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- PDB-5k7b: Beclin 2 CCD homodimer -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5k7b
TitleBeclin 2 CCD homodimer
ComponentsBeclin-2
KeywordsAPOPTOSIS / Coiled-coil Domain / Autophagy
Function / homology
Function and homology information


G protein-coupled receptor catabolic process / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / late endosome to vacuole transport / phagophore assembly site / cellular response to nitrogen starvation / endosome to lysosome transport / autophagosome assembly / phosphatidylinositol 3-kinase binding / mitophagy ...G protein-coupled receptor catabolic process / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / late endosome to vacuole transport / phagophore assembly site / cellular response to nitrogen starvation / endosome to lysosome transport / autophagosome assembly / phosphatidylinositol 3-kinase binding / mitophagy / autophagy / glucose homeostasis / protein-macromolecule adaptor activity / protein-containing complex binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3110 / Atg6/Beclin / Atg6/Beclin C-terminal domain superfamily / Atg6, BARA domain / Atg6/beclin, coiled-coil domain / Apg6 BARA domain / Apg6 coiled-coil region / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSu, M. / Sinha, S.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)RO3 NS090939 United States
National Science Foundation (NSF, United States)MCB-1413525 United States
National Science Foundation (NSF, United States)IIA-1355466 Doctoral Dissertation Award United States
North Dakota EPSCoR Track 1 United States
CitationJournal: Protein Sci. / Year: 2017
Title: BECN2 interacts with ATG14 through a metastable coiled-coil to mediate autophagy.
Authors: Su, M. / Li, Y. / Wyborny, S. / Neau, D. / Chakravarthy, S. / Levine, B. / Colbert, C.L. / Sinha, S.C.
History
DepositionMay 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beclin-2
B: Beclin-2
C: Beclin-2
D: Beclin-2


Theoretical massNumber of molelcules
Total (without water)45,2014
Polymers45,2014
Non-polymers00
Water2,504139
1
A: Beclin-2
B: Beclin-2


Theoretical massNumber of molelcules
Total (without water)22,6012
Polymers22,6012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-44 kcal/mol
Surface area13360 Å2
MethodPISA
2
C: Beclin-2
D: Beclin-2


Theoretical massNumber of molelcules
Total (without water)22,6012
Polymers22,6012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-40 kcal/mol
Surface area13100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.460, 44.320, 97.957
Angle α, β, γ (deg.)90.00, 96.77, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein
Beclin-2 / Beclin-1 autophagy-related pseudogene 1 / Beclin-1-like protein 1


Mass: 11300.361 Da / Num. of mol.: 4 / Fragment: UNP residues 158-250
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BECN2, BECN1L1, BECN1P1 / Production host: Escherichia coli (E. coli) / References: UniProt: A8MW95
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 45.96 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Bis-Tris pH 6.5, 0.1 M NaCl and 1.5 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.19→40.33 Å / Num. obs: 17947 / % possible obs: 84.6 % / Redundancy: 3.4 % / CC1/2: 0.997 / Net I/σ(I): 7.7
Reflection shellResolution: 2.19→2.26 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.6 / % possible all: 87

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→40.33 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.236 791 5.14 %
Rwork0.221 --
obs-15375 83.48 %
Refinement stepCycle: LAST / Resolution: 2.3→40.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2877 0 0 139 3016
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.022
X-RAY DIFFRACTIONf_angle_d1.548
X-RAY DIFFRACTIONf_dihedral_angle_d16.873
X-RAY DIFFRACTIONf_chiral_restr0.148
X-RAY DIFFRACTIONf_plane_restr0.005
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.44410.28991390.2582484X-RAY DIFFRACTION86
2.4441-2.63280.30391280.24042271X-RAY DIFFRACTION80
2.6328-2.89760.25011260.23432527X-RAY DIFFRACTION87
2.8976-3.31680.25721260.23472305X-RAY DIFFRACTION80
3.3168-4.17810.21061330.18662451X-RAY DIFFRACTION84
4.1781-40.330.20461390.22392546X-RAY DIFFRACTION85
Refinement TLS params.Method: refined / Origin x: 44.981 Å / Origin y: 28.763 Å / Origin z: 10.585 Å
111213212223313233
T0.1902 Å20.0088 Å2-0.0462 Å2-0.1855 Å20.0071 Å2--0.1519 Å2
L2.1763 °20.0118 °2-1.3465 °2-0.2947 °20.0796 °2--0.9822 °2
S0.1393 Å °0.0198 Å °0.0539 Å °-0.0141 Å °-0.0317 Å °0.0256 Å °-0.1071 Å °-0.0135 Å °-0.122 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA160 - 246
2X-RAY DIFFRACTION1ALLC-2 - 241
3X-RAY DIFFRACTION1ALLB-1 - 247
4X-RAY DIFFRACTION1ALLD162 - 249

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