[English] 日本語
Yorodumi
- PDB-7zeg: Human cytosolic 5' nucleotidase IIIB in complex with 3,4-diF-Bn7GMP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7zeg
TitleHuman cytosolic 5' nucleotidase IIIB in complex with 3,4-diF-Bn7GMP
Components7-methylguanosine phosphate-specific 5'-nucleotidase
KeywordsHYDROLASE / Cytosolic 5' nucleotidase / N7 methylguanosine monophosphate dephosphorylation / mRNA cap degradation
Function / homology
Function and homology information


mRNA decay by 3' to 5' exoribonuclease / 7-methylguanosine nucleotidase / : / 5'-nucleotidase / 5'-nucleotidase activity / nucleotide metabolic process / nucleotide binding / magnesium ion binding / cytoplasm / cytosol
Similarity search - Function
Pyrimidine 5'-nucleotidase, eukaryotic / Pyrimidine 5'-nucleotidase (UMPH-1) / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Chem-IOO / 7-methylguanosine phosphate-specific 5'-nucleotidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsKubacka, D. / Kozarski, M. / Baranowski, M.R. / Wojcik, R. / Jemielity, J. / Kowalska, J. / Basquin, J.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science CentreUMO- 2017/24/C/NZ1/00169 Poland
CitationJournal: Pharmaceuticals / Year: 2022
Title: Substrate-Based Design of Cytosolic Nucleotidase IIIB Inhibitors and Structural Insights into Inhibition Mechanism.
Authors: Kubacka, D. / Kozarski, M. / Baranowski, M.R. / Wojcik, R. / Panecka-Hofman, J. / Strzelecka, D. / Basquin, J. / Jemielity, J. / Kowalska, J.
History
DepositionMar 31, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1May 25, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Jun 8, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 7-methylguanosine phosphate-specific 5'-nucleotidase
B: 7-methylguanosine phosphate-specific 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,69111
Polymers69,3512
Non-polymers1,3409
Water6,954386
1
A: 7-methylguanosine phosphate-specific 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3145
Polymers34,6761
Non-polymers6394
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 7-methylguanosine phosphate-specific 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3776
Polymers34,6761
Non-polymers7015
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.755, 79.135, 94.388
Angle α, β, γ (deg.)90.000, 93.227, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRALAALA(chain 'A' and ((resid 7 and (name N or name...AA7 - 2099 - 211
12GLYGLYLEULEU(chain 'A' and ((resid 7 and (name N or name...AA221 - 289223 - 291
13IOOIOOIOOIOO(chain 'A' and ((resid 7 and (name N or name...AC401
14HOHHOHHOHHOH(chain 'A' and ((resid 7 and (name N or name...AL501
25THRTHRALAALA(chain 'B' and (resid 7 through 70 or (resid 71...BB7 - 2099 - 211
26GLYGLYLEULEU(chain 'B' and (resid 7 through 70 or (resid 71...BB221 - 289223 - 291
27HOHHOHHOHHOH(chain 'B' and (resid 7 through 70 or (resid 71...BM501
28HOHHOHHOHHOH(chain 'B' and (resid 7 through 70 or (resid 71...BM601

-
Components

#1: Protein 7-methylguanosine phosphate-specific 5'-nucleotidase / 7-methylguanosine nucleotidase / Cytosolic 5'-nucleotidase 3B / Cytosolic 5'-nucleotidase III-like ...7-methylguanosine nucleotidase / Cytosolic 5'-nucleotidase 3B / Cytosolic 5'-nucleotidase III-like protein / cN-III-like protein / N(7)-methylguanylate 5'-phosphatase


Mass: 34675.684 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NT5C3B, NT5C3L / Production host: Escherichia coli (E. coli)
References: UniProt: Q969T7, 7-methylguanosine nucleotidase, 5'-nucleotidase
#2: Chemical ChemComp-IOO / N7-(3,4-difluorobenzyl) guanosine 5'-monophosphate / [(2R,3S,4R,5R)-5-[2-azanyl-7-[[3,4-bis(fluoranyl)phenyl]methyl]-6-oxidanylidene-1H-purin-7-ium-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate


Type: L-RNA linking / Mass: 490.332 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H19F2N5O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 386 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.92 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion / pH: 6.2 / Details: 22% PEG 3350, 0.1M MES pH 6.2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.556→40.69 Å / Num. obs: 85124 / % possible obs: 99.15 % / Redundancy: 6.6 % / Biso Wilson estimate: 24.02 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.09054 / Rpim(I) all: 0.03799 / Rrim(I) all: 0.09835 / Net I/σ(I): 10.66
Reflection shellResolution: 1.556→1.612 Å / Mean I/σ(I) obs: 0.68 / Num. unique obs: 8109 / CC1/2: 0.439 / CC star: 0.781

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2bdu

2bdu


Resolution: 1.56→40.69 Å / SU ML: 0.2851 / Cross valid method: NONE / σ(F): 1.33 / Phase error: 36.571 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.273 3129 3.69 %
Rwork0.2396 81777 -
obs0.2409 84906 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.89 Å2
Refinement stepCycle: LAST / Resolution: 1.56→40.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4372 0 88 386 4846
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00384543
X-RAY DIFFRACTIONf_angle_d0.63616149
X-RAY DIFFRACTIONf_chiral_restr0.0473688
X-RAY DIFFRACTIONf_plane_restr0.004787
X-RAY DIFFRACTIONf_dihedral_angle_d10.74662688
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.580.49991290.46363383X-RAY DIFFRACTION91.34
1.58-1.610.44851400.41583667X-RAY DIFFRACTION99.22
1.61-1.630.41771440.39523735X-RAY DIFFRACTION99.16
1.63-1.660.44591420.37273700X-RAY DIFFRACTION99.15
1.66-1.70.39931420.3443720X-RAY DIFFRACTION99.08
1.7-1.730.39421400.33333668X-RAY DIFFRACTION99.06
1.73-1.770.36061410.30733737X-RAY DIFFRACTION99.16
1.77-1.810.34981420.29483690X-RAY DIFFRACTION99.27
1.81-1.850.3241440.27593751X-RAY DIFFRACTION99.62
1.85-1.90.36761410.27793699X-RAY DIFFRACTION99.53
1.9-1.960.30461430.27083725X-RAY DIFFRACTION99.64
1.96-2.020.2971440.25093760X-RAY DIFFRACTION99.82
2.02-2.10.31731430.24873719X-RAY DIFFRACTION99.69
2.1-2.180.27561430.24463731X-RAY DIFFRACTION99.9
2.18-2.280.32031430.24313755X-RAY DIFFRACTION99.77
2.28-2.40.29071440.23483746X-RAY DIFFRACTION99.79
2.4-2.550.25211430.23993764X-RAY DIFFRACTION99.74
2.55-2.750.27171420.23853706X-RAY DIFFRACTION99.66
2.75-3.020.26391430.23423748X-RAY DIFFRACTION99.72
3.02-3.460.26151440.22133767X-RAY DIFFRACTION99.64
3.46-4.360.20581440.19233760X-RAY DIFFRACTION99.64
4.36-40.690.23811480.21983846X-RAY DIFFRACTION99.7

+
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