[English] 日本語
Yorodumi
- PDB-7mu5: Human DCTPP1 bound to Triptolide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7mu5
TitleHuman DCTPP1 bound to Triptolide
ComponentsdCTP pyrophosphatase 1
KeywordsHYDROLASE/INHIBITOR / Inhibitor / pyrophosphatase / HYDROLASE / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


dCTP catabolic process / dCTP diphosphatase / dCTP diphosphatase activity / pyrimidine deoxyribonucleotide binding / nucleoside triphosphate catabolic process / nucleoside triphosphate diphosphatase activity / DNA protection / Interconversion of nucleotide di- and triphosphates / magnesium ion binding / mitochondrion ...dCTP catabolic process / dCTP diphosphatase / dCTP diphosphatase activity / pyrimidine deoxyribonucleotide binding / nucleoside triphosphate catabolic process / nucleoside triphosphate diphosphatase activity / DNA protection / Interconversion of nucleotide di- and triphosphates / magnesium ion binding / mitochondrion / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
dCTP pyrophosphatase 1 / : / MazG-like family
Similarity search - Domain/homology
triptolide / dCTP pyrophosphatase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHauk, G. / Berger, J.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Triptolide sensitizes cancer cells to nucleoside DNA methyltransferase inhibitors through inhibition of DCTPP1 mediated cell-intrinsic resistance
Authors: Liu, J. / He, Q.-L. / Zhou, J. / Chikarmane, R.V. / Hauk, G. / Rachakonda, A. / Vaghasia, A.M. / Castagna, N. / Steinberg, R.C. / Anders, N.M. / Wanjiku, T.M. / Nuhn, P. / Shim, J.S. / ...Authors: Liu, J. / He, Q.-L. / Zhou, J. / Chikarmane, R.V. / Hauk, G. / Rachakonda, A. / Vaghasia, A.M. / Castagna, N. / Steinberg, R.C. / Anders, N.M. / Wanjiku, T.M. / Nuhn, P. / Shim, J.S. / Giovinazzo, H. / Esopi, D.M. / Kim, K. / Coulter, J. / Wang, R. / Zhou, J. / Rudek, M.A. / Berger, J.M. / Liu, J.O. / Nelson, W.G. / Yegnasubramanian, S.
History
DepositionMay 14, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: dCTP pyrophosphatase 1
B: dCTP pyrophosphatase 1
C: dCTP pyrophosphatase 1
D: dCTP pyrophosphatase 1
E: dCTP pyrophosphatase 1
F: dCTP pyrophosphatase 1
G: dCTP pyrophosphatase 1
H: dCTP pyrophosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,52022
Polymers101,4918
Non-polymers3,02914
Water4,414245
1
A: dCTP pyrophosphatase 1
C: dCTP pyrophosphatase 1
E: dCTP pyrophosphatase 1
G: dCTP pyrophosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,28412
Polymers50,7464
Non-polymers1,5398
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17270 Å2
ΔGint-173 kcal/mol
Surface area17720 Å2
MethodPISA
2
B: dCTP pyrophosphatase 1
D: dCTP pyrophosphatase 1
F: dCTP pyrophosphatase 1
H: dCTP pyrophosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,23610
Polymers50,7464
Non-polymers1,4906
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16780 Å2
ΔGint-161 kcal/mol
Surface area18270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.163, 60.924, 73.458
Angle α, β, γ (deg.)91.459, 101.306, 104.131
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

-
Components

#1: Protein
dCTP pyrophosphatase 1 / Deoxycytidine-triphosphatase 1 / dCTPase 1 / RS21C6 / XTP3-transactivated gene A protein


Mass: 12686.380 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCTPP1, XTP3TPA, CDA03 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H773, dCTP diphosphatase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-TLI / triptolide / (3bS,4aS,5aS,6R,6aR,7aS,7bS,8aS,8bS)-6-hydroxy-8b-methyl-6a-(propan-2-yl)-3b,4,4a,6,6a,7a,7b,8b,9,10-decahydrotrisoxireno[6,7:8a,9:4b,5]phenanthro[1,2-c]furan-1(3H)-one


Mass: 360.401 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C20H24O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.43 Å3/Da / Density % sol: 49.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100mM Tris 7.5; 8% PEG3350; 300mM Proline

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92009 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92009 Å / Relative weight: 1
ReflectionResolution: 2.2→29.45 Å / Num. obs: 47686 / % possible obs: 98.18 % / Redundancy: 3.6 % / Biso Wilson estimate: 36.03 Å2 / CC1/2: 0.989 / CC star: 0.997 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.06693 / Rrim(I) all: 0.1275 / Net I/σ(I): 7.56
Reflection shellResolution: 2.2→2.279 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.4369 / Mean I/σ(I) obs: 2.22 / Num. unique obs: 4737 / CC1/2: 0.842 / CC star: 0.956 / Rpim(I) all: 0.2824 / Rrim(I) all: 0.5225 / % possible all: 97.59

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Cootmodel building
PHASERphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OIG

2oig


Resolution: 2.2→29.45 Å / SU ML: 0.2856 / Cross valid method: FREE R-VALUE / σ(F): 2.03 / Phase error: 24.0458
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2346 1726 3.62 %
Rwork0.184 45945 -
obs0.1858 47671 98.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.46 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6753 0 214 245 7212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01317170
X-RAY DIFFRACTIONf_angle_d1.72299863
X-RAY DIFFRACTIONf_chiral_restr0.26311081
X-RAY DIFFRACTIONf_plane_restr0.00891235
X-RAY DIFFRACTIONf_dihedral_angle_d17.85752679
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.32251440.26393803X-RAY DIFFRACTION97.63
2.26-2.340.27551420.22213837X-RAY DIFFRACTION97.62
2.34-2.420.26251430.21113796X-RAY DIFFRACTION97.86
2.42-2.520.27371440.21833817X-RAY DIFFRACTION98.07
2.52-2.630.26451440.20723845X-RAY DIFFRACTION98.15
2.63-2.770.2671440.19773851X-RAY DIFFRACTION98.21
2.77-2.940.2691430.19713802X-RAY DIFFRACTION98.48
2.95-3.170.23121440.19683830X-RAY DIFFRACTION98.71
3.17-3.490.22671450.18293859X-RAY DIFFRACTION98.38
3.49-3.990.22481430.16673805X-RAY DIFFRACTION98.16
3.99-5.030.19311440.14613823X-RAY DIFFRACTION98.14
5.03-29.450.22371460.18323877X-RAY DIFFRACTION99.28

+
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