[English] 日本語
Yorodumi
- PDB-4czx: Complex of Neurospora crassa PAN2 (WD40) with PAN3 (C-TERM) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4czx
TitleComplex of Neurospora crassa PAN2 (WD40) with PAN3 (C-TERM)
Components(PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT ...) x 2
KeywordsGENE REGULATION / WD40 DOMAIN / C-TERMINAL KNOB DOMAIN / DEADENYLATION / MRNA DECAY / PAN2-PAN3 COMPLEX
Function / homology
Function and homology information


PAN complex / poly(A)-specific ribonuclease / poly(A)-specific ribonuclease activity / nuclear-transcribed mRNA poly(A) tail shortening / poly(A) binding / P-body / mRNA processing / nucleic acid binding / ATP binding / metal ion binding
Similarity search - Function
Helix Hairpins - #3700 / PAN2-PAN3 deadenylation complex subunit PAN3 / Pan3 pseudokinase domain / Pan3 Pseudokinase domain / PAN2, UCH domain / PAN2-PAN3 deadenylation complex catalytic subunit PAN2 / : / Ubiquitin carboxyl-terminal hydrolase / PAN2 N-terminal / Exonuclease ...Helix Hairpins - #3700 / PAN2-PAN3 deadenylation complex subunit PAN3 / Pan3 pseudokinase domain / Pan3 Pseudokinase domain / PAN2, UCH domain / PAN2-PAN3 deadenylation complex catalytic subunit PAN2 / : / Ubiquitin carboxyl-terminal hydrolase / PAN2 N-terminal / Exonuclease / Exonuclease, RNase T/DNA polymerase III / EXOIII / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Quinoprotein alcohol dehydrogenase-like superfamily / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Papain-like cysteine peptidase superfamily / Helix Hairpins / Ribonuclease H superfamily / Ribonuclease H-like superfamily / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / PAN2-PAN3 deadenylation complex catalytic subunit pan2 / PAN2-PAN3 deadenylation complex subunit pan3
Similarity search - Component
Biological speciesNEUROSPORA CRASSA (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsJonas, S. / Izaurralde, E. / Weichenrieder, O.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: An Asymmetric Pan3 Dimer Recruits a Single Pan2 Exonuclease to Mediate Mrna Deadenylation and Decay.
Authors: Jonas, S. / Christie, M. / Peter, D. / Bhandari, D. / Loh, B. / Huntzinger, E. / Weichenrieder, O. / Izaurralde, E.
History
DepositionApr 22, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Database references
Revision 1.2Jul 16, 2014Group: Database references
Revision 1.3Apr 29, 2015Group: Data collection
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN2
B: PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1635
Polymers52,7812
Non-polymers3823
Water5,549308
1
A: PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN2
B: PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN3
hetero molecules

A: PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN2
B: PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,32610
Polymers105,5614
Non-polymers7656
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area6520 Å2
ΔGint-39.3 kcal/mol
Surface area36980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.925, 160.651, 124.515
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2085-

HOH

-
Components

-
PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT ... , 2 types, 2 molecules AB

#1: Protein PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN2 / PAB1P-DEPENDENT POLY(A)-NUCLEASE / PAN DEADENYLATION COMPLEX CATALYTIC SUBUNIT 2 / A-SPECIFIC ...PAB1P-DEPENDENT POLY(A)-NUCLEASE / PAN DEADENYLATION COMPLEX CATALYTIC SUBUNIT 2 / A-SPECIFIC RIBONUCLEASE SUBUNIT PAN2


Mass: 36235.258 Da / Num. of mol.: 1 / Fragment: WD40 DOMAIN, RESIDUES 1-321
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NEUROSPORA CRASSA (fungus) / Plasmid: PETMCN (PNYC) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: P0C581, poly(A)-specific ribonuclease
#2: Protein PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN3 / PAB1P-DEPENDENT POLY(A)-NUCLEASE / PAN DEADENYLATION COMPLEX SUBUNIT 3 / A-SPECIFIC RIBONUCLEASE SUBUNIT PAN3


Mass: 16545.453 Da / Num. of mol.: 1 / Fragment: C-TERM, RESIDUES 538-656
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NEUROSPORA CRASSA (fungus) / Plasmid: PETMCN (PNEA) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: Q7SDP4

-
Non-polymers , 4 types, 311 molecules

#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsTHE 3 N-TERMINAL RESIDUES OF CHAIN A REMAIN FROM THE PURIFICATION TAG THE N-TERMINAL 28 RESIDUES OF ...THE 3 N-TERMINAL RESIDUES OF CHAIN A REMAIN FROM THE PURIFICATION TAG THE N-TERMINAL 28 RESIDUES OF CHAIN B CORRESPOND TO THE HIS-TAG AND TEV SITE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 58 %
Description: MOLECULAR REPLACEMENT PHASES WERE USED FOR AU-SITE IDENTIFICATION
Crystal growpH: 6.5
Details: 10% PEG 4000, 20% GLYCEROL, 0.1M MES/IMIDAZOLE (PH 6.5), 30MM SODIUM NITRATE, 30MM DI-SODIUM HYDROGEN PHOSPHATE, 30MM AMMONIUM SULFATE

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONSLS X10SA10.97938
SYNCHROTRONSLS X10SA21.03996
Detector
TypeIDDetectorDateDetails
DECTRIS PILATUS 6M1PIXELSep 17, 2013DYNAMICALLY BENDABLE MIRROR
DECTRIS PILATUS 6M2PIXEL
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI(111)SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979381
21.039961
ReflectionResolution: 1.85→49.21 Å / Num. obs: 48059 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 28.8 Å2 / Rsym value: 0.05 / Net I/σ(I): 19.9
Reflection shellResolution: 1.85→1.96 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 2.95 / Rsym value: 0.57 / % possible all: 98.3

-
Processing

Software
NameVersionClassification
PHENIXPHENIX.REFINE 1.8.4_1496)refinement
XDSdata reduction
XSCALEdata scaling
PHASEREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BWX

4bwx


Resolution: 1.85→49.21 Å / SU ML: 0.19 / σ(F): 1.35 / Phase error: 23.58 / Stereochemistry target values: ML
Details: THE FOLLOWING RESIDUES WERE DISORDERED, CHAIN B 538, 560-563, 646-656. THE FOLLOWING RESIDUES WERE TRUNCATED AT CB, CHAIN A 316, 318, 321, CHAIN B 564. THE FOLLOWING RESIDUES WERE REFINED ...Details: THE FOLLOWING RESIDUES WERE DISORDERED, CHAIN B 538, 560-563, 646-656. THE FOLLOWING RESIDUES WERE TRUNCATED AT CB, CHAIN A 316, 318, 321, CHAIN B 564. THE FOLLOWING RESIDUES WERE REFINED WITH DOUBLE CONFORMATIONS CHAIN A 11, 23, 85, 122, 131, 133, 134, 184, CHAIN B 603, 617, 635.
RfactorNum. reflection% reflection
Rfree0.1967 2431 5.1 %
Rwork0.1675 --
obs0.169 48015 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.9 Å2
Refinement stepCycle: LAST / Resolution: 1.85→49.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3370 0 23 308 3701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073534
X-RAY DIFFRACTIONf_angle_d1.0554807
X-RAY DIFFRACTIONf_dihedral_angle_d13.7221314
X-RAY DIFFRACTIONf_chiral_restr0.041533
X-RAY DIFFRACTIONf_plane_restr0.005619
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8508-1.88860.28021450.30342524X-RAY DIFFRACTION96
1.8886-1.92960.30621370.26772650X-RAY DIFFRACTION99
1.9296-1.97450.29431430.232654X-RAY DIFFRACTION100
1.9745-2.02390.25321270.20662636X-RAY DIFFRACTION100
2.0239-2.07860.23941370.19492683X-RAY DIFFRACTION100
2.0786-2.13980.20681480.17582644X-RAY DIFFRACTION100
2.1398-2.20890.20821340.17152685X-RAY DIFFRACTION100
2.2089-2.28780.22271620.17562642X-RAY DIFFRACTION100
2.2878-2.37940.19341550.16652664X-RAY DIFFRACTION100
2.3794-2.48770.23641220.17132699X-RAY DIFFRACTION100
2.4877-2.61880.22151270.17892703X-RAY DIFFRACTION100
2.6188-2.78290.22941420.17992710X-RAY DIFFRACTION100
2.7829-2.99780.19411450.18192680X-RAY DIFFRACTION100
2.9978-3.29940.21191510.17342697X-RAY DIFFRACTION100
3.2994-3.77660.1791480.15762717X-RAY DIFFRACTION100
3.7766-4.75760.15051520.13622737X-RAY DIFFRACTION100
4.7576-49.22510.17611560.14832859X-RAY DIFFRACTION99
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)
11.2298-0.3337-0.56772.13660.01421.92410.05550.161-0.1269-0.3868-0.10720.0325-0.1722-0.1331-0.0170.24570.0079-0.04110.1399-0.05130.14041.230662.8157-6.092
21.25940.01230.66850.8763-0.61721.5969-0.0472-0.05430.0661-0.0318-0.1113-0.0089-0.12150.0742-0.0010.2317-0.01640.02790.26490.00010.2547-1.11640.05221.4267
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN 'A' AND RESID -2 THROUGH 321)
2X-RAY DIFFRACTION2(CHAIN 'B' AND RESID 539 THROUGH 645)

+
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