[English] 日本語
Yorodumi
- PDB-8pc2: SelDeg51 in complex with FKBP51FK1 domain and pVHL:EloB:EloC -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8pc2
TitleSelDeg51 in complex with FKBP51FK1 domain and pVHL:EloB:EloC
Components
  • Elongin-B
  • Elongin-C
  • Peptidyl-prolyl cis-trans isomerase FKBP5
  • von Hippel-Lindau disease tumor suppressor
KeywordsISOMERASE / FKBP51 / SAFit / Complex / PROTAC
Function / homology
Function and homology information


regulation of cellular response to hypoxia / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / transcription elongation factor activity / target-directed miRNA degradation / elongin complex / VCB complex / Replication of the SARS-CoV-1 genome / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex ...regulation of cellular response to hypoxia / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / transcription elongation factor activity / target-directed miRNA degradation / elongin complex / VCB complex / Replication of the SARS-CoV-1 genome / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / FK506 binding / intracellular non-membrane-bounded organelle / SUMOylation of ubiquitinylation proteins / negative regulation of transcription elongation by RNA polymerase II / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / ubiquitin-like ligase-substrate adaptor activity / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / negative regulation of signal transduction / chaperone-mediated protein folding / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / MECP2 regulates neuronal receptors and channels / negative regulation of TORC1 signaling / RNA Polymerase II Pre-transcription Events / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / ESR-mediated signaling / negative regulation of autophagy / transcription corepressor binding / peptidylprolyl isomerase / Evasion by RSV of host interferon responses / peptidyl-prolyl cis-trans isomerase activity / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / positive regulation of cell differentiation / TP53 Regulates Transcription of DNA Repair Genes / Vif-mediated degradation of APOBEC3G / response to bacterium / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / cell morphogenesis / Inactivation of CSF3 (G-CSF) signaling / Regulation of expression of SLITs and ROBOs / ubiquitin-protein transferase activity / transcription corepressor activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / protein folding / protein-macromolecule adaptor activity / Neddylation / Replication of the SARS-CoV-2 genome / cellular response to hypoxia / ubiquitin-dependent protein catabolic process / regulation of gene expression / proteasome-mediated ubiquitin-dependent protein catabolic process / protein-containing complex assembly / DNA-binding transcription factor binding / amyloid fibril formation / molecular adaptor activity / protein stabilization / protein ubiquitination / negative regulation of cell population proliferation / negative regulation of gene expression / ubiquitin protein ligase binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / mitochondrion / proteolysis / extracellular exosome / nucleoplasm / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
von Hippel-Lindau disease tumour suppressor, beta/alpha domain / von Hippel-Lindau disease tumour suppressor, alpha domain / von Hippel-Lindau disease tumour suppressor, beta domain / VHL superfamily / von Hippel-Lindau disease tumour suppressor, alpha domain superfamily / von Hippel-Lindau disease tumour suppressor, beta domain superfamily / VHL beta domain / VHL box domain / Tetratricopeptide repeat / Elongin B ...von Hippel-Lindau disease tumour suppressor, beta/alpha domain / von Hippel-Lindau disease tumour suppressor, alpha domain / von Hippel-Lindau disease tumour suppressor, beta domain / VHL superfamily / von Hippel-Lindau disease tumour suppressor, alpha domain superfamily / von Hippel-Lindau disease tumour suppressor, beta domain superfamily / VHL beta domain / VHL box domain / Tetratricopeptide repeat / Elongin B / Elongin-C / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / TPR repeat region circular profile. / TPR repeat profile. / SKP1/BTB/POZ domain superfamily / Tetratricopeptide repeats / Tetratricopeptide repeat / Ubiquitin family / Ubiquitin homologues / Tetratricopeptide-like helical domain superfamily / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Chem-XZW / von Hippel-Lindau disease tumor suppressor / Peptidyl-prolyl cis-trans isomerase FKBP5 / Elongin-C / Elongin-B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMeyners, C. / Walz, M. / Geiger, T.M. / Hausch, F.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2024
Title: Discovery of a Potent Proteolysis Targeting Chimera Enables Targeting the Scaffolding Functions of FK506-Binding Protein 51 (FKBP51).
Authors: Geiger, T.M. / Walz, M. / Meyners, C. / Kuehn, A. / Dreizler, J.K. / Sugiarto, W.O. / Maciel, E.V.S. / Zheng, M. / Lermyte, F. / Hausch, F.
History
DepositionJun 9, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 27, 2023Group: Database references / Category: citation / citation_author
Item: _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Jan 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.4Jan 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: von Hippel-Lindau disease tumor suppressor
C: Elongin-C
D: Elongin-B
G: Peptidyl-prolyl cis-trans isomerase FKBP5
A: von Hippel-Lindau disease tumor suppressor
E: Elongin-C
F: Elongin-B
H: Peptidyl-prolyl cis-trans isomerase FKBP5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,54610
Polymers110,8598
Non-polymers2,6872
Water25214
1
B: von Hippel-Lindau disease tumor suppressor
C: Elongin-C
D: Elongin-B
G: Peptidyl-prolyl cis-trans isomerase FKBP5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7735
Polymers55,4294
Non-polymers1,3441
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: von Hippel-Lindau disease tumor suppressor
E: Elongin-C
F: Elongin-B
H: Peptidyl-prolyl cis-trans isomerase FKBP5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7735
Polymers55,4294
Non-polymers1,3441
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.646, 68.425, 159.256
Angle α, β, γ (deg.)90.000, 114.453, 90.000
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21B
32B
42B
53B
63B
74B
84B

NCS domain segments:
Dom-IDComponent-IDEns-IDAuth asym-IDAuth seq-ID
111B61 - 209
211B61 - 209
322B16 - 112
422B16 - 112
533B1 - 104
633B1 - 104
744B22 - 138
844B22 - 138

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8

-
Components

-
Protein , 4 types, 8 molecules BACEDFGH

#1: Protein von Hippel-Lindau disease tumor suppressor / Protein G7 / pVHL


Mass: 18702.291 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VHL / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P40337
#2: Protein Elongin-C / EloC / Elongin 15 kDa subunit / RNA polymerase II transcription factor SIII subunit C / SIII p15 / ...EloC / Elongin 15 kDa subunit / RNA polymerase II transcription factor SIII subunit C / SIII p15 / Transcription elongation factor B polypeptide 1


Mass: 10974.616 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOC, TCEB1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15369
#3: Protein Elongin-B / EloB / Elongin 18 kDa subunit / RNA polymerase II transcription factor SIII subunit B / SIII p18 / ...EloB / Elongin 18 kDa subunit / RNA polymerase II transcription factor SIII subunit B / SIII p18 / Transcription elongation factor B polypeptide 2


Mass: 11748.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOB, TCEB2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15370
#4: Protein Peptidyl-prolyl cis-trans isomerase FKBP5 / PPIase FKBP5 / 51 kDa FK506-binding protein / FKBP-51 / 54 kDa progesterone receptor-associated ...PPIase FKBP5 / 51 kDa FK506-binding protein / FKBP-51 / 54 kDa progesterone receptor-associated immunophilin / Androgen-regulated protein 6 / FF1 antigen / FK506-binding protein 5 / FKBP-5 / FKBP54 / p54 / HSP90-binding immunophilin / Rotamase


Mass: 14004.026 Da / Num. of mol.: 2 / Mutation: A19T, C103A, C107I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP5, AIG6, FKBP51 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q13451, peptidylprolyl isomerase

-
Non-polymers , 2 types, 16 molecules

#5: Chemical ChemComp-XZW / [(1~{R})-3-(3,4-dimethoxyphenyl)-1-[4-[[1-[3-[2-[[[(2~{S},4~{R})-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidin-2-yl]carbonylamino]methyl]-5-(4-methyl-1,3-thiazol-5-yl)phenoxy]propyl]-1,2,3-triazol-4-yl]methoxy]phenyl]propyl] (2~{S})-1-[(2~{S})-2-cyclohexyl-2-(3,4,5-trimethoxyphenyl)ethanoyl]piperidine-2-carboxylate


Mass: 1343.602 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C72H91FN8O14S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 15% PEG3350, 0.2 M tri-sodium citrate, 0.1 M HEPES-NaOH pH 7.5 and 10% glycol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.8→48.74 Å / Num. obs: 33478 / % possible obs: 99.1 % / Redundancy: 4.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.07 / Rrim(I) all: 0.113 / Net I/σ(I): 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
9.29-48.7440.0289460.9990.0220.036
2.8-2.944.70.52344590.9250.4090.668

-
Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→48.739 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.911 / SU B: 36.246 / SU ML: 0.304 / Cross valid method: THROUGHOUT / ESU R: 0.948 / ESU R Free: 0.355
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2607 1674 5 %
Rwork0.2104 31803 -
all0.213 --
obs-33477 98.889 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 74.69 Å2
Baniso -1Baniso -2Baniso -3
1-3.195 Å2-0 Å26.89 Å2
2---9.174 Å20 Å2
3----0.204 Å2
Refinement stepCycle: LAST / Resolution: 2.8→48.739 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7018 0 192 14 7224
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0127390
X-RAY DIFFRACTIONr_bond_other_d0.0030.0166848
X-RAY DIFFRACTIONr_angle_refined_deg1.5811.69110082
X-RAY DIFFRACTIONr_angle_other_deg0.7931.61215726
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8625908
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.829546
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.272101108
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.43110302
X-RAY DIFFRACTIONr_chiral_restr0.0590.21143
X-RAY DIFFRACTIONr_chiral_restr_other1.2030.260
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028546
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021634
X-RAY DIFFRACTIONr_nbd_refined0.2270.21429
X-RAY DIFFRACTIONr_symmetry_nbd_other0.20.26537
X-RAY DIFFRACTIONr_nbtor_refined0.1860.23649
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.23876
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2135
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0360.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0990.214
X-RAY DIFFRACTIONr_nbd_other0.190.232
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2750.23
X-RAY DIFFRACTIONr_mcbond_it4.5155.6143668
X-RAY DIFFRACTIONr_mcbond_other4.5145.6133667
X-RAY DIFFRACTIONr_mcangle_it6.70710.0844564
X-RAY DIFFRACTIONr_mcangle_other6.70710.0844565
X-RAY DIFFRACTIONr_scbond_it4.7035.7543722
X-RAY DIFFRACTIONr_scbond_other4.7025.7553723
X-RAY DIFFRACTIONr_scangle_it6.97610.4875512
X-RAY DIFFRACTIONr_scangle_other6.97510.4885513
X-RAY DIFFRACTIONr_lrange_it8.85952.0397855
X-RAY DIFFRACTIONr_lrange_other8.8652.0357855
X-RAY DIFFRACTIONr_ncsr_local_group_10.1030.054562
X-RAY DIFFRACTIONr_ncsr_local_group_20.0830.052603
X-RAY DIFFRACTIONr_ncsr_local_group_30.0960.052913
X-RAY DIFFRACTIONr_ncsr_local_group_40.1010.052977
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11BX-RAY DIFFRACTIONLocal ncs0.103270.0501
12BX-RAY DIFFRACTIONLocal ncs0.103270.0501
23BX-RAY DIFFRACTIONLocal ncs0.083030.05009
24BX-RAY DIFFRACTIONLocal ncs0.083030.05009
35BX-RAY DIFFRACTIONLocal ncs0.096380.05009
36BX-RAY DIFFRACTIONLocal ncs0.096380.05009
47BX-RAY DIFFRACTIONLocal ncs0.101220.05008
48BX-RAY DIFFRACTIONLocal ncs0.101220.05008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.8-2.8720.3651150.31623400.31824760.910.92999.15190.298
2.872-2.9510.3581370.29523030.29924580.8950.93199.26770.274
2.951-3.0360.3581050.29422040.29723260.8960.93599.26910.271
3.036-3.1290.3331220.25721410.26222790.9220.9599.29790.235
3.129-3.2310.3291120.23520740.23922010.9250.95999.31850.213
3.231-3.3440.32970.22120220.22621360.9440.96699.20410.199
3.344-3.470.305890.23119560.23420640.9440.96599.07950.216
3.47-3.6110.334890.25218870.25620140.9390.95998.11320.234
3.611-3.770.298880.21817790.22119030.9480.97298.10830.204
3.77-3.9530.245950.17917260.18218270.9630.98299.67160.166
3.953-4.1660.2840.1516450.15317360.9770.98699.59680.141
4.166-4.4160.178920.14815550.1516550.9780.98699.51660.142
4.416-4.7180.166660.1414660.14115400.9830.98899.48050.136
4.718-5.0920.196710.14813750.1514650.9770.98998.70310.143
5.092-5.5720.259680.19812350.20113450.9640.98296.87730.189
5.572-6.220.276660.21311620.21712360.9570.97699.35280.204
6.22-7.1630.231630.2069880.20710600.9640.97799.15090.197
7.163-8.7260.237510.2038780.2059450.9640.97498.30690.206
8.726-12.1470.205420.1986520.1987210.9810.98296.25520.208
12.147-48.7390.301220.354150.3484500.9570.93797.11110.376
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)
11.58331.14620.26383.04811.89241.7819-0.02910.1126-0.17830.18020.0238-0.27060.19990.18440.00520.03870.00630.01820.11950.05210.0853-27.412720.0544-20.5866
20.85430.1-1.23482.60560.61395.08110.1523-0.45670.04270.4278-0.1429-0.2623-0.18210.3646-0.00940.0958-0.0867-0.02710.2712-0.02040.0941-30.070636.22183.7523
33.46650.85-2.08261.0975-1.01172.82630.1798-0.26540.35040.1157-0.06270.2532-0.2168-0.281-0.11720.0725-0.02240.03960.1917-0.11390.1494-46.667939.43719.3145
43.33980.2421-0.58582.5491-0.89343.6762-0.05710.2496-0.04440.0365-0.11850.40380.2232-0.55230.17560.04130.0057-0.00220.2253-0.14130.1404-37.22890.3219-46.4265
53.7022-1.00870.33061.4355-0.40941.24290.1126-0.0068-0.48020.0368-0.14430.12010.2381-0.11180.03180.158-0.08020.07650.0539-0.03760.1268-49.35470.7343-9.3988
63.3613-0.02690.23660.9865-0.20341.02810.03660.6665-0.0525-0.3297-0.04120.16490.0367-0.20970.00460.1538-0.01480.02320.3259-0.11380.1821-69.024514.6773-25.7424
72.38620.3584-0.25843.3918-0.36931.38410.11130.4820.499-0.1454-0.0266-0.0911-0.4401-0.047-0.08480.19210.02770.09760.35970.06610.2235-68.923932.8217-25.7425
83.07510.80040.72673.5476-2.30916.53120.2743-0.23060.06990.5546-0.1242-0.5324-0.51310.859-0.15010.5916-0.2187-0.1190.61750.00060.4656-22.0734-2.70959.7216
Refinement TLS groupSelection: ALL

+
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