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- PDB-2zne: Crystal structure of Zn2+-bound form of des3-23ALG-2 complexed wi... -

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Basic information

Entry
Database: PDB / ID: 2zne
TitleCrystal structure of Zn2+-bound form of des3-23ALG-2 complexed with Alix ABS peptide
Components
  • 16-meric peptide from Programmed cell death 6-interacting protein
  • Programmed cell death protein 6
KeywordsAPOPTOSIS / PENTA-EF-HAND PROTEIN / CALCIUM BINDING PROTEIN / Endoplasmic reticulum / Membrane / Nucleus / Polymorphism / Cytoplasm / Host-virus interaction / Protein transport / Transport
Function / homology
Function and homology information


proteinase activated receptor binding / actomyosin contractile ring assembly / ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway / regulation of extracellular exosome assembly / positive regulation of protein monoubiquitination / neural crest formation / extracellular exosome biogenesis / viral budding / maintenance of epithelial cell apical/basal polarity / positive regulation of extracellular exosome assembly ...proteinase activated receptor binding / actomyosin contractile ring assembly / ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway / regulation of extracellular exosome assembly / positive regulation of protein monoubiquitination / neural crest formation / extracellular exosome biogenesis / viral budding / maintenance of epithelial cell apical/basal polarity / positive regulation of extracellular exosome assembly / regulation of membrane permeability / vascular endothelial growth factor receptor-2 signaling pathway / neural crest cell development / COPII vesicle coating / COPII vesicle coat / regulation of centrosome duplication / bicellular tight junction assembly / positive regulation of exosomal secretion / midbody abscission / actomyosin / multivesicular body assembly / Flemming body / negative regulation of TOR signaling / RIPK1-mediated regulated necrosis / Cul3-RING ubiquitin ligase complex / negative regulation of vascular endothelial growth factor receptor signaling pathway / viral budding via host ESCRT complex / endoplasmic reticulum exit site / mitotic cytokinesis / Uptake and function of anthrax toxins / immunological synapse / bicellular tight junction / endoplasmic reticulum to Golgi vesicle-mediated transport / ubiquitin-like ligase-substrate adaptor activity / protein-membrane adaptor activity / positive regulation of endothelial cell proliferation / positive regulation of endothelial cell migration / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Budding and maturation of HIV virion / macroautophagy / intracellular protein transport / apoptotic signaling pathway / Regulation of necroptotic cell death / response to calcium ion / protein homooligomerization / positive regulation of angiogenesis / calcium-dependent protein binding / melanosome / protein transport / extracellular vesicle / cellular response to heat / cytoplasmic vesicle / angiogenesis / protein-macromolecule adaptor activity / protein dimerization activity / endosome / positive regulation of apoptotic process / protein heterodimerization activity / focal adhesion / apoptotic process / calcium ion binding / centrosome / endoplasmic reticulum membrane / perinuclear region of cytoplasm / magnesium ion binding / endoplasmic reticulum / protein homodimerization activity / extracellular exosome / nucleoplasm / identical protein binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
: / ALIX V-shaped domain / ALIX V-shaped domain binding to HIV / BRO1 domain / BRO1 domain superfamily / BRO1-like domain / BRO1 domain profile. / BRO1-like domain / EF hand / EF-hand ...: / ALIX V-shaped domain / ALIX V-shaped domain binding to HIV / BRO1 domain / BRO1 domain superfamily / BRO1-like domain / BRO1 domain profile. / BRO1-like 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 / Programmed cell death 6-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 10, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Programmed cell death protein 6
B: Programmed cell death protein 6
C: 16-meric peptide from Programmed cell death 6-interacting protein
D: 16-meric peptide from Programmed cell death 6-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,86714
Polymers43,2984
Non-polymers56910
Water1,22568
1
A: Programmed cell death protein 6
C: 16-meric peptide from Programmed cell death 6-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9347
Polymers21,6492
Non-polymers2855
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-170 kcal/mol
Surface area10730 Å2
MethodPISA
2
B: Programmed cell death protein 6
D: 16-meric peptide from Programmed cell death 6-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9347
Polymers21,6492
Non-polymers2855
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-144 kcal/mol
Surface area11050 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6690 Å2
ΔGint-342 kcal/mol
Surface area18830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.449, 88.509, 211.556
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 19877.145 Da / Num. of mol.: 2 / Fragment: residues 2-191
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: Protein/peptide 16-meric peptide from Programmed cell death 6-interacting protein / PDCD6-interacting protein / ALG-2-interacting protein 1 / Hp95


Mass: 1771.879 Da / Num. of mol.: 2 / Fragment: ALG-2 binding site, residues 799-814 / Mutation: C15S / Source method: obtained synthetically
Details: chemical synthesis; This sequence occurs naturally in humans.
References: UniProt: Q8WUM4
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.56 Å3/Da / Density % sol: 52.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10% 2-propanol, 0.1M Cacodylate, 0.2M zinc acetate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 11, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 23278 / % possible obs: 98 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 11.8
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 4 / Num. unique all: 2099 / % possible all: 91.1

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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: 2.2→33.94 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.903 / SU B: 6.862 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.29 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27388 1163 5.1 %RANDOM
Rwork0.2228 ---
obs0.22547 21603 97.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.722 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2--0.67 Å20 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 2.2→33.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3002 0 10 68 3080
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223086
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4371.9214179
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.8915359
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.05523.693176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.19115499
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.4711526
X-RAY DIFFRACTIONr_chiral_restr0.120.2426
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022446
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2190.21506
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3160.22159
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2152
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0950.217
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.256
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2230.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8621.51798
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.63522914
X-RAY DIFFRACTIONr_scbond_it2.12231354
X-RAY DIFFRACTIONr_scangle_it3.514.51265
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.198→2.255 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 71 -
Rwork0.26 1462 -
obs--90.55 %

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