[English] 日本語
Yorodumi
- PDB-5ulj: Crystal structure of Scheffersomyces stipitis Rai1 in complex wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ulj
TitleCrystal structure of Scheffersomyces stipitis Rai1 in complex with (3'-NADP)+ and calcium ion
ComponentsRAI1
KeywordsHYDROLASE / NADP
Function / homology
Function and homology information


RNA polymerase II termination complex / positive regulation of termination of RNA polymerase II transcription / termination of RNA polymerase II transcription, poly(A)-coupled / Las1 complex / phosphodiesterase decapping endonuclease activity / deadenylation-independent decapping of nuclear-transcribed mRNA / mRNA 5'-diphosphatase activity / NAD-cap decapping / nuclear polyadenylation-dependent rRNA catabolic process / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...RNA polymerase II termination complex / positive regulation of termination of RNA polymerase II transcription / termination of RNA polymerase II transcription, poly(A)-coupled / Las1 complex / phosphodiesterase decapping endonuclease activity / deadenylation-independent decapping of nuclear-transcribed mRNA / mRNA 5'-diphosphatase activity / NAD-cap decapping / nuclear polyadenylation-dependent rRNA catabolic process / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / enzyme regulator activity / mRNA processing / nucleotide binding / RNA binding / metal ion binding
Similarity search - Function
RAI1-like / RAI1-like family / RAI1 like PD-(D/E)XK nuclease
Similarity search - Domain/homology
Chem-0WD / PYROPHOSPHATE / Decapping nuclease RAI1
Similarity search - Component
Biological speciesScheffersomyces stipitis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.911 Å
AuthorsDoamekpor, S.K. / Tong, L.
CitationJournal: Cell / Year: 2017
Title: 5' End Nicotinamide Adenine Dinucleotide Cap in Human Cells Promotes RNA Decay through DXO-Mediated deNADding.
Authors: Jiao, X. / Doamekpor, S.K. / Bird, J.G. / Nickels, B.E. / Tong, L. / Hart, R.P. / Kiledjian, M.
History
DepositionJan 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RAI1
B: RAI1
C: RAI1
D: RAI1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,48010
Polymers186,5534
Non-polymers1,9276
Water15,457858
1
A: RAI1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4243
Polymers46,6381
Non-polymers7852
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RAI1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4243
Polymers46,6381
Non-polymers7852
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RAI1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8162
Polymers46,6381
Non-polymers1781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: RAI1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8162
Polymers46,6381
Non-polymers1781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.350, 102.476, 101.194
Angle α, β, γ (deg.)90.000, 112.850, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
RAI1 / RAI1


Mass: 46638.223 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scheffersomyces stipitis (strain ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545) (fungus)
References: UniProt: A3LNL5
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-0WD / [[(2R,3S,4R,5R)-5-(3-aminocarbonyl-4H-pyridin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methyl hydrogen phosphate


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Chemical ChemComp-PPV / PYROPHOSPHATE


Mass: 177.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4O7P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 858 / 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: 2.29 Å3/Da / Density % sol: 46.25 % / Mosaicity: 0.926 ° / Mosaicity esd: 0.006 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 15% (w/v) PEG 3350 and 0.2 M NH4Cl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 23, 2016 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.91→50 Å / Num. obs: 129210 / % possible obs: 99.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 25.84 Å2 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.05 / Rrim(I) all: 0.097 / Χ2: 0.986 / Net I/σ(I): 10.7 / Num. measured all: 470441
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.91-1.9830.483126100.7220.3380.5930.74897.9
1.98-2.063.30.345128660.8540.2270.4150.84399.4
2.06-2.153.70.248128950.9350.1480.2890.95399.6
2.15-2.263.70.189128860.9590.1130.221.199.7
2.26-2.413.70.146129000.9730.0870.171.12999.8
2.41-2.593.70.114129210.9830.0680.1331.13699.9
2.59-2.853.80.087129690.9880.0510.1011.082100
2.85-3.273.80.068130110.9910.040.0790.918100
3.27-4.113.80.069130070.990.0410.0810.96199.9
4.11-503.80.061131450.9920.0360.0710.89599.7

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.12 Å49.68 Å
Translation7.12 Å49.68 Å

-
Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHASER2.5.6phasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.911→49.679 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.44
RfactorNum. reflection% reflection
Rfree0.2542 2009 1.56 %
Rwork0.2076 --
obs0.2083 129162 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 82.25 Å2 / Biso mean: 29.692 Å2 / Biso min: 10.83 Å2
Refinement stepCycle: final / Resolution: 1.911→49.679 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12520 0 97 858 13475
Biso mean--36.78 33.59 -
Num. residues----1527
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312869
X-RAY DIFFRACTIONf_angle_d0.68617338
X-RAY DIFFRACTIONf_chiral_restr0.0291871
X-RAY DIFFRACTIONf_plane_restr0.0032198
X-RAY DIFFRACTIONf_dihedral_angle_d13.9925006
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9107-1.95850.31371360.2698618875495
1.9585-2.01150.26911480.25199054920299
2.0115-2.07070.26731420.23949052919499
2.0707-2.13750.28781390.231690489187100
2.1375-2.21390.27141500.227590729222100
2.2139-2.30250.28141360.226991259261100
2.3025-2.40730.25021460.219790839229100
2.4073-2.53420.28391400.224990879227100
2.5342-2.6930.29731460.224691409286100
2.693-2.90090.26081410.225291439284100
2.9009-3.19280.24651470.221891369283100
3.1928-3.65470.26791430.200291529295100
3.6547-4.6040.22881470.169991819328100
4.604-49.69550.21351480.18429262941099

+
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