[English] 日本語
Yorodumi
- PDB-4z0v: The structure of human PDE12 residues 161-609 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4z0v
TitleThe structure of human PDE12 residues 161-609
Components2',5'-phosphodiesterase 12
KeywordsHYDROLASE / PDE12 2'-5'A EEP nuclease
Function / homology
Function and homology information


oligoribonucleotidase activity / mitochondrial mRNA catabolic process / regulation of mitochondrial mRNA stability / poly(A)-specific ribonuclease / cellular response to interferon-alpha / poly(A)-specific ribonuclease activity / nucleic acid metabolic process / OAS antiviral response / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / cellular response to dsRNA ...oligoribonucleotidase activity / mitochondrial mRNA catabolic process / regulation of mitochondrial mRNA stability / poly(A)-specific ribonuclease / cellular response to interferon-alpha / poly(A)-specific ribonuclease activity / nucleic acid metabolic process / OAS antiviral response / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / cellular response to dsRNA / exonuclease activity / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of viral genome replication / antiviral innate immune response / cellular response to type II interferon / mRNA processing / 3'-5'-RNA exonuclease activity / defense response to virus / mitochondrial matrix / mitochondrion / metal ion binding / cytosol
Similarity search - Function
: / 2',5'-phosphodiesterase 12-like, N-terminal domain / : / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily
Similarity search - Domain/homology
2',5'-phosphodiesterase 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.78 Å
AuthorsNolte, R.T. / Wisely, B. / Wang, L. / Wood, E.R.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: The Role of Phosphodiesterase 12 (PDE12) as a Negative Regulator of the Innate Immune Response and the Discovery of Antiviral Inhibitors.
Authors: Wood, E.R. / Bledsoe, R. / Chai, J. / Daka, P. / Deng, H. / Ding, Y. / Harris-Gurley, S. / Kryn, L.H. / Nartey, E. / Nichols, J. / Nolte, R.T. / Prabhu, N. / Rise, C. / Sheahan, T. / ...Authors: Wood, E.R. / Bledsoe, R. / Chai, J. / Daka, P. / Deng, H. / Ding, Y. / Harris-Gurley, S. / Kryn, L.H. / Nartey, E. / Nichols, J. / Nolte, R.T. / Prabhu, N. / Rise, C. / Sheahan, T. / Shotwell, J.B. / Smith, D. / Tai, V. / Taylor, J.D. / Tomberlin, G. / Wang, L. / Wisely, B. / You, S. / Xia, B. / Dickson, H.
History
DepositionMar 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Aug 19, 2015Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 2',5'-phosphodiesterase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2348
Polymers49,6571
Non-polymers5777
Water6,485360
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.688, 62.554, 65.393
Angle α, β, γ (deg.)90.00, 110.40, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein 2',5'-phosphodiesterase 12 / 2-PDE / Mitochondrial deadenylase


Mass: 49657.113 Da / Num. of mol.: 1 / Fragment: UNP residues 155-609
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDE12 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3
References: UniProt: Q6L8Q7, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases, poly(A)-specific ribonuclease
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 360 / 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: 2.23 Å3/Da / Density % sol: 44.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2M MgCl2 0.1M Tris pH 8.5 24% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 31, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 41250 / % possible obs: 100 % / Redundancy: 3.8 % / Biso Wilson estimate: 19.41 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 16.694
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.78-1.843.80.40241160.8630.2420.471.091100
1.84-1.923.80.29540800.930.1760.3441.109100
1.92-23.80.20641190.9620.1240.2411.048100
2-2.113.80.14941120.9780.0890.1741.048100
2.11-2.243.80.11940860.9840.0710.1380.988100
2.24-2.423.80.09241460.990.0550.1080.952100
2.42-2.663.80.07640800.9930.0450.0881.007100
2.66-3.043.80.07341400.9930.0430.0851.151100
3.04-3.833.70.0641490.9940.0360.071.00799.8
3.83-503.70.03542220.9980.0210.040.89199.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.8 Å43.78 Å
Translation1.8 Å43.78 Å

-
Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
HKL-2000data collection
SCALEPACKdata scaling
PHASER2.5.4phasing
PDB_EXTRACT3.15data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NG0

3ng0


Resolution: 1.78→43.78 Å / Cor.coef. Fo:Fc: 0.9543 / Cor.coef. Fo:Fc free: 0.9413 / SU R Cruickshank DPI: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.116 / SU Rfree Blow DPI: 0.11 / SU Rfree Cruickshank DPI: 0.109
RfactorNum. reflection% reflectionSelection details
Rfree0.201 1291 3.13 %RANDOM
Rwork0.1645 ---
obs0.1657 41211 99.96 %-
Displacement parametersBiso mean: 21.18 Å2
Baniso -1Baniso -2Baniso -3
1-3.9537 Å20 Å2-0.7934 Å2
2---2.0526 Å20 Å2
3----1.9011 Å2
Refine analyzeLuzzati coordinate error obs: 0.172 Å
Refinement stepCycle: LAST / Resolution: 1.78→43.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3453 0 37 360 3850
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013584HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.014878HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1623SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes77HARMONIC2
X-RAY DIFFRACTIONt_gen_planes531HARMONIC5
X-RAY DIFFRACTIONt_it3584HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.11
X-RAY DIFFRACTIONt_other_torsion2.61
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion461SEMIHARMONIC5
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_contact4361SEMIHARMONIC4
LS refinement shellResolution: 1.78→1.83 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2086 93 3.05 %
Rwork0.202 2959 -
all0.2022 3052 -
obs--99.96 %

+
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