[English] 日本語
Yorodumi
- PDB-6cw2: Crystal structure of a yeast SAGA transcriptional coactivator Ada... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6cw2
TitleCrystal structure of a yeast SAGA transcriptional coactivator Ada2/Gcn5 HAT subcomplex, crystal form 1
Components
  • Histone acetyltransferase GCN5
  • Transcriptional adapter 2
  • antibody heavy chain
  • antibody light chain
KeywordsGENE REGULATION / Ada2/Gcn5 structure
Function / homology
Function and homology information


ADA complex / SAGA-type complex / histone crotonyltransferase activity / replication-born double-strand break repair via sister chromatid exchange / SLIK (SAGA-like) complex / rDNA heterochromatin formation / histone H3 acetyltransferase activity / SAGA complex / peptide-lysine-N-acetyltransferase activity / phosphatidylserine binding ...ADA complex / SAGA-type complex / histone crotonyltransferase activity / replication-born double-strand break repair via sister chromatid exchange / SLIK (SAGA-like) complex / rDNA heterochromatin formation / histone H3 acetyltransferase activity / SAGA complex / peptide-lysine-N-acetyltransferase activity / phosphatidylserine binding / Estrogen-dependent gene expression / chromosome, centromeric region / histone acetyltransferase complex / subtelomeric heterochromatin formation / Ub-specific processing proteases / histone acetyltransferase activity / histone acetyltransferase / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / lysine-acetylated histone binding / chromatin organization / chromosome, telomeric region / transcription coactivator activity / chromatin remodeling / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleus / cytosol
Similarity search - Function
Transcriptional adaptor 2 / ADA2-like, zinc finger, ZZ-type / Histone acetyltransferase GCN5 / SWIRM domain / SWIRM domain / SWIRM domain profile. / SANT domain profile. / SANT domain / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. ...Transcriptional adaptor 2 / ADA2-like, zinc finger, ZZ-type / Histone acetyltransferase GCN5 / SWIRM domain / SWIRM domain / SWIRM domain profile. / SANT domain profile. / SANT domain / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Myb-like DNA-binding domain / Acetyltransferase (GNAT) family / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Homeobox-like domain superfamily / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Winged helix-like DNA-binding domain superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Transcriptional adapter 2 / Histone acetyltransferase GCN5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsSun, J. / Paduch, M. / Kim, S.A. / Kramer, R.M. / Barrios, A.F. / Lu, V. / Luke, J. / Usatyuk, S. / Kossiakoff, A.A. / Tan, S.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM088236 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM111651 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U01GM094588 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM072688 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54HG006436 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structural basis for activation of SAGA histone acetyltransferase Gcn5 by partner subunit Ada2.
Authors: Sun, J. / Paduch, M. / Kim, S.A. / Kramer, R.M. / Barrios, A.F. / Lu, V. / Luke, J. / Usatyuk, S. / Kossiakoff, A.A. / Tan, S.
History
DepositionMar 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity.formula_weight
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Structure summary / Category: entity / pdbx_audit_support
Item: _entity.formula_weight / _pdbx_audit_support.funding_organization

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
D: Histone acetyltransferase GCN5
C: Transcriptional adapter 2
A: antibody heavy chain
B: antibody light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9706
Polymers90,8394
Non-polymers1312
Water91951
1
A: antibody heavy chain
B: antibody light chain


Theoretical massNumber of molelcules
Total (without water)47,9522
Polymers47,9522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-36 kcal/mol
Surface area18040 Å2
MethodPISA
2
D: Histone acetyltransferase GCN5
C: Transcriptional adapter 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0174
Polymers42,8862
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-26 kcal/mol
Surface area18980 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10770 Å2
ΔGint-73 kcal/mol
Surface area33890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)191.816, 191.816, 92.674
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

-
Protein , 2 types, 2 molecules DC

#1: Protein Histone acetyltransferase GCN5


Mass: 29081.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: GCN5, ADA4, SWI9, YGR252W / Plasmid: PST44 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: Q03330, histone acetyltransferase
#2: Protein Transcriptional adapter 2


Mass: 13804.530 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ADA2, SCKG_0090 / Plasmid: PST44 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: A0A250W8G8, UniProt: Q02336*PLUS

-
Antibody , 2 types, 2 molecules AB

#3: Antibody antibody heavy chain


Mass: 24548.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Antibody antibody light chain


Mass: 23403.943 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

-
Non-polymers , 2 types, 53 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 5.52 Å3/Da / Density % sol: 77.72 %
Crystal growTemperature: 294 K / Method: microbatch / pH: 8.5
Details: 10 mM Tris-Cl pH 8.5, 200 mM Li2SO4, 25% w/v PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.67→166.12 Å / Num. obs: 55876 / % possible obs: 100 % / Redundancy: 20.1 % / Rpim(I) all: 0.045 / Net I/σ(I): 15.4
Reflection shellResolution: 2.67→2.75 Å / Redundancy: 19.9 % / Num. unique obs: 4546 / Rpim(I) all: 0.947 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.67→95.908 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2838 2712 4.87 %
Rwork0.2501 53001 -
obs0.2517 55713 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 245 Å2 / Biso mean: 86.9959 Å2 / Biso min: 42.37 Å2
Refinement stepCycle: final / Resolution: 2.67→95.908 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5895 0 2 51 5948
Biso mean--91.51 67.45 -
Num. residues----772
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096043
X-RAY DIFFRACTIONf_angle_d1.7338221
X-RAY DIFFRACTIONf_chiral_restr0.073916
X-RAY DIFFRACTIONf_plane_restr0.0111051
X-RAY DIFFRACTIONf_dihedral_angle_d15.2712130
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6702-2.71870.36521510.30722688283997
2.7187-2.7710.29981160.29752785290199
2.771-2.82760.32651450.28432730287599
2.8276-2.88910.29341440.273227792923100
2.8891-2.95630.33561450.276427582903100
2.9563-3.03020.34421460.264327642910100
3.0302-3.11210.29331530.255927832936100
3.1121-3.20370.28551430.239127692912100
3.2037-3.30710.24971280.245628112939100
3.3071-3.42530.2791180.234928052923100
3.4253-3.56250.3151800.246727522932100
3.5625-3.72460.31371300.255527802910100
3.7246-3.9210.29121550.248727842939100
3.921-4.16670.27951280.236328232951100
4.1667-4.48840.23831390.21227762915100
4.4884-4.940.23551410.222728322973100
4.94-5.65480.2771090.234128452954100
5.6548-7.12410.27851570.27128433000100
7.1241-95.96990.30021840.28328943078100
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)
13.39212.97850.46455.47120.7915.3445-0.6748-0.2813-1.04190.60380.491-0.18270.8590.80570.27910.92090.2392-0.00990.7804-0.17560.844539.3594106.7664-9.4437
22.45772.1292-1.55667.7157-0.06382.75130.02280.16690.00370.87040.5199-0.6242-0.1727-0.3687-0.47650.65330.36690.05481.07-0.02060.579227.071687.6286-3.1244
33.10940.1529-0.47622.519-0.40793.62030.1316-0.10920.14790.07320.09410.623-0.2225-1.2406-0.2280.55480.25770.07971.02740.04930.685216.680283.6239-9.4367
43.11651.0586-1.02913.53472.352.87730.0117-0.0019-0.3437-0.2070.22770.507-0.4982-0.7141-0.25470.63220.34310.04970.99950.04930.608922.351190.5454-20.9035
50.2723-0.6036-1.02865.57171.40123.879-0.3176-0.033-0.0533-0.5852-0.15431.0333-0.1554-1.1780.4080.68120.2269-0.01711.1179-0.05130.750220.721986.0445-26.6315
60.2942-0.4830.25436.6151-1.26970.26450.2209-0.11790.2047-0.1739-0.6598-1.3203-0.10530.0520.37680.88630.35480.14920.7955-0.04120.872437.8414120.8705-21.2401
74.42232.42412.84325.84340.22969.3296-0.03111.4548-0.81890.95510.7885-1.72840.5599-0.3505-0.92211.11920.0284-0.04620.5827-0.09720.927834.1497138.3879-32.1168
83.46891.8996-2.99274.0743-0.16013.2920.6368-0.5543-0.9781-0.38310.01290.32130.54210.6371-0.19871.00450.21790.00940.4672-0.01950.987523.3759128.9692-27.0851
93.86523.67242.26993.85872.65442.00060.7049-0.8463-0.6590.7414-0.41340.26951.00750.2177-0.10681.16480.256-0.09310.56290.05260.858129.5303131.3966-19.2119
104.79341.5636-2.44744.65173.50456.0621-0.19890.2940.69460.4077-0.3261-0.2561-1.0541-0.12090.48971.20020.08810.05160.57260.16020.955928.4223139.9734-19.8646
110.9924-2.1142-1.11214.61532.6812.002-0.11330.35450.8289-0.8989-0.7316-0.168-0.65450.25360.85641.21960.37440.01590.77620.01621.120436.5522119.7185-31.946
126.98712.5106-3.34392.67981.69467.33450.61650.40410.02420.48310.2163-1.0988-1.9624-1.2751-0.72481.02040.38030.11170.84380.12090.744329.9768110.2617-25.8088
138.93850.6365-3.03093.99661.75852.0224-0.23811.31710.4506-0.6062-0.12620.5439-0.7087-1.32530.26160.82090.49370.01150.9622-0.03410.606527.798103.6112-31.6453
142.7332-3.3546-0.44354.9816-0.77562.53560.87820.16520.1161-1.2868-0.5447-0.2061-1.1548-0.4316-0.40590.7750.2990.10510.7429-0.12630.618343.5501102.602-27.1967
153.3299-2.7799-0.00252.5431-1.11745.115-0.7213-1.3472-0.31421.04580.65960.49690.55091.2447-0.14770.70750.45870.15791.13440.0470.698656.856173.0008-11.9792
164.216-1.47040.46423.7137-0.78651.4796-0.3569-0.9573-0.14030.48970.2431-0.121-0.17-0.3960.09580.73690.44370.09041.02890.06920.600848.418579.8739-12.7619
173.1953-3.71640.27286.381-1.07371.1781-0.2362-0.4910.0005-0.14440.2144-0.14850.21320.1967-00.58570.26840.02090.83240.03040.405951.370979.5766-17.6839
183.1741-1.4868-1.22051.06670.71910.516-0.00930.0388-0.3818-0.2115-0.332-0.10370.46821.25450.31330.89630.63960.14281.60920.24610.832874.710760.059-22.2512
195.68514.62883.71035.3132.23545.72060.5355-0.0854-0.82321.23750.2935-1.06750.68610.4134-0.61260.75390.4110.0351.3652-0.06510.727374.503965.957-26.5149
207.2959-1.1072-4.55182.34370.02793.03730.14510.30420.1481-0.0074-0.2949-0.94220.62811.91340.32380.79180.47070.08271.93270.32120.846580.699963.1189-25.3459
213.5417-0.2285-2.98692.09610.97542.8389-0.2983-0.73350.1643-0.3645-0.403-0.12630.11351.83720.63290.94460.61170.08361.66860.18770.68176.219461.8373-14.8517
224.4165-0.881-1.3891.75590.23334.0902-0.13550.3947-0.27290.1209-0.00780.1497-0.05190.45720.11470.55960.20280.04170.831-0.04450.542151.987385.5893-36.0703
237.5022-1.0103-4.51032.9324-0.10194.2258-0.6821-0.2501-0.2130.01450.29360.04090.2080.49580.45390.54550.1974-0.04920.8966-0.0480.511952.169581.9102-32.8456
240.5923-0.3722-0.48271.49090.41770.3543-0.1911-0.289-0.1213-0.0759-0.0946-1.07490.86031.0024-0.08841.06311.02690.37751.79690.00920.609775.060261.6513-35.6707
250.6388-0.95811.36126.907-3.07513.02010.11250.2138-0.2516-0.42470.29880.08290.8720.1523-0.30790.97790.44590.15751.23260.08180.705372.763758.1995-40.0746
263.94520.7834-2.68762.1479-0.96824.05010.2048-0.1933-0.0194-0.3938-0.2355-0.49470.69441.2353-0.18310.80370.51760.13051.47520.02260.651570.144768.5496-36.6331
271.0297-1.4133-0.55594.12741.62150.636-0.33740.4178-1.2049-1.8153-0.26830.63191.98430.17930.64941.84570.56080.33341.1822-0.17381.020474.514652.9816-38.3577
281.7177-0.7987-0.56950.92030.74830.6017-0.2676-0.053-0.9914-0.1932-0.11910.00090.57650.2923-0.13481.73970.92640.50411.76450.17251.252980.766252.0353-43.0358
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'D' and (resid 72 through 89 )D72 - 89
2X-RAY DIFFRACTION2chain 'D' and (resid 90 through 110 )D90 - 110
3X-RAY DIFFRACTION3chain 'D' and (resid 111 through 187 )D111 - 187
4X-RAY DIFFRACTION4chain 'D' and (resid 188 through 233 )D188 - 233
5X-RAY DIFFRACTION5chain 'D' and (resid 234 through 259 )D234 - 259
6X-RAY DIFFRACTION6chain 'D' and (resid 260 through 298 )D260 - 298
7X-RAY DIFFRACTION7chain 'D' and (resid 299 through 312 )D299 - 312
8X-RAY DIFFRACTION8chain 'C' and (resid 6 through 18 )C6 - 18
9X-RAY DIFFRACTION9chain 'C' and (resid 19 through 31 )C19 - 31
10X-RAY DIFFRACTION10chain 'C' and (resid 32 through 49 )C32 - 49
11X-RAY DIFFRACTION11chain 'C' and (resid 50 through 66 )C50 - 66
12X-RAY DIFFRACTION12chain 'C' and (resid 67 through 80 )C67 - 80
13X-RAY DIFFRACTION13chain 'C' and (resid 81 through 107 )C81 - 107
14X-RAY DIFFRACTION14chain 'C' and (resid 108 through 120 )C108 - 120
15X-RAY DIFFRACTION15chain 'A' and (resid 4 through 20 )A4 - 20
16X-RAY DIFFRACTION16chain 'A' and (resid 21 through 86 )A21 - 86
17X-RAY DIFFRACTION17chain 'A' and (resid 87 through 138 )A87 - 138
18X-RAY DIFFRACTION18chain 'A' and (resid 139 through 173 )A139 - 173
19X-RAY DIFFRACTION19chain 'A' and (resid 174 through 191 )A174 - 191
20X-RAY DIFFRACTION20chain 'A' and (resid 192 through 217 )A192 - 217
21X-RAY DIFFRACTION21chain 'A' and (resid 218 through 232 )A218 - 232
22X-RAY DIFFRACTION22chain 'B' and (resid 1 through 76 )B1 - 76
23X-RAY DIFFRACTION23chain 'B' and (resid 77 through 102 )B77 - 102
24X-RAY DIFFRACTION24chain 'B' and (resid 103 through 130 )B103 - 130
25X-RAY DIFFRACTION25chain 'B' and (resid 131 through 159 )B131 - 159
26X-RAY DIFFRACTION26chain 'B' and (resid 160 through 175 )B160 - 175
27X-RAY DIFFRACTION27chain 'B' and (resid 176 through 199 )B176 - 199
28X-RAY DIFFRACTION28chain 'B' and (resid 200 through 215 )B200 - 215

+
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