[English] 日本語
Yorodumi
- PDB-6tzc: Crystal Structure of African Swine Fever Virus A179L with the Aut... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6tzc
TitleCrystal Structure of African Swine Fever Virus A179L with the Autophagy Regulator Beclin
Components
  • Apoptosis regulator Bcl-2 homolog
  • Beclin-1BECN1
  • Maltose/maltodextrin-binding periplasmic protein
KeywordsSTRUCTURAL PROTEIN/APOPTOSIS / Apoptosis / Autophagy / Bcl-2 virus / STRUCTURAL PROTEIN / STRUCTURAL PROTEIN-APOPTOSIS complex
Function / homology
Function and homology information


phosphatidylinositol 3-kinase complex, class III / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / : / suppression by virus of host autophagy / early endosome to late endosome transport / cellular response to nitrogen starvation / late endosome to vacuole transport / phagophore assembly site / host cell endoplasmic reticulum ...phosphatidylinositol 3-kinase complex, class III / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / : / suppression by virus of host autophagy / early endosome to late endosome transport / cellular response to nitrogen starvation / late endosome to vacuole transport / phagophore assembly site / host cell endoplasmic reticulum / detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / host cell mitochondrion / autophagosome assembly / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / autophagosome / cellular response to glucose starvation / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / regulation of cytokinesis / mitochondrial membrane / macroautophagy / : / autophagy / endocytosis / outer membrane-bounded periplasmic space / regulation of apoptotic process / defense response to virus / periplasmic space / endosome membrane / cell cycle / cell division / apoptotic process / DNA damage response / endoplasmic reticulum membrane / Golgi apparatus / membrane / nucleus / cytosol
Similarity search - Function
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 / Apoptosis regulator, Bcl-2, BH1 motif, conserved site ...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 / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl-2 family / Bcl-2, Bcl-2 homology region 1-3 / Bcl2-like / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
alpha-maltose / Maltose/maltodextrin-binding periplasmic protein / Apoptosis regulator Bcl-2 homolog / Beclin-1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
African swine fever virus
Sus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsBanjara, S. / Kvansakul, M. / Hinds, M.G.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)FT130101349 Australia
CitationJournal: Viruses / Year: 2019
Title: Crystal Structure of African Swine Fever Virus A179L with the Autophagy Regulator Beclin.
Authors: Banjara, S. / Shimmon, G.L. / Dixon, L.K. / Netherton, C.L. / Hinds, M.G. / Kvansakul, M.
History
DepositionAug 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_2
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Maltose/maltodextrin-binding periplasmic protein
B: Apoptosis regulator Bcl-2 homolog
C: Beclin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9994
Polymers61,6573
Non-polymers3421
Water2,270126
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-15 kcal/mol
Surface area22390 Å2
Unit cell
Length a, b, c (Å)54.565, 44.347, 129.022
Angle α, β, γ (deg.)90.000, 94.532, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein Maltose/maltodextrin-binding periplasmic protein / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP


Mass: 40684.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: malE, b4034, JW3994 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9
#2: Protein Apoptosis regulator Bcl-2 homolog


Mass: 18126.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus (strain Badajoz 1971 Vero-adapted)
Strain: Badajoz 1971 Vero-adapted / Gene: Ba71V-041, A179L / Production host: Escherichia coli (E. coli) / References: UniProt: P42485
#3: Protein/peptide Beclin-1 / BECN1


Mass: 2845.193 Da / Num. of mol.: 1 / Fragment: BH3 motif, residues 103-128 / Source method: obtained synthetically / Source: (synth.) Sus scrofa (pig) / References: UniProt: Q4A1L5
#4: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.5 % / Description: Thin Plate
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M Ammonium sulfate, 0.1M Bis-Tris pH 5.5, 25% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.41→51.59 Å / Num. obs: 24021 / % possible obs: 99.4 % / Redundancy: 2.9 % / Biso Wilson estimate: 34.28 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.12 / Net I/σ(I): 4.6
Reflection shellResolution: 2.41→2.47 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2373 / CC1/2: 0.48 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
AMBER1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UA5

5ua5


Resolution: 2.41→51.58 Å / SU ML: 0.3476 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 27.2483
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2527 1182 4.92 %
Rwork0.2139 22839 -
obs0.2159 24021 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.93 Å2
Refinement stepCycle: LAST / Resolution: 2.41→51.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4140 0 23 126 4289
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00474297
X-RAY DIFFRACTIONf_angle_d0.59035849
X-RAY DIFFRACTIONf_chiral_restr0.0439655
X-RAY DIFFRACTIONf_plane_restr0.0032749
X-RAY DIFFRACTIONf_dihedral_angle_d19.32031550
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.41-2.520.32981320.30122829X-RAY DIFFRACTION98.5
2.52-2.650.36041420.27852817X-RAY DIFFRACTION99.13
2.65-2.820.30611240.26262858X-RAY DIFFRACTION98.61
2.82-3.030.29921760.24712807X-RAY DIFFRACTION99.14
3.03-3.340.2631640.23792851X-RAY DIFFRACTION99.83
3.34-3.820.25191460.19282857X-RAY DIFFRACTION99.57
3.82-4.810.18771530.16632862X-RAY DIFFRACTION98.69
4.82-51.580.2281450.19112958X-RAY DIFFRACTION98.01
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.33282671775-0.738900472331-0.6170219449921.42702698612-0.5048234772762.287987973990.1144280031460.2727044004510.518270361150.0327508698150.132116630050.0240583204576-0.389337281403-0.194810711469-0.2046112113080.3234318713990.00698738967261-0.01226605694370.2906983299620.0637495444510.360083349024-15.447598951-6.10298838892-27.0462563021
20.804406382105-0.353928415017-0.02725773923840.9276381486430.5846141105661.82312774227-0.002290573455120.189760360759-0.6228943698050.2451367247180.0596219930627-0.4393263708070.6748415000880.313025512562-0.09887856909140.3655686950010.05782481552120.0599228483140.366650207287-0.03094903527120.542794103857-8.58986784656-22.083655068-30.1412261445
31.117577630290.645660779978-0.9097695491551.91958384234-1.346363448211.30468502999-0.06820681521680.7272201589290.103699488207-0.4885331574430.1647570537130.06000612196950.142796833157-0.108950882572-0.04864689141360.53484153747-0.02318640245660.01139299798040.8239542160740.03747365303650.357122252626-5.31616509006-3.28799332697-54.7843548128
41.304501769140.462985923298-0.1073457635272.07880171089-0.08637131801430.78649273741-0.2711233031220.33328774327-0.3769013753560.138820249510.0407032983360.00343162983586-0.06122518373210.5659609255390.2014750574540.4395128615920.0944690267880.07663479517790.9765692267280.1246975695880.4362597561778.89580535765-4.00473724388-49.0511779071
51.782773161190.376664424422-0.9011756315041.10173341129-0.8571902528221.94845766113-0.02396252618240.6740394066980.00362699757837-0.297396280660.133415191270.1143979516420.0123114097755-0.280100524197-0.0288577486610.3667710319730.00756618355896-0.01965837246010.530070435093-0.01096038264270.296421208601-13.9085305779-8.97983698733-44.9256526016
63.202887679340.4699573730810.3283112938832.6657670148-1.127670238191.981095790590.05211276259460.05187119675450.4064971971430.374195080601-0.0488204727939-0.133589018027-0.722749200540.799514852486-0.03604888654750.50378762251-0.0519814752045-0.02656098376970.727687983437-0.002088561392050.5807041502678.167329874541.7031418186-41.8405481553
76.6523416262-1.047534246151.075405057423.60010288198-0.3477722257743.11736467318-0.150111074896-0.1358790035380.5312400175330.01243768460580.08896896690690.0902022991886-0.03142260773360.09575311038270.1746870770390.247688184611-0.0133134132521-0.02805841946380.277290001239-0.02697423943890.36630312582913.2013394412-13.2462364202-3.75173751835
83.27172850123-0.505654314737-0.03094734011411.49479658933-0.1071370455141.72496595466-0.05631369346650.166902323139-0.1349392635750.02250862197220.009701610505270.0009730178339550.1446379001930.002610346154850.03764652814090.1976060392770.00264093213669-0.01547155712810.07280026118890.01479878184050.24389416234312.9503625115-20.5834832841-11.2344317066
98.06851265674-4.3548371041-2.44577281733.936482491571.585117001685.675363459440.1259300354270.0594763720698-0.978418999735-0.1477079097-0.00671012356819-0.4212787041830.431884875534-0.0585327739439-0.02503221336950.311681692275-0.0128267613188-0.02586410218990.2198122226410.05184568510260.6365990919066.64883584158-30.4076743385-5.85160180723
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 98 )
2X-RAY DIFFRACTION2chain 'A' and (resid 99 through 131 )
3X-RAY DIFFRACTION3chain 'A' and (resid 132 through 198 )
4X-RAY DIFFRACTION4chain 'A' and (resid 199 through 226 )
5X-RAY DIFFRACTION5chain 'A' and (resid 227 through 359 )
6X-RAY DIFFRACTION6chain 'A' and (resid 360 through 394 )
7X-RAY DIFFRACTION7chain 'B' and (resid 3 through 53 )
8X-RAY DIFFRACTION8chain 'B' and (resid 54 through 146 )
9X-RAY DIFFRACTION9chain 'C' and (resid 106 through 125 )

+
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