[English] 日本語
Yorodumi
- PDB-4ddp: crystal structure of Beclin 1 evolutionarily conserved domain(ECD) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ddp
Titlecrystal structure of Beclin 1 evolutionarily conserved domain(ECD)
ComponentsBeclin-1
KeywordsMEMBRANE PROTEIN / Beclin 1 / ECD / autophagy / membrane binding
Function / homology
Function and homology information


cellular response to aluminum ion / phosphatidylinositol 3-kinase complex, class III / phosphatidylinositol 3-kinase complex, class III, type II / positive regulation of stress granule assembly / cellular response to oxygen-glucose deprivation / phosphatidylinositol 3-kinase complex, class III, type I / response to mitochondrial depolarisation / positive regulation of attachment of mitotic spindle microtubules to kinetochore / cytoplasmic side of mitochondrial outer membrane / negative regulation of lysosome organization ...cellular response to aluminum ion / phosphatidylinositol 3-kinase complex, class III / phosphatidylinositol 3-kinase complex, class III, type II / positive regulation of stress granule assembly / cellular response to oxygen-glucose deprivation / phosphatidylinositol 3-kinase complex, class III, type I / response to mitochondrial depolarisation / positive regulation of attachment of mitotic spindle microtubules to kinetochore / cytoplasmic side of mitochondrial outer membrane / negative regulation of lysosome organization / positive regulation of autophagosome assembly / negative regulation of autophagosome assembly / receptor catabolic process / engulfment of apoptotic cell / suppression by virus of host autophagy / protein targeting to lysosome / early endosome to late endosome transport / late endosome to vacuole transport / cellular response to nitrogen starvation / SMAD protein signal transduction / Translation of Replicase and Assembly of the Replication Transcription Complex / phagophore assembly site / negative regulation of programmed cell death / response to iron(II) ion / phosphatidylinositol-3-phosphate biosynthetic process / mitotic metaphase chromosome alignment / cytoplasmic pattern recognition receptor signaling pathway / Macroautophagy / RSV-host interactions / lysosome organization / positive regulation of cardiac muscle hypertrophy / p38MAPK cascade / mitophagy / autophagosome maturation / autophagosome assembly / negative regulation of reactive oxygen species metabolic process / neuron development / autophagosome / response to vitamin E / regulation of macroautophagy / amyloid-beta metabolic process / cellular defense response / cellular response to glucose starvation / positive regulation of autophagy / phosphatidylinositol 3-kinase binding / positive regulation of intrinsic apoptotic signaling pathway / JNK cascade / cellular response to epidermal growth factor stimulus / cellular response to copper ion / cellular response to amino acid starvation / phagocytic vesicle / regulation of cytokinesis / regulation of autophagy / macroautophagy / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / response to lead ion / trans-Golgi network / ISG15 antiviral mechanism / autophagy / cellular response to hydrogen peroxide / GTPase binding / protein-macromolecule adaptor activity / Translation of Replicase and Assembly of the Replication Transcription Complex / protein-containing complex assembly / defense response to virus / molecular adaptor activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / nuclear body / endosome membrane / response to hypoxia / Ub-specific processing proteases / endosome / response to xenobiotic stimulus / negative regulation of cell population proliferation / cell division / apoptotic process / ubiquitin protein ligase binding / dendrite / endoplasmic reticulum membrane / negative regulation of apoptotic process / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / endoplasmic reticulum / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Autophagy protein 6/Beclin 1 / Beclin-1, BH3 domain / Beclin-1 BH3 domain, Bcl-2-interacting / Atg6/Beclin / Atg6/Beclin C-terminal domain superfamily / Atg6, BARA domain / Atg6/beclin, coiled-coil domain / Apg6 BARA domain / Apg6 coiled-coil region / Actin-binding Protein, T-fimbrin; domain 1 ...Autophagy protein 6/Beclin 1 / Beclin-1, BH3 domain / Beclin-1 BH3 domain, Bcl-2-interacting / Atg6/Beclin / Atg6/Beclin C-terminal domain superfamily / Atg6, BARA domain / Atg6/beclin, coiled-coil domain / Apg6 BARA domain / Apg6 coiled-coil region / Actin-binding Protein, T-fimbrin; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.547 Å
AuthorsHuang, W.J. / Choi, W.Y. / Wang, J.W. / Shi, Y.G.
CitationJournal: Cell Res. / Year: 2012
Title: Crystal structure and biochemical analyses reveal Beclin 1 as a novel membrane binding protein
Authors: Huang, W. / Choi, W. / Hu, W. / Mi, N. / Guo, Q. / Ma, M. / Liu, M. / Tian, Y. / Lu, P. / Wang, F.L. / Deng, H. / Liu, L. / Gao, N. / Yu, L. / Shi, Y.
History
DepositionJan 19, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beclin-1


Theoretical massNumber of molelcules
Total (without water)24,4601
Polymers24,4601
Non-polymers00
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.746, 33.563, 74.765
Angle α, β, γ (deg.)90.00, 113.49, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Beclin-1 / Coiled-coil myosin-like BCL2-interacting protein / Protein GT197


Mass: 24459.807 Da / Num. of mol.: 1 / Fragment: UNP residues 241-450
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BECN1, GT197 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14457
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG 3350, 0.3M NaCl, 0.1M Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Dec 2, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.547→50 Å / Num. obs: 26572 / % possible obs: 97.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.55→1.61 Å / % possible all: 93.3

-
Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: dev_596)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.547→32.408 Å / FOM work R set: 0.7867 / SU ML: 0.13 / σ(F): 0 / Phase error: 26.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2034 1243 5.03 %RANDOM
Rwork0.1755 ---
all0.177 25256 --
obs0.177 24700 90.74 %-
Solvent computationShrinkage radii: 1.01 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.947 Å2 / ksol: 0.436 e/Å3
Displacement parametersBiso mean: 40.9722 Å2
Baniso -1Baniso -2Baniso -3
1-19.2043 Å20 Å2-6.5855 Å2
2---9.6744 Å20 Å2
3----9.5299 Å2
Refinement stepCycle: LAST / Resolution: 1.547→32.408 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1590 0 0 115 1705
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121625
X-RAY DIFFRACTIONf_angle_d1.2742190
X-RAY DIFFRACTIONf_dihedral_angle_d16.034582
X-RAY DIFFRACTIONf_chiral_restr0.083225
X-RAY DIFFRACTIONf_plane_restr0.007277
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5466-1.60850.32691240.2951205572
1.6085-1.68170.28971500.252235884
1.6817-1.77040.23241120.2132250588
1.7704-1.88130.25791200.1894262992
1.8813-2.02650.20781430.1788272396
2.0265-2.23040.18161480.1614279797
2.2304-2.5530.20161470.1514282598
2.553-3.21610.2141520.1655284098
3.2161-32.41510.17671470.17272592
Refinement TLS params.Method: refined / Origin x: 28.8198 Å / Origin y: -3.9292 Å / Origin z: 17.324 Å
111213212223313233
T0.2124 Å20.0417 Å20.0034 Å2-0.2068 Å20.0037 Å2--0.1896 Å2
L0.8275 °20.2464 °20.0823 °2-1.8621 °20.056 °2--1.5292 °2
S-0.0182 Å °0.022 Å °-0.0268 Å °-0.0437 Å °-0.0418 Å °-0.0853 Å °0.0665 Å °0.1095 Å °0.0077 Å °
Refinement TLS groupSelection details: chain A

+
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