[English] 日本語
Yorodumi
- PDB-4qde: Dcps in complex with covalent inhibitor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4qde
TitleDcps in complex with covalent inhibitor
Componentsm7GpppX diphosphatase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Decapping scavenger enzyme / residual cap structure cleavage / mRNA degradation / 3'->5' exosome-mediated mRNA decay pathway / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


mRNA methylguanosine-cap decapping / 5'-(N7-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase / 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity / mRNA decay by 3' to 5' exoribonuclease / RNA exonuclease activity / : / deadenylation-dependent decapping of nuclear-transcribed mRNA / RNA 7-methylguanosine cap binding / mRNA cis splicing, via spliceosome / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay ...mRNA methylguanosine-cap decapping / 5'-(N7-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase / 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity / mRNA decay by 3' to 5' exoribonuclease / RNA exonuclease activity / : / deadenylation-dependent decapping of nuclear-transcribed mRNA / RNA 7-methylguanosine cap binding / mRNA cis splicing, via spliceosome / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / P-body / mitochondrion / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
mRNA decapping enzyme DcpS N-terminal fold / mRNA decapping enzyme DcpS N-terminal domain / Scavenger mRNA decapping enzyme, N-terminal domain / Scavenger mRNA decapping enzyme DcpS/DCS2 / Scavenger mRNA decapping enzyme, N-terminal / Scavenger mRNA decapping enzyme (DcpS) N-terminal / Scavenger mRNA decapping enzyme C-term binding / Histidine triad, conserved site / HIT domain signature. / HIT-like ...mRNA decapping enzyme DcpS N-terminal fold / mRNA decapping enzyme DcpS N-terminal domain / Scavenger mRNA decapping enzyme, N-terminal domain / Scavenger mRNA decapping enzyme DcpS/DCS2 / Scavenger mRNA decapping enzyme, N-terminal / Scavenger mRNA decapping enzyme (DcpS) N-terminal / Scavenger mRNA decapping enzyme C-term binding / Histidine triad, conserved site / HIT domain signature. / HIT-like / HIT family, subunit A / HIT-like superfamily / Phosphorylase Kinase; domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-30S / PHOSPHATE ION / m7GpppX diphosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.9 Å
AuthorsLiu, S.
CitationJournal: To be Published
Title: Dcps in complex with covalent inhibitors
Authors: Liu, S.
History
DepositionMay 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / database_2 / pdbx_initial_refinement_model / software / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: m7GpppX diphosphatase
B: m7GpppX diphosphatase
C: m7GpppX diphosphatase
D: m7GpppX diphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,71213
Polymers154,3544
Non-polymers1,3589
Water0
1
A: m7GpppX diphosphatase
B: m7GpppX diphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,8086
Polymers77,1772
Non-polymers6314
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10250 Å2
ΔGint-58 kcal/mol
Surface area25670 Å2
MethodPISA
2
C: m7GpppX diphosphatase
D: m7GpppX diphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9037
Polymers77,1772
Non-polymers7265
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10550 Å2
ΔGint-74 kcal/mol
Surface area26240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.370, 105.610, 137.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
m7GpppX diphosphatase / / DCS-1 / Decapping scavenger enzyme / Hint-related 7meGMP-directed hydrolase / Histidine triad ...DCS-1 / Decapping scavenger enzyme / Hint-related 7meGMP-directed hydrolase / Histidine triad nucleotide-binding protein 5 / Histidine triad protein member 5 / HINT-5 / Scavenger mRNA-decapping enzyme DcpS


Mass: 38588.602 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCPS, DCS1, HINT5, HSPC015 / Production host: Escherichia coli (E. coli)
References: UniProt: Q96C86, 5'-(N7-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-30S / 2-{[(2,4-diaminoquinazolin-5-yl)oxy]methyl}benzenesulfonic acid


Mass: 346.361 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H14N4O4S

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 1:1 protein (4 mg/mL in 25 mM sodium chloride, 20 mM Tris-HCl, pH 8.0, 1 mM TCEP) to precipitant (23-25% PEG3350, 0.1 M potassium phosphate monobasic, 0.05 M sodium chloride, 26% glycerol), ...Details: 1:1 protein (4 mg/mL in 25 mM sodium chloride, 20 mM Tris-HCl, pH 8.0, 1 mM TCEP) to precipitant (23-25% PEG3350, 0.1 M potassium phosphate monobasic, 0.05 M sodium chloride, 26% glycerol), VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 3, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→81.51 Å / Num. obs: 33336 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 60.43 Å2 / Rmerge(I) obs: 0.211 / Rsym value: 0.083
Reflection shellResolution: 2.9→3.24 Å / Rmerge(I) obs: 0.808 / Mean I/σ(I) obs: 2.5 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
autoPROCdata scaling
BUSTERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1XMM

1xmm


Resolution: 2.9→38.68 Å / Cor.coef. Fo:Fc: 0.9267 / Cor.coef. Fo:Fc free: 0.894 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.381 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2514 1683 5.06 %RANDOM
Rwork0.2088 ---
obs0.2109 33254 99.88 %-
Displacement parametersBiso mean: 65.73 Å2
Baniso -1Baniso -2Baniso -3
1-10.0095 Å20 Å20 Å2
2---1.2744 Å20 Å2
3----8.7351 Å2
Refine analyzeLuzzati coordinate error obs: 0.413 Å
Refinement stepCycle: LAST / Resolution: 2.9→38.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9561 0 81 0 9642
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3475SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes269HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1456HARMONIC5
X-RAY DIFFRACTIONt_it9877HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1219SEMIHARMONIC5
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_contact10948SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d9877HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg13414HARMONIC21.19
X-RAY DIFFRACTIONt_omega_torsion3.21
X-RAY DIFFRACTIONt_other_torsion21.83
LS refinement shellResolution: 2.9→2.99 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.2816 149 5.21 %
Rwork0.2237 2713 -
all0.2268 2862 -
obs--99.88 %
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)
12.91930.45110.67181.3326-0.39921.2145-0.01130.18660.0671-0.1001-0.1033-0.1848-0.02730.02650.1147-0.38840.01430.0118-0.2050.0264-0.259334.703240.51824.3861
24.1012-0.6210.93861.1006-0.35190.74940.0368-0.156-0.31980.07270.07230.09840.1293-0.0724-0.1091-0.4173-0.0159-0.0157-0.30620.0313-0.260846.175523.593241.6582
33.91580.4369-0.75890.8872-0.511.11640.07220.27260.4664-0.04510.12120.0762-0.0978-0.1131-0.1934-0.4482-0.0060.0015-0.25960.0541-0.296796.601432.719626.7681
42.47530.3773-0.222.0318-0.19781.1495-0.0673-0.03750.06550.13320.0504-0.1120.00930.05810.0169-0.39250.0027-0.0308-0.24430.0267-0.293185.258416.208144.3794
51.4893-2.70041.23744.5471-0.87313.55590.00210.4727-0.6866-0.52810.05630.1360.59580.0226-0.05830.24190.10830.24790.4054-0.0660.49441.193718.96467.0344
60.26931.3861-0.9514.5884-0.99532.8786-0.1613-0.55710.78890.39190.2364-0.0534-0.61620.1399-0.07520.413-0.0873-0.2530.4544-0.18480.774791.910338.155460.6742
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|146 - A|336 }A146 - 336
2X-RAY DIFFRACTION2{ B|146 - B|336 }B146 - 336
3X-RAY DIFFRACTION3{ C|146 - C|336 }C146 - 336
4X-RAY DIFFRACTION4{ D|146 - D|336 }D146 - 336
5X-RAY DIFFRACTION5{ A|40 - A|145 B|40 - B|145 }A40 - 145
6X-RAY DIFFRACTION5{ A|40 - A|145 B|40 - B|145 }B40 - 145
7X-RAY DIFFRACTION6{ C|39 - C|145 D|40 - D|145 }C39 - 145
8X-RAY DIFFRACTION6{ C|39 - C|145 D|40 - D|145 }D40 - 145

+
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