[English] 日本語
Yorodumi
- PDB-3wxa: X-ray crystal structural analysis of the complex between ALG-2 an... -

+
Open data


ID or keywords:

Loading...

-
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 / vascular endothelial growth factor receptor-2 signaling pathway / COPII-coated vesicle cargo loading / neural crest cell development / COPII vesicle coating / COPII vesicle coat / XBP1(S) activates chaperone genes / COPII-coated ER to Golgi transport vesicle / endoplasmic reticulum organization ...vesicle coat / neural crest formation / vascular endothelial growth factor receptor-2 signaling pathway / COPII-coated vesicle cargo loading / neural crest cell development / COPII vesicle coating / COPII vesicle coat / XBP1(S) activates chaperone genes / COPII-coated ER to Golgi transport vesicle / endoplasmic reticulum organization / negative regulation of TOR signaling / COPII-mediated vesicle transport / positive regulation of protein monoubiquitination / negative regulation of vascular endothelial growth factor receptor signaling pathway / Cul3-RING ubiquitin ligase complex / endoplasmic reticulum exit site / 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 / MHC class II antigen presentation / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / apoptotic signaling pathway / 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 / cytoplasmic vesicle / angiogenesis / protein-macromolecule adaptor activity / endosome / protein dimerization activity / positive regulation of apoptotic process / 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 / cytoplasm / cytosol
Similarity search - Function
: / Protein transport protein SEC31-like / Ancestral coatomer element 1, Sec16/Sec31 / Sec16 Sec23-binding domain / 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 / Sec16 Sec23-binding 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
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