[English] 日本語
Yorodumi
- PDB-4bwk: Structure of Neurospora crassa PAN3 pseudokinase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4bwk
TitleStructure of Neurospora crassa PAN3 pseudokinase
ComponentsPAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN-3
KeywordsGENE REGULATION / DEADENYLASE / PAN2 / MIRNA / MRNA DECAY
Function / homology
Function and homology information


PAN complex / nuclear-transcribed mRNA poly(A) tail shortening / poly(A) binding / P-body / mRNA processing / ATP binding / metal ion binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #5160 / Helix Hairpins - #3700 / PAN2-PAN3 deadenylation complex subunit PAN3 / Pan3 pseudokinase domain / Pan3 Pseudokinase domain / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix Hairpins / Transferase(Phosphotransferase) domain 1 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #5160 / Helix Hairpins - #3700 / PAN2-PAN3 deadenylation complex subunit PAN3 / Pan3 pseudokinase domain / Pan3 Pseudokinase domain / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix Hairpins / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase-like domain superfamily / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / PAN2-PAN3 deadenylation complex subunit pan3
Similarity search - Component
Biological speciesNEUROSPORA CRASSA (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsChristie, M. / Boland, A. / Huntzinger, E. / Weichenrieder, O. / Izaurralde, E.
CitationJournal: Mol.Cell / Year: 2013
Title: Structure of the Pan3 Pseudokinase Reveals the Basis for Interactions with the Pan2 Deadenylase and the Gw182 Proteins
Authors: Christie, M. / Boland, A. / Huntzinger, E. / Weichenrieder, O. / Izaurralde, E.
History
DepositionJul 4, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN-3
B: PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,5854
Polymers98,5382
Non-polymers1,0462
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8400 Å2
ΔGint-51.2 kcal/mol
Surface area37990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.521, 89.521, 228.789
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.998, 0.014, 0.057), (0.037, 0.904, 0.426), (-0.046, 0.428, -0.903)
Vector: -61.72517, 16.72507, -60.32031)

-
Components

#1: Protein PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN-3 / PAB1P-DEPENDENT POLY(A)-NUCLEASE / PAB-DEPENDENT POLYA-SPECIFIC RIBONUCLEASE SUBUNIT PAN-3


Mass: 49269.078 Da / Num. of mol.: 2
Fragment: PSEUDOKINASE DOMAIN, COILED COIL, CTERMINAL KNOB, RESIDUES 234-656
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NEUROSPORA CRASSA (fungus) / Plasmid: PNEA-NPM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7SDP4
#2: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.5 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1 M HEPES PH 7.5, 7% PEG 6000, 6% ISOPROPANOL

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00001
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 26, 2012 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 3.3→46.03 Å / Num. obs: 15611 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.9 % / Biso Wilson estimate: 117.45 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.9
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 3 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→46.027 Å / SU ML: 0.4 / σ(F): 1.36 / Phase error: 37.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2937 779 5 %
Rwork0.2521 --
obs0.2541 15516 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→46.027 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6345 0 62 0 6407
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086545
X-RAY DIFFRACTIONf_angle_d1.5248866
X-RAY DIFFRACTIONf_dihedral_angle_d14.0022426
X-RAY DIFFRACTIONf_chiral_restr0.057993
X-RAY DIFFRACTIONf_plane_restr0.0071124
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3002-3.50690.39341170.3622445X-RAY DIFFRACTION99
3.5069-3.77750.31371240.30642454X-RAY DIFFRACTION100
3.7775-4.15740.37811310.28032441X-RAY DIFFRACTION100
4.1574-4.75850.31371440.26642458X-RAY DIFFRACTION100
4.7585-5.99310.30441370.26412462X-RAY DIFFRACTION100
5.9931-46.03110.24181260.21112477X-RAY DIFFRACTION100
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)
10.71940.0108-0.07660.58830.27260.57650.89690.6930.0354-0.0327-0.7471-0.23650.52980.23220.07170.54070.06590.36670.26250.13730.5009-23.673527.7266-34.2508
20.3692-0.0794-0.01680.52790.25820.24860.4872-0.13380.04420.0145-0.63-0.14110.0535-0.768-0.15251.2172-0.85990.38840.3648-0.30730.5627-39.742626.6032-16.769
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESSEQ 235:646)
2X-RAY DIFFRACTION2(CHAIN B AND RESSEQ 235:646)

+
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