DNA-directed RNA polymerase II subunit RPB1 / Regulation of nuclear pre-mRNA domain-containing protein 1B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMoreno, R.Y. / Zhang, Y.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-104896 United States
CitationJournal: To Be Published
Title: Thr4 phosphorylation primes Ser2 phosphorylation on RNA polymerase II and mediates regulation in elongation and 3'end processing
Authors: Moreno, R.Y. / Panina, S.B. / Irani, S. / Hardtke, H.A. / Richardson, R. / Floyd, B.M. / Marcotte, E.M. / Zhang, Q. / Zhang, Y.J.
History
DepositionApr 2, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Regulation of nuclear pre-mRNA domain-containing protein 1B
B: Regulation of nuclear pre-mRNA domain-containing protein 1B
C: SER-PRO-THR-SER-PRO-SER-TYR-SER-PRO-TPO-SER-PRO-SER-TYR-SER


Theoretical massNumber of molelcules
Total (without water)32,0893
Polymers32,0893
Non-polymers00
Water68538
1
A: Regulation of nuclear pre-mRNA domain-containing protein 1B
C: SER-PRO-THR-SER-PRO-SER-TYR-SER-PRO-TPO-SER-PRO-SER-TYR-SER


Theoretical massNumber of molelcules
Total (without water)16,8572
Polymers16,8572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-4 kcal/mol
Surface area7470 Å2
MethodPISA
2
B: Regulation of nuclear pre-mRNA domain-containing protein 1B


Theoretical massNumber of molelcules
Total (without water)15,2321
Polymers15,2321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.317, 90.231, 135.074
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Regulation of nuclear pre-mRNA domain-containing protein 1B / Cell cycle-related and expression-elevated protein in tumor


Mass: 15232.341 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPRD1B, C20orf77, CREPT / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NQG5
#2: Protein/peptide SER-PRO-THR-SER-PRO-SER-TYR-SER-PRO-TPO-SER-PRO-SER-TYR-SER


Mass: 1624.554 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CTD peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: P24928
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.15 Å3/Da / Density % sol: 60.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Co-crystallization of CID with CTD peptide occurred in a reservoir solution of 20-32% PEG3350 and 0.1M lithium sulfate. 1:3 molar ratio of protein to peptide was used

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 13291 / % possible obs: 92.1 % / Redundancy: 3.9 % / CC1/2: 0.93 / Rsym value: 0.073 / Net I/σ(I): 5.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.5-2.543.70.4944070.8860.9690.260.5620.61956.4
2.54-2.593.70.4424220.930.9820.2290.50.6461.3
2.59-2.643.60.5655300.8780.9670.2980.6430.673.9
2.64-2.693.70.5735750.9180.9780.3070.6540.680.5
2.69-2.753.80.5796060.8420.9560.3090.6590.61787.6
2.75-2.823.80.4726840.90.9730.2540.5390.72493.3
2.82-2.893.70.436730.8880.970.2410.4950.89396.1
2.89-2.964.10.4447100.9110.9760.240.5070.88999.2
2.96-3.054.10.3597000.9370.9830.1930.4090.94999.7
3.05-3.154.10.2837190.9740.9930.1510.3221.178100
3.15-3.264.30.2667140.9750.9940.1380.3011.34699.9
3.26-3.394.20.2017160.9890.9970.1060.2281.571100
3.39-3.554.20.1917190.9910.9980.10.2171.64499.7
3.55-3.733.90.1527210.9890.9970.0850.1752.29298.8
3.73-3.9740.1337190.9880.9970.0720.1512.59399.7
3.97-4.273.90.1137180.9840.9960.0620.132.59499.6
4.27-4.740.0967140.9910.9980.0530.1112.6998.1
4.7-5.383.90.0867210.9910.9980.0470.0992.69398.5
5.38-6.783.90.0717480.9930.9980.0390.0811.98299.7
6.78-503.80.0517750.9960.9990.030.0591.76397

-
Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→42.79 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 45.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.347 1320 10.01 %
Rwork0.2656 --
obs0.2737 13183 91.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→42.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2134 0 0 38 2172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092181
X-RAY DIFFRACTIONf_angle_d1.3142937
X-RAY DIFFRACTIONf_dihedral_angle_d21.464284
X-RAY DIFFRACTIONf_chiral_restr0.07319
X-RAY DIFFRACTIONf_plane_restr0.009369
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.60.4097880.3434788X-RAY DIFFRACTION55
2.6-2.710.47231240.39521130X-RAY DIFFRACTION80
2.71-2.860.47461460.39251321X-RAY DIFFRACTION93
2.86-3.040.42441580.35141411X-RAY DIFFRACTION99
3.04-3.270.4061580.32631414X-RAY DIFFRACTION99
3.27-3.60.39171580.30921405X-RAY DIFFRACTION99
3.6-4.120.33721590.2581442X-RAY DIFFRACTION99
4.12-5.190.34211610.23211445X-RAY DIFFRACTION98
5.19-42.790.28971680.21911507X-RAY DIFFRACTION98

+
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