[English] 日本語
Yorodumi
- PDB-9t4k: Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1) ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9t4k
TitleHuman Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1) H91M mutant in complex with IP6
ComponentsDiphosphoinositol polyphosphate phosphohydrolase 1
KeywordsHYDROLASE / Inositol metabolism / phosphatase / NUDIX hydrolases / DIPP1 / IP6
Function / homology
Function and homology information


inositol diphosphate pentakisphosphate diphosphatase activity / diphosphoinositol polyphosphate catabolic process / inositol diphosphate tetrakisphosphate diphosphatase activity / endopolyphosphatase / diadenosine polyphosphate catabolic process / 5'-(N7-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase / bis(5'-adenosyl)-hexaphosphatase activity / inositol-3,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity / diadenosine pentaphosphate catabolic process / diadenosine hexaphosphate catabolic process ...inositol diphosphate pentakisphosphate diphosphatase activity / diphosphoinositol polyphosphate catabolic process / inositol diphosphate tetrakisphosphate diphosphatase activity / endopolyphosphatase / diadenosine polyphosphate catabolic process / 5'-(N7-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase / bis(5'-adenosyl)-hexaphosphatase activity / inositol-3,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity / diadenosine pentaphosphate catabolic process / diadenosine hexaphosphate catabolic process / adenosine 5'-(hexahydrogen pentaphosphate) catabolic process / endopolyphosphatase activity / diphosphoinositol polyphosphate metabolic process / diphosphoinositol-polyphosphate diphosphatase activity / inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity / 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity / diadenosine hexaphosphate hydrolase (ATP-forming) / bis(5'-adenosyl)-pentaphosphatase activity / Synthesis of pyrophosphates in the cytosol / diphosphoinositol-polyphosphate diphosphatase / RNA decapping / 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / manganese ion binding / cell-cell signaling / glutamatergic synapse / magnesium ion binding / zinc ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily
Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / PHOSPHATE ION / Diphosphoinositol polyphosphate phosphohydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.394 Å
AuthorsCasas-Florez, D. / Marquez-Monino, M.A. / Gonzalez, B.
Funding support Spain, 2items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2020-117400GB-I00 Spain
Spanish Ministry of Science, Innovation, and UniversitiesPID2023-147659NB-I00 Spain
CitationJournal: Int.J.Biol.Macromol. / Year: 2026
Title: The DIPP1 family binds IP 8 in catalytically-productive twist-boat and chair conformations and associates in a ligand-dependent manner.
Authors: Casas-Florez, D. / Whitfield, H. / Perez-Canadillas, J.M. / Monterroso, B. / Riley, A.M. / Marquez-Monino, M.A. / Shipton, M.L. / Sanz-Aparicio, J. / Brearley, C.A. / Potter, B.V.L. / Gonzalez, B.
History
DepositionOct 30, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Diphosphoinositol polyphosphate phosphohydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1058
Polymers17,1081
Non-polymers9967
Water3,369187
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-59 kcal/mol
Surface area8330 Å2
Unit cell
Length a, b, c (Å)34.412, 64.869, 78.644
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Diphosphoinositol polyphosphate phosphohydrolase 1 / DIPP-1 / Diadenosine hexaphosphate hydrolase / Ap6A hydrolase / Endopolyphosphatase / Nucleoside ...DIPP-1 / Diadenosine hexaphosphate hydrolase / Ap6A hydrolase / Endopolyphosphatase / Nucleoside diphosphate-linked moiety X motif 3 / Nudix motif 3 / m7GpppN-mRNA hydrolase / m7GpppX diphosphatase


Mass: 17108.416 Da / Num. of mol.: 1
Mutation: Deletion of the last 24 C-terminal residues (149-172) and H91M
Source method: isolated from a genetically manipulated source
Details: Deletion of the last 24 C-terminal residues (149-172), the first three amino acids (GHM) remain as residual residues after removal of the expression tag.
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT3, DIPP, DIPP1 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: O95989, diphosphoinositol-polyphosphate diphosphatase, diadenosine hexaphosphate hydrolase (ATP-forming), endopolyphosphatase, 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] ...References: UniProt: O95989, diphosphoinositol-polyphosphate diphosphatase, diadenosine hexaphosphate hydrolase (ATP-forming), endopolyphosphatase, 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase, 5'-(N7-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase

-
Non-polymers , 6 types, 194 molecules

#2: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 53.4 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Protein: 19.5mg/mL IP6: 10mM Precipitant condition: 32% PEG 6K, 0.1M NaOAc pH 5, 0.2M LiCl, 1mM MgCl2 Ratio: 1:1

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.39→39.35 Å / Num. obs: 26701 / % possible obs: 94.4 % / Redundancy: 13.2 % / Biso Wilson estimate: 15.8 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.05 / Net I/σ(I): 9.5
Reflection shellResolution: 1.394→1.492 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1304 / CC1/2: 0.62 / Rpim(I) all: 0.81

-
Processing

Software
NameVersionClassification
autoPROC1.1.7data processing
REFMAC5.8.0419refinement
Coot0.9.8.92model building
autoPROC1.1.7data reduction
autoPROC1.1.7data scaling
REFMAC5.8.0419phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.394→39.35 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.417 / SU ML: 0.054 / Cross valid method: FREE R-VALUE / ESU R: 0.084 / ESU R Free: 0.089
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2271 1283 4.921 %
Rwork0.1872 24788 -
all0.189 --
obs-26071 72.532 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 19.011 Å2
Baniso -1Baniso -2Baniso -3
1-0.005 Å20 Å2-0 Å2
2--0.044 Å2-0 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.394→39.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1200 0 53 187 1440
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0121368
X-RAY DIFFRACTIONr_bond_other_d0.0020.0161255
X-RAY DIFFRACTIONr_angle_refined_deg1.9451.8741869
X-RAY DIFFRACTIONr_angle_other_deg0.6831.7842912
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2725167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.806512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.53910245
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.3931064
X-RAY DIFFRACTIONr_chiral_restr0.1040.2203
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021617
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02309
X-RAY DIFFRACTIONr_nbd_refined0.2130.2247
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.21100
X-RAY DIFFRACTIONr_nbtor_refined0.180.2610
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.2692
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2260.2142
X-RAY DIFFRACTIONr_metal_ion_refined0.1680.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.220.29
X-RAY DIFFRACTIONr_nbd_other0.1640.227
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2020.218
X-RAY DIFFRACTIONr_mcbond_it2.3471.699644
X-RAY DIFFRACTIONr_mcbond_other2.3471.699644
X-RAY DIFFRACTIONr_mcangle_it3.7963.037819
X-RAY DIFFRACTIONr_mcangle_other3.7943.037820
X-RAY DIFFRACTIONr_scbond_it3.4442.302724
X-RAY DIFFRACTIONr_scbond_other3.4462.287721
X-RAY DIFFRACTIONr_scangle_it5.5854.0331050
X-RAY DIFFRACTIONr_scangle_other5.5914.0021045
X-RAY DIFFRACTIONr_lrange_it8.25821.9451552
X-RAY DIFFRACTIONr_lrange_other8.03520.8991485
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.394-1.430.52350.445146X-RAY DIFFRACTION5.7262
1.43-1.4690.447340.397625X-RAY DIFFRACTION26.182
1.469-1.5120.349510.333926X-RAY DIFFRACTION39.1426
1.512-1.5580.241550.2881153X-RAY DIFFRACTION50.1661
1.558-1.6090.26780.261261X-RAY DIFFRACTION57.6907
1.609-1.6660.317760.2361457X-RAY DIFFRACTION67.3846
1.666-1.7290.245750.2341572X-RAY DIFFRACTION75
1.729-1.7990.244800.211669X-RAY DIFFRACTION83.1669
1.799-1.8790.208860.1971765X-RAY DIFFRACTION91.6337
1.879-1.970.189910.1911869X-RAY DIFFRACTION99.8981
1.97-2.0770.1751000.1761731X-RAY DIFFRACTION100
2.077-2.2020.196890.1711678X-RAY DIFFRACTION100
2.202-2.3540.208840.1681569X-RAY DIFFRACTION100
2.354-2.5420.283680.1811488X-RAY DIFFRACTION100
2.542-2.7830.238560.1721375X-RAY DIFFRACTION100
2.783-3.110.235830.1621228X-RAY DIFFRACTION100
3.11-3.5870.175510.1571109X-RAY DIFFRACTION100
3.587-4.3840.207530.144955X-RAY DIFFRACTION100
4.384-6.1620.288490.205745X-RAY DIFFRACTION100
6.162-39.350.227190.298467X-RAY DIFFRACTION100

+
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