[English] 日本語
Yorodumi
- PDB-6hay: Crystal structure of PROTAC 1 in complex with the bromodomain of ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hay
TitleCrystal structure of PROTAC 1 in complex with the bromodomain of human SMARCA2 and pVHL:ElonginC:ElonginB
Components
  • Elongin-B
  • Elongin-C
  • Probable global transcription activator SNF2L2
  • von Hippel-Lindau disease tumor suppressor
KeywordsGENE REGULATION / bromodomain / E3 Ubiquitin Protein Ligase
Function / homology
Function and homology information


bBAF complex / npBAF complex / brahma complex / nBAF complex / regulation of cellular response to hypoxia / GBAF complex / regulation of G0 to G1 transition / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / transcription elongation factor activity ...bBAF complex / npBAF complex / brahma complex / nBAF complex / regulation of cellular response to hypoxia / GBAF complex / regulation of G0 to G1 transition / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / transcription elongation factor activity / regulation of nucleotide-excision repair / target-directed miRNA degradation / elongin complex / VCB complex / SWI/SNF complex / ATP-dependent chromatin remodeler activity / regulation of mitotic metaphase/anaphase transition / Replication of the SARS-CoV-1 genome / Cul5-RING ubiquitin ligase complex / positive regulation of double-strand break repair / positive regulation of T cell differentiation / intermediate filament cytoskeleton / Cul2-RING ubiquitin ligase complex / positive regulation of stem cell population maintenance / intracellular non-membrane-bounded organelle / SUMOylation of ubiquitinylation proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / negative regulation of transcription elongation by RNA polymerase II / spermatid development / regulation of G1/S transition of mitotic cell cycle / negative regulation of cell differentiation / 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 / positive regulation of myoblast differentiation / ATP-dependent activity, acting on DNA / Formation of HIV elongation complex in the absence of HIV Tat / negative regulation of signal transduction / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / negative regulation of TORC1 signaling / RNA Polymerase II Pre-transcription Events / negative regulation of autophagy / transcription corepressor binding / helicase 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 / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Vif-mediated degradation of APOBEC3G / cell morphogenesis / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Inactivation of CSF3 (G-CSF) signaling / negative regulation of cell growth / RMTs methylate histone arginines / Regulation of expression of SLITs and ROBOs / ubiquitin-protein transferase activity / transcription corepressor activity / protein-macromolecule adaptor activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / nervous system development / Replication of the SARS-CoV-2 genome / histone binding / ubiquitin-dependent protein catabolic process / cellular response to hypoxia / proteasome-mediated ubiquitin-dependent protein catabolic process / regulation of gene expression / protein-containing complex assembly / DNA-binding transcription factor binding / amyloid fibril formation / transcription coactivator activity / molecular adaptor activity / protein stabilization / protein ubiquitination / transcription cis-regulatory region binding / hydrolase activity / chromatin remodeling / negative regulation of cell population proliferation / negative regulation of gene expression / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / chromatin binding / positive regulation of cell population proliferation / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / enzyme binding / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II
Similarity search - Function
BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / von Hippel-Lindau disease tumour suppressor, alpha domain / von Hippel-Lindau disease tumour suppressor, beta domain / Elongin C; Chain C, domain 1 / domain in helicases and associated with SANT domains / Glutamine-Leucine-Glutamine, QLQ / QLQ ...BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / von Hippel-Lindau disease tumour suppressor, alpha domain / von Hippel-Lindau disease tumour suppressor, beta domain / Elongin C; Chain C, domain 1 / domain in helicases and associated with SANT domains / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / Snf2-ATP coupling, chromatin remodelling complex / HSA domain / 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 / Helicase/SANT-associated domain / HSA domain profile. / Elongin B / Elongin-C / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / SKP1/BTB/POZ domain superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Helicase conserved C-terminal domain / Bromodomain-like / Histone Acetyltransferase; Chain A / Ubiquitin-like (UB roll) / Ubiquitin family / Bromodomain, conserved site / Bromodomain signature. / Ubiquitin homologues / Ubiquitin-like domain / Bromodomain / Ubiquitin domain profile. / Bromodomain profile. / bromo domain / helicase superfamily c-terminal domain / Bromodomain / Bromodomain-like superfamily / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Ubiquitin-like domain superfamily / Roll / Up-down Bundle / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Chem-FX8 / von Hippel-Lindau disease tumor suppressor / Probable global transcription activator SNF2L2 / Elongin-C / Elongin-B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.24 Å
AuthorsRoy, M. / Bader, G. / Diers, E. / Trainor, N. / Farnaby, W. / Ciulli, A.
Funding support1items
OrganizationGrant numberCountry
European Research CouncilERC-2012-StG-311460 DrugE3CRLs
CitationJournal: Nat.Chem.Biol. / Year: 2019
Title: BAF complex vulnerabilities in cancer demonstrated via structure-based PROTAC design.
Authors: Farnaby, W. / Koegl, M. / Roy, M.J. / Whitworth, C. / Diers, E. / Trainor, N. / Zollman, D. / Steurer, S. / Karolyi-Oezguer, J. / Riedmueller, C. / Gmaschitz, T. / Wachter, J. / Dank, C. / ...Authors: Farnaby, W. / Koegl, M. / Roy, M.J. / Whitworth, C. / Diers, E. / Trainor, N. / Zollman, D. / Steurer, S. / Karolyi-Oezguer, J. / Riedmueller, C. / Gmaschitz, T. / Wachter, J. / Dank, C. / Galant, M. / Sharps, B. / Rumpel, K. / Traxler, E. / Gerstberger, T. / Schnitzer, R. / Petermann, O. / Greb, P. / Weinstabl, H. / Bader, G. / Zoephel, A. / Weiss-Puxbaum, A. / Ehrenhofer-Wolfer, K. / Wohrle, S. / Boehmelt, G. / Rinnenthal, J. / Arnhof, H. / Wiechens, N. / Wu, M.Y. / Owen-Hughes, T. / Ettmayer, P. / Pearson, M. / McConnell, D.B. / Ciulli, A.
History
DepositionAug 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 3, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable global transcription activator SNF2L2
B: von Hippel-Lindau disease tumor suppressor
C: Elongin-C
D: Elongin-B
E: Probable global transcription activator SNF2L2
F: von Hippel-Lindau disease tumor suppressor
G: Elongin-C
H: Elongin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,09834
Polymers111,6128
Non-polymers3,48626
Water5,405300
1
A: Probable global transcription activator SNF2L2
B: von Hippel-Lindau disease tumor suppressor
C: Elongin-C
D: Elongin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,45317
Polymers55,8064
Non-polymers1,64713
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
E: Probable global transcription activator SNF2L2
F: von Hippel-Lindau disease tumor suppressor
G: Elongin-C
H: Elongin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,64517
Polymers55,8064
Non-polymers1,83913
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.725, 117.260, 121.557
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 4 types, 8 molecules AEBFCGDH

#1: Protein Probable global transcription activator SNF2L2 / ATP-dependent helicase SMARCA2 / BRG1-associated factor 190B / BAF190B / Protein brahma homolog / ...ATP-dependent helicase SMARCA2 / BRG1-associated factor 190B / BAF190B / Protein brahma homolog / hBRM / SNF2-alpha / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2


Mass: 14380.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCA2, BAF190B, BRM, SNF2A, SNF2L2 / Plasmid: pDEST15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P51531, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: 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 / Plasmid: pHAT4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P40337
#3: 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 / Plasmid: pCDF-1b DUET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15369
#4: 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 / Plasmid: pCDF-1b DUET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15370

-
Non-polymers , 5 types, 326 molecules

#5: Chemical ChemComp-FX8 / (2~{S},4~{R})-~{N}-[[2-[2-[2-[2-[4-[3-azanyl-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl]ethoxy]ethoxy]ethoxy]-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide


Mass: 918.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C46H60FN9O8S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#8: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.61 Å3/Da / Density % sol: 52.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.75
Details: 18% (w/v) PEG 3350, 0.2 M sodium formate, 0.1 M HEPES, pH 7.75

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 2.24→48.33 Å / Num. obs: 105978 / % possible obs: 99.6 % / Redundancy: 6.97 % / Biso Wilson estimate: 52.59 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rrim(I) all: 0.088 / Net I/σ(I): 16.1
Reflection shellResolution: 2.24→2.37 Å / Redundancy: 6.94 % / Rmerge(I) obs: 0.851 / Mean I/σ(I) obs: 2 / Num. unique obs: 16832 / CC1/2: 0.81 / Rrim(I) all: 0.919 / % possible all: 97.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.25 Å48.33 Å
Translation2.25 Å48.33 Å

-
Processing

Software
NameVersionClassification
XDSJun 1, 2017data reduction
XSCALEJun 1, 2017data scaling
PHASER2.4.0phasing
BUSTER2.10.2refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T35, 4QY4

5t35

4qy4


Resolution: 2.24→48.33 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.938 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.252 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.254 / SU Rfree Blow DPI: 0.188 / SU Rfree Cruickshank DPI: 0.19
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2774 5 %RANDOM
Rwork0.192 ---
obs0.193 55493 100 %-
Displacement parametersBiso max: 165.73 Å2 / Biso mean: 55.66 Å2 / Biso min: 25.09 Å2
Baniso -1Baniso -2Baniso -3
1-4.4546 Å20 Å20 Å2
2--5.7471 Å20 Å2
3----10.2017 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: final / Resolution: 2.24→48.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7424 0 236 300 7960
Biso mean--57.44 52.23 -
Num. residues----930
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2798SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes200HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1112HARMONIC5
X-RAY DIFFRACTIONt_it7889HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1015SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9182SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7889HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg10674HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion3.38
X-RAY DIFFRACTIONt_other_torsion17.43
LS refinement shellResolution: 2.24→2.3 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 203 5.02 %
Rwork0.202 3841 -
all0.204 4044 -
obs--99.41 %
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)
17.63232.04080.83892.61661.03991.3978-0.2326-0.39450.8144-0.1490.00070.5237-0.1781-0.11860.2319-0.11710.0024-0.1279-0.16560.023-0.0511-49.744215.0301-30.5413
22.43170.06561.75570.92010.13412.1643-0.29420.22970.1171-0.02280.12990.0533-0.2830.03520.1642-0.0161-0.0071-0.0221-0.11240.0356-0.0853-14.562814.9976-21.3984
32.736-0.90931.05950.9082-0.27632.5587-0.11830.19890.0173-0.0786-0.0379-0.213-0.22080.39170.1562-0.0382-0.00760.001-0.07860.0335-0.0269.150111.8912-4.8239
41.1624-1.24491.3212.6365-1.28882.4781-0.0027-0.1766-0.2085-0.10910.13280.29380.0212-0.1501-0.1301-0.11670.02730.0003-0.07270.04380.037.0228-0.48348.6922
54.46450.91910.21962.8250.32451.7061-0.0682-0.1669-0.61730.4009-0.0536-0.64220.41460.11490.1219-0.04830.0141-0.0088-0.16960.0111-0.019115.1898-16.9151-33.6418
63.10130.2336-1.78770.6819-0.27781.6022-0.35180.1547-0.6664-0.00530.08040.14580.1786-0.060.2715-0.0939-0.03190.1415-0.183-0.03570.0817-18.7872-17.4908-21.1752
73.6298-1.4648-1.56322.53230.42422.1632-0.30780.1016-0.7080.0261-0.14660.32640.2115-0.14840.4543-0.1052-0.00480.1256-0.12990.01570.0627-40.5362-14.8959-4.6521
82.5958-0.8674-1.81822.79461.77472.4441-0.1678-0.4223-0.1954-0.0067-0.0003-0.13710.04660.31630.1681-0.1270.0320.01920.01390.1108-0.0899-40.4934-1.95858.2372
91.1934-0.62830.43070-0.38960-0.13420.22690.0061-0.12470.06990.0666-0.0202-0.05790.06430.0348-0.05740.0194-0.0271-0.00880.0059-16.7438-0.892-28.7452
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1374 - 1493
2X-RAY DIFFRACTION2{ B|* }B59 - 210
3X-RAY DIFFRACTION3{ C|* }C16 - 112
4X-RAY DIFFRACTION4{ D|* }D1 - 104
5X-RAY DIFFRACTION5{ E|* }E1377 - 1491
6X-RAY DIFFRACTION6{ F|* }F59 - 209
7X-RAY DIFFRACTION7{ G|* }G16 - 112
8X-RAY DIFFRACTION8{ H|* }H1 - 103
9X-RAY DIFFRACTION9{ I|* }I1 - 2

+
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