[English] 日本語
Yorodumi
- PDB-2zn9: Crystal structure of Ca2+-bound form of des3-20ALG-2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2zn9
TitleCrystal structure of Ca2+-bound form of des3-20ALG-2
ComponentsProgrammed cell death protein 6
KeywordsAPOPTOSIS / PENTA-EF-HAND PROTEIN / CALCIUM BINDING PROTEIN / Endoplasmic reticulum / Membrane / Nucleus / Polymorphism
Function / homology
Function and homology information


neural crest formation / vascular endothelial growth factor receptor-2 signaling pathway / neural crest cell development / COPII vesicle coat / COPII vesicle coating / negative regulation of TOR signaling / positive regulation of protein monoubiquitination / Cul3-RING ubiquitin ligase complex / negative regulation of vascular endothelial growth factor receptor signaling pathway / : ...neural crest formation / vascular endothelial growth factor receptor-2 signaling pathway / neural crest cell development / COPII vesicle coat / COPII vesicle coating / negative regulation of TOR signaling / positive regulation of protein monoubiquitination / Cul3-RING ubiquitin ligase complex / negative regulation of vascular endothelial growth factor receptor signaling pathway / : / endoplasmic reticulum exit site / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / ubiquitin-like ligase-substrate adaptor activity / endoplasmic reticulum to Golgi vesicle-mediated transport / protein-membrane adaptor activity / positive regulation of endothelial cell proliferation / positive regulation of endothelial cell migration / apoptotic signaling pathway / intracellular protein transport / response to calcium ion / positive regulation of angiogenesis / calcium-dependent protein binding / cellular response to heat / protein-macromolecule adaptor activity / cytoplasmic vesicle / angiogenesis / protein dimerization activity / endosome / protein heterodimerization activity / calcium ion binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / magnesium ion binding / endoplasmic reticulum / protein homodimerization activity / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / EF hand / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain ...: / EF hand / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Programmed cell death protein 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSuzuki, H. / Kawasaki, M. / Inuzuka, T. / Kakiuchi, T. / Shibata, H. / Wakatsuki, S. / Maki, M.
CitationJournal: Structure / Year: 2008
Title: Structural Basis for Ca(2+)-Dependent Formation of ALG-2/Alix Peptide Complex: Ca(2+)/EF3-Driven Arginine Switch Mechanism
Authors: Suzuki, H. / Kawasaki, M. / Inuzuka, T. / Okumura, M. / Kakiuchi, T. / Shibata, H. / Wakatsuki, S. / Maki, M.
History
DepositionApr 22, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 6
B: Programmed cell death protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,55911
Polymers40,3172
Non-polymers1,2429
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-108 kcal/mol
Surface area18840 Å2
MethodPISA
2
A: Programmed cell death protein 6
hetero molecules

B: Programmed cell death protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,55911
Polymers40,3172
Non-polymers1,2429
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_565-y,x+1,z+1/41
Buried area3800 Å2
ΔGint-100 kcal/mol
Surface area19780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.024, 72.024, 91.663
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

-
Components

#1: Protein Programmed cell death protein 6 / Apoptosis-linked gene 2 protein / Probable calcium-binding protein ALG-2


Mass: 20158.492 Da / Num. of mol.: 2 / Fragment: residues 20-191
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD6, ALG2 / Plasmid: pET3d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: O75340
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#4: Chemical ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 546.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsBOTH POLYETHYLENE GLYCOLS(12P AND 2PE) ARE A PART OF PEG 8000 USED IN THE CRYSTALLIZATION CONDITION.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 18% PEG 8000, 0.1M Sodium Cacodylate, 0.2M Calcium Acetate hydrate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 27, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 18354 / % possible obs: 99.8 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 11.8
Reflection shellResolution: 2.4→2.5 Å / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 8.2 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HQV

1hqv


Resolution: 2.4→38.66 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.898 / SU B: 10.789 / SU ML: 0.251 / Cross valid method: THROUGHOUT / ESU R: 0.411 / ESU R Free: 0.299 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29843 941 5.1 %RANDOM
Rwork0.23433 ---
obs0.23749 17411 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.565 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20 Å20 Å2
2--0.42 Å20 Å2
3----0.83 Å2
Refinement stepCycle: LAST / Resolution: 2.4→38.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2816 0 69 46 2931
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222942
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3391.933953
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4255337
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.04523.81168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.18515486
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4961526
X-RAY DIFFRACTIONr_chiral_restr0.0980.2404
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022266
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2190.21374
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.22015
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.287
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1360.218
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.262
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0090.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5941.51718
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.07722713
X-RAY DIFFRACTIONr_scbond_it1.53731406
X-RAY DIFFRACTIONr_scangle_it2.4044.51240
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.398→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 66 -
Rwork0.318 1247 -
obs--99.09 %

+
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