[English] 日本語
Yorodumi
- PDB-6uxm: Crystal structure of BAK core domain BH3-groove-dimer in complex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6uxm
TitleCrystal structure of BAK core domain BH3-groove-dimer in complex with E. coli lipid
ComponentsBcl-2 homologous antagonist/killer
KeywordsAPOPTOSIS / Pore-forming Protein
Function / homology
Function and homology information


Activation and oligomerization of BAK protein / BH domain binding / B cell negative selection / BAK complex / negative regulation of endoplasmic reticulum calcium ion concentration / response to fungus / response to mycotoxin / limb morphogenesis / Release of apoptotic factors from the mitochondria / apoptotic process involved in blood vessel morphogenesis ...Activation and oligomerization of BAK protein / BH domain binding / B cell negative selection / BAK complex / negative regulation of endoplasmic reticulum calcium ion concentration / response to fungus / response to mycotoxin / limb morphogenesis / Release of apoptotic factors from the mitochondria / apoptotic process involved in blood vessel morphogenesis / post-embryonic camera-type eye morphogenesis / endocrine pancreas development / establishment or maintenance of transmembrane electrochemical gradient / B cell apoptotic process / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / endoplasmic reticulum calcium ion homeostasis / regulation of mitochondrial membrane permeability / calcium ion transport into cytosol / fibroblast apoptotic process / response to UV-C / mitochondrial fusion / Bcl-2 family protein complex / myeloid cell homeostasis / porin activity / thymocyte apoptotic process / negative regulation of release of cytochrome c from mitochondria / pore complex / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / vagina development / B cell homeostasis / positive regulation of calcium ion transport into cytosol / positive regulation of proteolysis / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / blood vessel remodeling / animal organ regeneration / cellular response to unfolded protein / Pyroptosis / heat shock protein binding / extrinsic apoptotic signaling pathway in absence of ligand / intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / epithelial cell proliferation / response to gamma radiation / regulation of mitochondrial membrane potential / apoptotic signaling pathway / positive regulation of protein-containing complex assembly / response to hydrogen peroxide / establishment of localization in cell / cellular response to mechanical stimulus / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to UV / protein-folding chaperone binding / channel activity / response to ethanol / transmembrane transporter binding / mitochondrial outer membrane / regulation of cell cycle / positive regulation of apoptotic process / response to xenobiotic stimulus / protein heterodimerization activity / negative regulation of cell population proliferation / negative regulation of gene expression / apoptotic process / protein-containing complex binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / metal ion binding / identical protein binding / cytosol
Similarity search - Function
Blc2-like / Apoptosis Regulator Bcl-x / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / 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-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions ...Blc2-like / Apoptosis Regulator Bcl-x / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / 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-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl2-like / Bcl-2, Bcl-2 homology region 1-3 / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Bcl-2 homologous antagonist/killer
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.49 Å
AuthorsCowan, A.D. / Colman, P.M. / Czabotar, P.E.
Funding support Australia, 3items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1079706 Australia
National Health and Medical Research Council (NHMRC, Australia)1059290 Australia
National Health and Medical Research Council (NHMRC, Australia)1113133 Australia
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2020
Title: BAK core dimers bind lipids and can be bridged by them.
Authors: Cowan, A.D. / Smith, N.A. / Sandow, J.J. / Kapp, E.A. / Rustam, Y.H. / Murphy, J.M. / Brouwer, J.M. / Bernardini, J.P. / Roy, M.J. / Wardak, A.Z. / Tan, I.K. / Webb, A.I. / Gulbis, J.M. / ...Authors: Cowan, A.D. / Smith, N.A. / Sandow, J.J. / Kapp, E.A. / Rustam, Y.H. / Murphy, J.M. / Brouwer, J.M. / Bernardini, J.P. / Roy, M.J. / Wardak, A.Z. / Tan, I.K. / Webb, A.I. / Gulbis, J.M. / Smith, B.J. / Reid, G.E. / Dewson, G. / Colman, P.M. / Czabotar, P.E.
History
DepositionNov 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0Oct 11, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
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_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.mon_nstd_flag / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bcl-2 homologous antagonist/killer
B: Bcl-2 homologous antagonist/killer
C: Bcl-2 homologous antagonist/killer
D: Bcl-2 homologous antagonist/killer
E: Bcl-2 homologous antagonist/killer
F: Bcl-2 homologous antagonist/killer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,46812
Polymers57,0046
Non-polymers4,4646
Water00
1
A: Bcl-2 homologous antagonist/killer
B: Bcl-2 homologous antagonist/killer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4894
Polymers19,0012
Non-polymers1,4882
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-47 kcal/mol
Surface area9290 Å2
MethodPISA
2
C: Bcl-2 homologous antagonist/killer
D: Bcl-2 homologous antagonist/killer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4894
Polymers19,0012
Non-polymers1,4882
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-43 kcal/mol
Surface area9190 Å2
MethodPISA
3
E: Bcl-2 homologous antagonist/killer
F: Bcl-2 homologous antagonist/killer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4894
Polymers19,0012
Non-polymers1,4882
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-45 kcal/mol
Surface area9280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.700, 55.040, 56.500
Angle α, β, γ (deg.)116.130, 109.670, 97.020
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 70 through 145 or (resid 200...
21(chain B and (resid 70 through 145 or (resid 200...
31(chain C and (resid 70 through 145 or (resid 200...
41(chain D and (resid 70 through 145 or (resid 200...
51(chain E and (resid 70 through 145 or (resid 200...
61(chain F and (resid 70 through 145 or (resid 200...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 70 through 145 or (resid 200...A0
211(chain B and (resid 70 through 145 or (resid 200...B0
311(chain C and (resid 70 through 145 or (resid 200...C0
411(chain D and (resid 70 through 145 or (resid 200...D0
511(chain E and (resid 70 through 145 or (resid 200...E0
611(chain F and (resid 70 through 145 or (resid 200...F0

-
Components

#1: Protein
Bcl-2 homologous antagonist/killer / Apoptosis regulator BAK / Bcl-2-like protein 7 / Bcl2-L-7


Mass: 9500.688 Da / Num. of mol.: 6 / Fragment: Core/dimerisation domain, residues 68-148
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAK1, BAK, BCL2L7, CDN1 / Plasmid: pGEX-6P-3 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q16611
#2: Chemical
ChemComp-PEE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE


Mass: 744.034 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C41H78NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: DOPE, phospholipid*YM
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: ammonium sulphate, PEG 10000, sodium acetate, bis-tris chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.49→25.665 Å / Num. obs: 15495 / % possible obs: 97.4 % / Redundancy: 9.436 % / Biso Wilson estimate: 75.759 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Rrim(I) all: 0.096 / Χ2: 1.016 / Net I/σ(I): 15.03 / Num. measured all: 146213 / Scaling rejects: 190
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.49-2.558.8061.9051.289449116610730.5182.02692
2.55-2.629.7821.41.910878114311120.7221.47797.3
2.62-2.79.7440.962.9510826113211110.8641.01498.1
2.7-2.789.7550.7743.7510028105810280.9260.81797.2
2.78-2.879.7410.6274.5410033104410300.9270.66198.7
2.87-2.989.7310.5195.51967310219940.9470.54897.4
2.98-3.099.680.3617.7693419819650.9750.38198.4
3.09-3.219.7690.24910.789299309140.9890.26298.3
3.21-3.369.670.16914.5187429299040.9940.17897.3
3.36-3.529.5920.11918.4581828588530.9960.12699.4
3.52-3.719.5560.10121.9276268167980.9970.10797.8
3.71-3.949.3780.07426.6572687937750.9970.07897.7
3.94-4.219.0990.06629.565067177150.9970.0799.7
4.21-4.559.1670.06130.9361606836720.9980.06598.4
4.55-4.988.8950.05832.1554886286170.9980.06198.2
4.98-5.578.8110.05533.0548555615510.9980.05998.2
5.57-6.438.7380.0632.3842644994880.9970.06497.8
6.43-7.879.1040.053538514344230.9980.05397.5
7.87-11.139.0430.04437.3329393313250.9970.04698.2
11.13-25.6657.9930.04235.4411751791470.9980.04582.1

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.49 Å46.91 Å
Translation2.49 Å46.91 Å

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.5.6phasing
PHENIX1.14refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U2V

4u2v


Resolution: 2.49→25.665 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 27.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2372 1546 10 %
Rwork0.1872 13914 -
obs0.1922 15460 98.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 205.69 Å2 / Biso mean: 92.0494 Å2 / Biso min: 42.69 Å2
Refinement stepCycle: final / Resolution: 2.49→25.665 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3775 0 173 0 3948
Biso mean--86.52 --
Num. residues----470
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1871X-RAY DIFFRACTION12.566TORSIONAL
12B1871X-RAY DIFFRACTION12.566TORSIONAL
13C1871X-RAY DIFFRACTION12.566TORSIONAL
14D1871X-RAY DIFFRACTION12.566TORSIONAL
15E1871X-RAY DIFFRACTION12.566TORSIONAL
16F1871X-RAY DIFFRACTION12.566TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.49-2.57020.38371300.3108117592
2.5702-2.66190.31131420.262124098
2.6619-2.76840.29351440.2395128898
2.7684-2.89420.29481430.2196126799
2.8942-3.04660.27651370.2168128199
3.0466-3.23710.27691430.2009126899
3.2371-3.48650.21581410.1764128199
3.4865-3.83630.2491380.1883128499
3.8363-4.38910.21571430.178127299
4.3891-5.52070.23131420.1859128199
5.5207-25.6650.20841430.1601127799
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)
19.12685.4318-6.49382.04162.1139.49930.40612.20091.7497-1.8085-0.14623.4797-0.592-1.82642.35881.5139-0.0516-0.78110.67560.06890.60515.21785.080511.5144
25.83470.79320.1062.63330.14230.0383-0.96671.7243-1.2705-0.89450.45270.07820.52830.6633-0.69832.01790.25760.50011.2069-0.39710.86928.0572-9.22219.8518
38.85041.24451.0996.949-2.19129.1522-0.12251.211-0.6774-1.32030.1822-0.94250.28520.6405-0.23160.57480.13280.2510.6637-0.02420.485926.841-4.480418.0723
42.0571-4.23371.07874.86141.25870.95940.80543.10552.4431-2.2945-0.732-1.0734-0.59970.38740.54081.5222-0.13650.3920.9750.16770.678127.86574.254710.8991
57.8733-0.78592.77449.7094.30626.2505-0.2222-0.21661.1616-1.3598-0.29771.3878-0.9385-0.51360.43350.8440.0456-0.25970.6970.08941.02574.12728.383120.5441
64.07144.71311.65146.25991.42825.79260.1316-0.06670.5725-1.4258-0.2360.6976-0.8911-0.19540.33730.56380.0729-0.14530.4903-0.00270.628311.119410.54523.3452
73.9281-3.5167-0.09363.49-1.22845.62131.145-1.77691.2351.5002-1.00262.1685-1.2536-0.7574-0.52010.88420.10450.36420.9914-0.34331.07874.46127.64646.428
86.93880.01510.97684.2244-1.62777.93070.1430.35831.21790.2836-0.2472-0.7158-1.37390.46650.1140.75140.01410.02970.65510.05750.817229.205411.368835.7619
96.59790.49823.60376.85440.08896.57280.12250.19841.34940.5369-0.09121.1329-2.0245-1.72550.21950.56570.11660.04230.51560.10030.552621.702411.253933.9739
105.77811.8737-7.50254.4448-2.57672.10791.4472-1.78382.41831.1137-0.7314-1.1449-1.79462.0373-0.36310.8938-0.2073-0.05231.1536-0.09130.856327.723110.065445.8272
113.68643.54960.41254.85571.2912.0671.5977-1.464-0.56723.5292-1.10250.54210.5375-0.6235-0.351.2277-0.38040.1671.21360.00180.79886.4466-4.050851.3059
125.2422-1.385-0.54638.97650.51058.00870.531-0.97130.12450.1667-0.67361.11140.58590.14670.19460.4515-0.04410.16290.549-0.05320.67187.3443-1.521742.0695
135.6464-3.65050.48055.3721-3.47124.4776-0.3486-0.609-2.321.03750.00871.20570.6945-0.94280.11820.9221-0.06850.0430.6585-0.04721.14675.3904-23.607731.7084
145.1465-0.0029-0.55655.32646.5178.0874-0.1826-1.5564-1.21112.0344-0.4055-1.13741.89050.7227-0.91351.06060.0169-0.34271.08180.38250.904625.8311-21.631244.4313
152.41532.89651.72225.87554.84245.360.2817-0.2256-0.08380.78070.6143-1.08310.20131.1946-1.03240.78450.0548-0.21790.88560.09311.227831.8899-11.228637.2692
166.176-2.3189-2.7737.93514.42823.7289-0.3466-0.9098-0.63721.4244-0.52751.24891.0883-0.2560.29030.6471-0.0878-0.02590.67340.23150.52622.2454-13.880940.6366
179.92096.0473.68023.94852.01566.7131-0.31131.1963-1.2212-0.63840.0277-2.47521.40741.8073-1.35350.7090.3349-0.24760.61360.1421.572928.6954-23.230533.749
184.0713-3.16451.11787.3462-6.51446.9508-0.63351.7722-1.1577-1.9972-0.4033-0.16342.59010.5232-0.07561.2007-0.0217-0.15430.7999-0.14851.10779.1358-25.080621.6168
194.99953.4956-0.04228.17341.32787.4624-0.01560.95220.4005-0.98330.50621.3539-0.137-0.8565-0.38770.56160.0342-0.12130.58520.09640.59037.1347-15.067524.2216
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'E' and (resid 67 through 88 )E67 - 88
2X-RAY DIFFRACTION2chain 'E' and (resid 89 through 106 )E89 - 106
3X-RAY DIFFRACTION3chain 'E' and (resid 107 through 145 )E107 - 145
4X-RAY DIFFRACTION4chain 'F' and (resid 70 through 88 )F70 - 88
5X-RAY DIFFRACTION5chain 'F' and (resid 89 through 124 )F89 - 124
6X-RAY DIFFRACTION6chain 'F' and (resid 125 through 148 )F125 - 148
7X-RAY DIFFRACTION7chain 'A' and (resid 67 through 88 )A67 - 88
8X-RAY DIFFRACTION8chain 'A' and (resid 89 through 124 )A89 - 124
9X-RAY DIFFRACTION9chain 'A' and (resid 125 through 145 )A125 - 145
10X-RAY DIFFRACTION10chain 'B' and (resid 69 through 88 )B69 - 88
11X-RAY DIFFRACTION11chain 'B' and (resid 89 through 106 )B89 - 106
12X-RAY DIFFRACTION12chain 'B' and (resid 107 through 145 )B107 - 145
13X-RAY DIFFRACTION13chain 'C' and (resid 67 through 88 )C67 - 88
14X-RAY DIFFRACTION14chain 'C' and (resid 89 through 100 )C89 - 100
15X-RAY DIFFRACTION15chain 'C' and (resid 101 through 124 )C101 - 124
16X-RAY DIFFRACTION16chain 'C' and (resid 125 through 145 )C125 - 145
17X-RAY DIFFRACTION17chain 'D' and (resid 69 through 88 )D69 - 88
18X-RAY DIFFRACTION18chain 'D' and (resid 89 through 100 )D89 - 100
19X-RAY DIFFRACTION19chain 'D' and (resid 101 through 145 )D101 - 145

+
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