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- PDB-3wxa: X-ray crystal structural analysis of the complex between ALG-2 an... -

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Basic information

Entry
Database: PDB / ID: 3wxa
TitleX-ray crystal structural analysis of the complex between ALG-2 and Sec31A peptide
Components
  • Programmed cell death protein 6
  • Protein transport protein Sec31A
KeywordsAPOPTOSIS/TRANSPORT PROTEIN / PENTA-EF-HAND PROTEIN / Endoplasmic reticulum / Membrane / Transport / Apoptosis / Calcium Binding / APOPTOSIS-TRANSPORT PROTEIN complex
Function / homology
Function and homology information


vesicle coat / neural crest formation / COPII-coated vesicle cargo loading / vascular endothelial growth factor receptor-2 signaling pathway / neural crest cell development / COPII vesicle coat / COPII vesicle coating / XBP1(S) activates chaperone genes / endoplasmic reticulum organization / negative regulation of TOR signaling ...vesicle coat / neural crest formation / COPII-coated vesicle cargo loading / vascular endothelial growth factor receptor-2 signaling pathway / neural crest cell development / COPII vesicle coat / COPII vesicle coating / XBP1(S) activates chaperone genes / endoplasmic reticulum organization / negative regulation of TOR signaling / COPII-mediated vesicle transport / positive regulation of protein monoubiquitination / Cul3-RING ubiquitin ligase complex / negative regulation of vascular endothelial growth factor receptor signaling pathway / COPII-coated ER to Golgi transport vesicle / : / 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 / MHC class II antigen presentation / positive regulation of endothelial cell migration / apoptotic signaling pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / ER to Golgi transport vesicle membrane / response to calcium ion / positive regulation of angiogenesis / calcium-dependent protein binding / Signaling by ALK fusions and activated point mutants / protein transport / cellular response to heat / protein-macromolecule adaptor activity / cytoplasmic vesicle / angiogenesis / protein dimerization activity / endosome / protein heterodimerization activity / intracellular membrane-bounded organelle / calcium ion binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / structural molecule activity / magnesium ion binding / endoplasmic reticulum / protein homodimerization activity / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Protein transport protein SEC31-like / Ancestral coatomer element 1, Sec16/Sec31 / Sec23-binding domain of Sec16 / EF hand / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site ...: / Protein transport protein SEC31-like / Ancestral coatomer element 1, Sec16/Sec31 / Sec23-binding domain of Sec16 / 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 / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Programmed cell death protein 6 / Protein transport protein Sec31A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsTakahashi, T. / Suzuki, H. / Kawasaki, M. / Shibata, H. / Wakatsuki, S. / Maki, M.
CitationJournal: Int J Mol Sci / Year: 2015
Title: Structural Analysis of the Complex between Penta-EF-Hand ALG-2 Protein and Sec31A Peptide Reveals a Novel Target Recognition Mechanism of ALG-2
Authors: Takahashi, T. / Kojima, K. / Zhang, W. / Sasaki, K. / Ito, M. / Suzuki, H. / Kawasaki, M. / Wakatsuki, S. / Takahara, T. / Shibata, H. / Maki, M.
History
DepositionJul 29, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Nov 8, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: Protein transport protein Sec31A
D: Protein transport protein Sec31A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,52814
Polymers42,8744
Non-polymers65410
Water50428
1
A: Programmed cell death protein 6
C: Protein transport protein Sec31A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7647
Polymers21,4372
Non-polymers3275
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-11 kcal/mol
Surface area11150 Å2
MethodPISA
2
B: Programmed cell death protein 6
D: Protein transport protein Sec31A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7647
Polymers21,4372
Non-polymers3275
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-9 kcal/mol
Surface area11040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.973, 81.973, 103.232
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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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: UNP 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: Protein/peptide Protein transport protein Sec31A / ABP125 / ABP130 / SEC31-like protein 1 / SEC31-related protein A / Web1-like protein


Mass: 1278.458 Da / Num. of mol.: 2 / Fragment: ALG-2 binding site, UNP residues 837-848 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo sapiens (human) / References: UniProt: O94979
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.34 Å3/Da / Density % sol: 47.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M Cacodylate, 20% MPD, 0.05M Zinc Acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1.28209 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 21, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28209 Å / Relative weight: 1
ReflectionResolution: 2.36→71 Å / Num. all: 16251 / Num. obs: 16160 / % possible obs: 99.4 % / Redundancy: 10.3 % / Biso Wilson estimate: 36.9 Å2 / Rsym value: 0.08 / Net I/σ(I): 33
Reflection shellResolution: 2.36→2.421 Å / Redundancy: 10.3 % / Mean I/σ(I) obs: 33 / Num. unique all: 16251 / Rsym value: 0.08 / % possible all: 99.4

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Processing

Software
NameVersionClassification
SERGUIdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZND

2znd


Resolution: 2.36→38.094 Å / σ(F): 1.37 / Phase error: 28.13 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.263 813 5.03 %RANDOM
Rwork0.2254 ---
obs0.2304 16147 99.54 %-
all-16251 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.36→38.094 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2960 0 10 28 2998
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033034
X-RAY DIFFRACTIONf_angle_d0.6124102
X-RAY DIFFRACTIONf_dihedral_angle_d13.91104
X-RAY DIFFRACTIONf_chiral_restr0.024422
X-RAY DIFFRACTIONf_plane_restr0.003540
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3607-2.50840.30111430.2976252094
2.5084-2.70180.30871300.2795256095
2.7018-2.97310.33151360.2761255995
2.9731-3.40190.28781400.2504255995
3.4019-4.28070.22511430.198256795
4.2807-21.84010.24681210.2012254893

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