[English] 日本語
Yorodumi
- PDB-4iir: Crystal Structure of AMPPNP-bound Human PRPF4B kinase domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4iir
TitleCrystal Structure of AMPPNP-bound Human PRPF4B kinase domain
ComponentsSerine/threonine-protein kinase PRP4 homolog
KeywordsTRANSFERASE / kinase
Function / homology
Function and homology information


mRNA cis splicing, via spliceosome / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / mRNA splicing, via spliceosome / chromosome / non-specific serine/threonine protein kinase / protein kinase activity / nuclear speck / protein phosphorylation ...mRNA cis splicing, via spliceosome / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / mRNA splicing, via spliceosome / chromosome / non-specific serine/threonine protein kinase / protein kinase activity / nuclear speck / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / RNA binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
Serine/threonine-protein PRP4, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. ...Serine/threonine-protein PRP4, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Serine/threonine-protein kinase PRP4 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMechin, I. / Haas, K. / Chen, X. / Zhang, Y. / McLean, L.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Evaluation of Cancer Dependence and Druggability of PRP4 Kinase Using Cellular, Biochemical, and Structural Approaches.
Authors: Gao, Q. / Mechin, I. / Kothari, N. / Guo, Z. / Deng, G. / Haas, K. / McManus, J. / Hoffmann, D. / Wang, A. / Wiederschain, D. / Rocnik, J. / Czechtizky, W. / Chen, X. / McLean, L. / Arlt, H. ...Authors: Gao, Q. / Mechin, I. / Kothari, N. / Guo, Z. / Deng, G. / Haas, K. / McManus, J. / Hoffmann, D. / Wang, A. / Wiederschain, D. / Rocnik, J. / Czechtizky, W. / Chen, X. / McLean, L. / Arlt, H. / Harper, D. / Liu, F. / Majid, T. / Patel, V. / Lengauer, C. / Garcia-Echeverria, C. / Zhang, B. / Cheng, H. / Dorsch, M. / Huang, S.M.
History
DepositionDec 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2013Group: Database references
Revision 1.2Nov 6, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine/threonine-protein kinase PRP4 homolog
B: Serine/threonine-protein kinase PRP4 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,2889
Polymers83,8672
Non-polymers1,4217
Water7,080393
1
A: Serine/threonine-protein kinase PRP4 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5604
Polymers41,9331
Non-polymers6273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serine/threonine-protein kinase PRP4 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7285
Polymers41,9331
Non-polymers7944
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.500, 52.500, 78.790
Angle α, β, γ (deg.)105.290, 103.050, 93.090
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Serine/threonine-protein kinase PRP4 homolog / PRP4 kinase / PRP4 pre-mRNA-processing factor 4 homolog


Mass: 41933.469 Da / Num. of mol.: 2 / Fragment: kinase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA0536, PRP4, PRP4H, PRP4K, PRPF4B / Plasmid: pFastBac1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9
References: UniProt: Q13523, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 393 / 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: 2.42 Å3/Da / Density % sol: 49.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M ammonium sulfate, 20-30% PEG 3350 and 0.1M HEPES pH7.0, 5 mM AMPPNP final concentration added to cryo-protectant solution for soaking of apo crystals, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 51485 / % possible obs: 97.5 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.055 / Χ2: 1.045 / Net I/σ(I): 10.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.072.20.38450951.025197
2.07-2.152.20.26851291.063197
2.15-2.252.20.18751501.065197.3
2.25-2.372.20.1551471.056197.5
2.37-2.522.20.11951671.042197.8
2.52-2.712.20.08951861.032197.9
2.71-2.992.20.06851681.032198.2
2.99-3.422.20.05652051.024198.1
3.42-4.312.20.04452031.037198.2
4.31-502.10.03450351.076195.5

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
BUSTER-TNTBUSTER 2.9.1refinement
PDB_EXTRACT3.11data extraction
BUSTER2.9.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20.16 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU R Cruickshank DPI: 0.223 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2648 2621 5.09 %RANDOM
Rwork0.2428 ---
obs0.2439 51445 97.14 %-
Displacement parametersBiso max: 128.8 Å2 / Biso mean: 44.9143 Å2 / Biso min: 17.93 Å2
Baniso -1Baniso -2Baniso -3
1--2.7612 Å26.0368 Å2-10.523 Å2
2--3.4009 Å21.3959 Å2
3----0.6397 Å2
Refine analyzeLuzzati coordinate error obs: 0.341 Å
Refinement stepCycle: LAST / Resolution: 2→20.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5347 0 83 393 5823
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2007SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes148HARMONIC2
X-RAY DIFFRACTIONt_gen_planes771HARMONIC5
X-RAY DIFFRACTIONt_it5484HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion691SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6496SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5550HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg7488HARMONIC20.97
X-RAY DIFFRACTIONt_omega_torsion1.81
X-RAY DIFFRACTIONt_other_torsion20.39
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2841 180 5.03 %
Rwork0.2687 3397 -
all0.2695 3577 -
obs--97.14 %

+
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://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