[English] 日本語
Yorodumi
- PDB-3ajm: Crystal structure of programmed cell death 10 in complex with ino... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ajm
TitleCrystal structure of programmed cell death 10 in complex with inositol 1,3,4,5-tetrakisphosphate
ComponentsProgrammed cell death protein 10
KeywordsAPOPTOSIS / adaptor protein / dimerization / four-helix bundle
Function / homology
Function and homology information


FAR/SIN/STRIPAK complex / intrinsic apoptotic signaling pathway in response to hydrogen peroxide / regulation of Golgi organization / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / Golgi reassembly / endothelium development / positive regulation of stress-activated MAPK cascade / establishment of Golgi localization / positive regulation of intracellular protein transport / negative regulation of cell migration involved in sprouting angiogenesis ...FAR/SIN/STRIPAK complex / intrinsic apoptotic signaling pathway in response to hydrogen peroxide / regulation of Golgi organization / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / Golgi reassembly / endothelium development / positive regulation of stress-activated MAPK cascade / establishment of Golgi localization / positive regulation of intracellular protein transport / negative regulation of cell migration involved in sprouting angiogenesis / wound healing, spreading of cells / positive regulation of Notch signaling pathway / regulation of angiogenesis / cellular response to leukemia inhibitory factor / positive regulation of MAP kinase activity / positive regulation of protein serine/threonine kinase activity / positive regulation of peptidyl-serine phosphorylation / angiogenesis / protein stabilization / intracellular signal transduction / positive regulation of cell migration / Golgi membrane / negative regulation of gene expression / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of apoptotic process / protein kinase binding / Golgi apparatus / protein homodimerization activity / extracellular exosome / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 - #70 / Programmed cell death protein 10 / Programmed cell death protein 10, C-terminal / Programmed cell death protein 10, dimerisation domain superfamily / : / Programmed cell death protein 10, dimerisation domain / Nucleotidyltransferases domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle ...Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 - #70 / Programmed cell death protein 10 / Programmed cell death protein 10, C-terminal / Programmed cell death protein 10, dimerisation domain superfamily / : / Programmed cell death protein 10, dimerisation domain / Nucleotidyltransferases domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE / Programmed cell death protein 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsDing, J. / Wang, D.C.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2010
Title: Crystal structure of human programmed cell death 10 complexed with inositol-(1,3,4,5)-tetrakisphosphate: a novel adaptor protein involved in human cerebral cavernous malformation.
Authors: Ding, J. / Wang, X. / Li, D.F. / Hu, Y. / Zhang, Y. / Wang, D.C.
History
DepositionJun 9, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: Programmed cell death protein 10
B: Programmed cell death protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2933
Polymers49,7932
Non-polymers5001
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-39 kcal/mol
Surface area20870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.830, 89.830, 114.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-3-

HOH

21A-221-

HOH

-
Components

#1: Protein Programmed cell death protein 10 / TF-1 cell apoptosis-related protein 15 / Cerebral cavernous malformations 3 protein


Mass: 24896.619 Da / Num. of mol.: 2 / Fragment: UNP residues 8-212
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD10 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9BUL8
#2: Chemical ChemComp-4IP / INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE


Mass: 500.075 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H16O18P4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 30% PEG, 0.1M sodium cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1951
2951
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-17A10.97888, 0.97928, 0.96405
SYNCHROTRONPhoton Factory BL-17A21
Detector
TypeIDDetectorDate
ADSC QUANTUM 2701CCDOct 26, 2008
ADSC QUANTUM 2702CCDOct 26, 2008
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.978881
20.979281
30.964051
411
ReflectionResolution: 2.3→48.17 Å / Num. all: 21459 / Num. obs: 21428 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 46.3 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 14.6
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 5.8 / Num. unique all: 3070 / Rsym value: 0.317 / % possible all: 100

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.3→44.915 Å / SU ML: 0.3 / σ(F): 1.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2641 1095 5.12 %RANDOM
Rwork0.2135 ---
obs0.216 21366 99.8 %-
all-21413 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.529 Å2 / ksol: 0.364 e/Å3
Displacement parametersBiso mean: 55.9 Å2
Baniso -1Baniso -2Baniso -3
1-4.6117 Å20 Å2-0 Å2
2--4.6117 Å20 Å2
3----9.2235 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.3→44.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3191 0 28 99 3318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053269
X-RAY DIFFRACTIONf_angle_d0.6764407
X-RAY DIFFRACTIONf_dihedral_angle_d18.1921303
X-RAY DIFFRACTIONf_chiral_restr0.051507
X-RAY DIFFRACTIONf_plane_restr0.002558
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.3001-2.40480.25541450.204224682468100
2.4048-2.53160.2771240.207324982498100
2.5316-2.69020.27171460.207324742474100
2.6902-2.89780.25931420.215225232523100
2.8978-3.18940.26641370.219925032503100
3.1894-3.65070.2671620.198925062506100
3.6507-4.59880.24981290.18225732573100
4.5988-44.92350.26141100.23162726272699
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)
11.875-1.93971.94912.5551-2.23462.1005-0.104-0.1031-0.05910.15840.31310.1178-0.1219-0.50920.00010.2350.0358-0.00620.38210.01410.174182.796832.364516.2286
23.43540.0423-1.0772.0408-0.0612.24750.1885-0.01370.33080.1310.10660.129-0.22720.17110.00010.21050.03560.06260.21850.05770.316165.641552.264117.1918
33.085-0.64790.3560.3173-0.71452.13710.0148-0.0524-0.08630.04430.02350.10010.3925-0.2302-0.00070.28440.02120.00830.22750.03940.200485.503431.056612.7872
41.5983-0.37690.07972.5772-0.26722.29660.23250.69150.0491-0.4575-0.2577-0.32010.08980.48590.00030.4010.13520.030.6630.06530.3424116.208633.617614.6177
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESSEQ 17:86
2X-RAY DIFFRACTION2CHAIN A AND RESSEQ 98:211
3X-RAY DIFFRACTION3CHAIN B AND RESSEQ 17:86
4X-RAY DIFFRACTION4CHAIN B AND RESSEQ 98:209

+
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