[English] 日本語
Yorodumi
- PDB-5aql: Fragment-based screening of HSP70 sheds light on the functional r... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5aql
TitleFragment-based screening of HSP70 sheds light on the functional role of ATP-binding site residues
Components
  • BAG FAMILY MOLECULAR CHAPERONE REGULATOR 1
  • HEAT SHOCK COGNATE 71 KDA PROTEIN
KeywordsCHAPERONE / HEAT SHOCK PROTEIN / HSP70 / HSP72 / HSC70 / ATPASE / BAG1 / FRAGMENT
Function / homology
Function and homology information


lumenal side of lysosomal membrane / regulation of protein import / negative regulation of supramolecular fiber organization / positive regulation of protein refolding / prostaglandin binding / positive regulation of lysosomal membrane permeability / lysosomal matrix / A1 adenosine receptor binding / protein carrier chaperone / response to nickel cation ...lumenal side of lysosomal membrane / regulation of protein import / negative regulation of supramolecular fiber organization / positive regulation of protein refolding / prostaglandin binding / positive regulation of lysosomal membrane permeability / lysosomal matrix / A1 adenosine receptor binding / protein carrier chaperone / response to nickel cation / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / Respiratory syncytial virus genome transcription / protein transmembrane import into intracellular organelle / Lipophagy / chaperone-mediated autophagy translocation complex disassembly / slow axonal transport / clathrin-uncoating ATPase activity / GABA synthesis, release, reuptake and degradation / protein targeting to lysosome involved in chaperone-mediated autophagy / adenyl-nucleotide exchange factor activity / late endosomal microautophagy / response to odorant / positive regulation by host of viral genome replication / synaptic vesicle uncoating / C3HC4-type RING finger domain binding / positive regulation of smooth muscle cell apoptotic process / negative regulation of NLRP3 inflammasome complex assembly / clathrin coat disassembly / ATP-dependent protein disaggregase activity / CHL1 interactions / regulation of protein complex stability / photoreceptor ribbon synapse / maintenance of postsynaptic specialization structure / membrane organization / Prp19 complex / glycinergic synapse / presynaptic cytosol / postsynaptic specialization membrane / protein folding chaperone complex / positive regulation of mRNA splicing, via spliceosome / postsynaptic cytosol / regulation of postsynapse organization / negative regulation of cardiac muscle cell apoptotic process / Lysosome Vesicle Biogenesis / intermediate filament / chaperone-mediated autophagy / cellular response to steroid hormone stimulus / Golgi Associated Vesicle Biogenesis / phosphatidylserine binding / non-chaperonin molecular chaperone ATPase / positive regulation of proteolysis / chaperone cofactor-dependent protein refolding / HSF1-dependent transactivation / response to unfolded protein / estrous cycle / Regulation of HSF1-mediated heat shock response / regulation of protein-containing complex assembly / autophagosome / Attenuation phase / Protein methylation / ATP metabolic process / protein folding chaperone / skeletal muscle tissue development / positive regulation of phagocytosis / forebrain development / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / cellular response to cadmium ion / cellular response to starvation / photoreceptor inner segment / lysosomal lumen / mRNA Splicing - Major Pathway / cerebellum development / dendritic shaft / response to activity / kidney development / AUF1 (hnRNP D0) binds and destabilizes mRNA / response to progesterone / G protein-coupled receptor binding / ATP-dependent protein folding chaperone / peptide binding / spliceosomal complex / Late endosomal microautophagy / regulation of protein stability / PKR-mediated signaling / terminal bouton / ADP binding / mRNA splicing, via spliceosome / Chaperone Mediated Autophagy / cellular response to hydrogen peroxide / G1/S transition of mitotic cell cycle / positive regulation of T cell mediated cytotoxicity / protein import into nucleus / unfolded protein binding / melanosome / synaptic vesicle / late endosome / protein folding / response to estradiol / MHC class II protein complex binding
Similarity search - Function
BAG domain / BAG domain superfamily / Molecular chaperone regulator BAG / BAG domain / BAG domain / BAG domain profile. / BAG domains, present in regulator of Hsp70 proteins / Defensin A-like - #30 / Defensin A-like / Heat shock hsp70 proteins family signature 2. ...BAG domain / BAG domain superfamily / Molecular chaperone regulator BAG / BAG domain / BAG domain / BAG domain profile. / BAG domains, present in regulator of Hsp70 proteins / Defensin A-like - #30 / Defensin A-like / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / ATPase, nucleotide binding domain / Ubiquitin family / Ubiquitin homologues / Nucleotidyltransferase; domain 5 / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Alpha-Beta Complex / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Heat shock cognate 71 kDa protein / BAG family molecular chaperone regulator 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsJones, A.M. / Westwood, I.M. / Osborne, J.D. / Matthews, T.P. / Cheeseman, M.D. / Rowlands, M.G. / Jeganathan, F. / Burke, R. / Lee, D. / Kadi, N. ...Jones, A.M. / Westwood, I.M. / Osborne, J.D. / Matthews, T.P. / Cheeseman, M.D. / Rowlands, M.G. / Jeganathan, F. / Burke, R. / Lee, D. / Kadi, N. / Liu, M. / Richards, M. / McAndrew, C. / Yahya, N. / Dobson, S.E. / Jones, K. / Workman, P. / Collins, I. / van Montfort, R.L.M.
CitationJournal: Sci Rep / Year: 2016
Title: A fragment-based approach applied to a highly flexible target: Insights and challenges towards the inhibition of HSP70 isoforms.
Authors: Jones, A.M. / Westwood, I.M. / Osborne, J.D. / Matthews, T.P. / Cheeseman, M.D. / Rowlands, M.G. / Jeganathan, F. / Burke, R. / Lee, D. / Kadi, N. / Liu, M. / Richards, M. / McAndrew, C. / ...Authors: Jones, A.M. / Westwood, I.M. / Osborne, J.D. / Matthews, T.P. / Cheeseman, M.D. / Rowlands, M.G. / Jeganathan, F. / Burke, R. / Lee, D. / Kadi, N. / Liu, M. / Richards, M. / McAndrew, C. / Yahya, N. / Dobson, S.E. / Jones, K. / Workman, P. / Collins, I. / van Montfort, R.L.
History
DepositionSep 22, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Data collection / Database references / Category: citation / citation_author / diffrn_detector
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _diffrn_detector.type
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: HEAT SHOCK COGNATE 71 KDA PROTEIN
B: BAG FAMILY MOLECULAR CHAPERONE REGULATOR 1
C: HEAT SHOCK COGNATE 71 KDA PROTEIN
D: BAG FAMILY MOLECULAR CHAPERONE REGULATOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,98413
Polymers112,0354
Non-polymers9499
Water16,358908
1
A: HEAT SHOCK COGNATE 71 KDA PROTEIN
B: BAG FAMILY MOLECULAR CHAPERONE REGULATOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5387
Polymers56,0182
Non-polymers5215
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint0.6 kcal/mol
Surface area27360 Å2
MethodPQS
2
C: HEAT SHOCK COGNATE 71 KDA PROTEIN
D: BAG FAMILY MOLECULAR CHAPERONE REGULATOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4466
Polymers56,0182
Non-polymers4284
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-1.1 kcal/mol
Surface area27570 Å2
MethodPQS
Unit cell
Length a, b, c (Å)232.027, 40.928, 116.546
Angle α, β, γ (deg.)90.00, 90.58, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-2011-

HOH

-
Components

#1: Protein HEAT SHOCK COGNATE 71 KDA PROTEIN / HEAT SHOCK 70 KDA PROTEIN 8 / LIPOPOLYSACCHARIDE-ASSOCIATED PROTEIN 1 / LAP-1 / LPS-ASSOCIATED PROTEIN 1


Mass: 42506.113 Da / Num. of mol.: 2 / Fragment: NUCLEOTIDE BINDING DOMAIN, RESIDUES 1-381 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): AI / References: UniProt: P11142, EC: 3.6.3.51
#2: Protein BAG FAMILY MOLECULAR CHAPERONE REGULATOR 1 / BAG-1 / BCL-2-ASSOCIATED ATHANOGENE 1


Mass: 13511.571 Da / Num. of mol.: 2 / Fragment: RESIDUES 222-334
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): AI / References: UniProt: Q99933
#3: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 908 / 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: 2.47 Å3/Da / Density % sol: 50.19 % / Description: NONE
Crystal growpH: 8.5
Details: 16-26% (W/V) PEG3350, 0.1 M K-NA TARTRATE, 0.1 M TRIS.HCL PH 8.5 AND 25% (V/V) GLYCEROL

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 23, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 1.69→58.27 Å / Num. obs: 120610 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 25.56 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 6.3
Reflection shellResolution: 1.69→1.72 Å / Redundancy: 2.5 % / Rmerge(I) obs: 1.31 / Mean I/σ(I) obs: 0.8 / % possible all: 72.9

-
Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HX1

1hx1


Resolution: 1.69→58.27 Å / Cor.coef. Fo:Fc: 0.9528 / Cor.coef. Fo:Fc free: 0.9397 / SU R Cruickshank DPI: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.095 / SU Rfree Blow DPI: 0.092 / SU Rfree Cruickshank DPI: 0.089
RfactorNum. reflection% reflectionSelection details
Rfree0.1965 6047 5.01 %RANDOM
Rwork0.1687 ---
obs0.1701 120580 97.41 %-
Displacement parametersBiso mean: 32.16 Å2
Baniso -1Baniso -2Baniso -3
1--2.7697 Å20 Å27.0239 Å2
2--4.7927 Å20 Å2
3----2.023 Å2
Refine analyzeLuzzati coordinate error obs: 0.218 Å
Refinement stepCycle: LAST / Resolution: 1.69→58.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7585 0 62 908 8555
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017800HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9510543HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2786SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes220HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1127HARMONIC5
X-RAY DIFFRACTIONt_it7800HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.03
X-RAY DIFFRACTIONt_other_torsion15.12
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1061SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies6HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9636SEMIHARMONIC4
LS refinement shellResolution: 1.69→1.73 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2113 337 4.64 %
Rwork0.2064 6922 -
all0.2067 7259 -
obs--80 %
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)
11.7516-0.24950.36431.94730.98830.9745-0.0220.14160.1244-0.108-0.03350.0238-0.16590.0170.0555-0.0529-0.0057-0.0231-0.02040.0028-0.0309-40.240914.333837.8254
21.16081.31140.50223.35220.7370.77660.1326-0.2406-0.16390.2394-0.0355-0.11750.16520.0306-0.0971-0.0113-0.0088-0.04520.0253-0.0197-0.018-33.3987-2.567752.1442
30.66890.20940.4351.09670.18071.05950.066-0.08160.00410.0813-0.04040.11620.0458-0.0935-0.0255-0.0589-0.0026-0.0140.0056-0.028-0.0082-45.73364.382542.2784
45.4804-1.001821.8756-1.31411.57960.09530.1826-0.355-0.12860.05440.2604-0.0459-0.0836-0.1498-0.03890.0211-0.06120.0459-0.0892-0.014-40.7231-2.09222.5868
52.8823-0.74331.94321.12380.35623.0245-0.0437-0.1782-0.0847-0.18770.03240.1899-0.0515-0.11330.01140.0307-0.0091-0.00210.0233-0.0289-0.0928-8.2310.426235.2015
62.4692-0.44391.11911.7793-0.13973.4034-0.05240.0186-0.03570.071-0.00050.094-0.0165-0.15210.0529-0.0442-0.0260.02080.0045-0.0387-0.0763-11.88185.751440.0336
71.74950.9871-0.19430.0520.80252.4482-0.01430.209-0.0789-0.12680.13460.0291-0.10910.0946-0.12030.0213-0.0051-0.01590.045-0.0052-0.1075-5.32310.94637.3183
84.97051.0951.93030.58370.54731.25340.090.5105-0.4158-0.0580.02050.00030.04640.1525-0.1105-0.01920.0185-0.03480.0499-0.1012-0.0762-24.8101-1.886922.2918
93.6329-1.5704-1.48021.15961.21352.12460.06420.39410.1576-0.1289-0.00670.0005-0.03110.021-0.0575-0.0171-0.0024-0.03520.0264-0.0101-0.0691-35.57275.968321.8771
101.141.3854-2.15231.707-2.89656.2880.1675-0.16710.3062-0.03480.04210.2188-0.02490.0789-0.2096-0.06290.02920.02830.0052-0.0747-0.0467-10.170724.033653.7625
110.88880.1013-0.42310.8091-0.00841.82550.0132-0.18810.1582-0.00320.02280.10570.0955-0.1099-0.036-0.08-0.0040.00650.0738-0.0406-0.0749-13.97513.738257.6963
121.20590.7414-1.26812.2315-2.72364.37550.0483-0.24470.1847-0.17-0.0176-0.01070.11090.1804-0.0306-0.0353-0.00790.01490.0872-0.0382-0.0624-5.844615.081254.4778
131.11830.38280.32912.70150.41691.16070.0904-0.0851-0.02750.3391-0.1419-0.02480.0837-0.03360.0516-0.0462-0.02660.0012-0.0394-0.0309-0.0973-39.093521.8461-5.6243
141.4360.45521.02441.04060.63373.0230.1175-0.0909-0.05610.0932-0.20440.23360.1572-0.37540.0869-0.0769-0.02530.02110.0303-0.07840.0066-50.746218.9458-13.1193
152.7492-0.08950.61761.7414-0.67460.87230.01240.1464-0.1849-0.11030.04140.2481-0.0123-0.0821-0.0539-0.05420.0208-0.04860.0576-0.0774-0.0163-45.719215.6732-29.1039
164.276-0.12842.83141.40250.65112.5743-0.0438-0.03460.0064-0.04910.02560.1201-0.0626-0.06710.01820.03150.00010.00770.0079-0.0181-0.0844-12.136117.5442-21.2151
172.2314-0.18771.45631.51960.02853.3654-0.0511-0.0608-0.00020.11630.03390.031-0.0743-0.15060.0173-0.0374-0.01730.02660.0098-0.0286-0.063-14.248622.98-16.0774
181.74840.9084-0.26290.5020.25091.96650.03080.16-0.04690.06390.0348-0.0619-0.08070.0923-0.06550.03070.002-0.01170.0513-0.0206-0.0289-8.0428.0398-19.8157
193.72540.92090.54230.7620.05510.353-0.0110.2075-0.2005-0.0986-0.05940.0417-0.08520.06250.0704-0.02050.0095-0.00190.0475-0.0787-0.0611-23.793214.5514-30.1435
201.9237-0.2827-0.0950.88450.12681.0156-0.00680.3453-0.0466-0.1601-0.02290.09660.03470.0210.0297-0.05430.0009-0.03960.0441-0.0548-0.084-40.270920.7018-31.6896
211.13280.8045-0.00432.993-2.32823.78540.1819-0.13770.11730.3403-0.00570.1084-0.05810.0286-0.17620.00550.00840.0392-0.0562-0.074-0.076-10.736141.4513-3.7203
221.2750.39030.14022.9655-0.4651.47690.1099-0.28680.02760.2286-0.00510.12020.0685-0.0581-0.1048-0.10430.001-0.0037-0.0022-0.0336-0.0966-13.489830.87941.7169
231.7240.0425-0.56442.4666-2.57164.35360.088-0.25390.0373-0.2059-0.019-0.0960.20160.2566-0.069-0.0191-0.01670.01380.0408-0.0491-0.0631-5.768232.6937-3.3639

+
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://pdbjlvh1.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