[English] 日本語
Yorodumi
- PDB-5vse: Structure of human G9a SET-domain (EHMT2) in complex with inhibit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vse
TitleStructure of human G9a SET-domain (EHMT2) in complex with inhibitor 17: N~2~-cyclopentyl-6,7-dimethoxy-N~2~-methyl-N~4~-(1-methylpiperidin-4-yl)quinazoline-2,4-diamine
ComponentsHistone-lysine N-methyltransferase EHMT2
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / protein-small molecule inhibitor complex / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


histone H3K56 methyltransferase activity / phenotypic switching / neuron fate specification / [histone H3]-lysine9 N-methyltransferase / peptidyl-lysine dimethylation / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / histone H3K27 methyltransferase activity / synaptonemal complex assembly / negative regulation of autophagosome assembly ...histone H3K56 methyltransferase activity / phenotypic switching / neuron fate specification / [histone H3]-lysine9 N-methyltransferase / peptidyl-lysine dimethylation / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / histone H3K27 methyltransferase activity / synaptonemal complex assembly / negative regulation of autophagosome assembly / oocyte development / C2H2 zinc finger domain binding / protein-lysine N-methyltransferase activity / fertilization / cellular response to cocaine / organ growth / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of gene expression via chromosomal CpG island methylation / Transcriptional Regulation by E2F6 / regulation of DNA replication / RNA Polymerase I Transcription Initiation / Transcriptional Regulation by VENTX / spermatid development / behavioral response to cocaine / Transferases; Transferring one-carbon groups; Methyltransferases / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / cellular response to starvation / epigenetic regulation of gene expression / transcription corepressor binding / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / RNA polymerase II transcription regulatory region sequence-specific DNA binding / promoter-specific chromatin binding / Regulation of TP53 Activity through Methylation / PKMTs methylate histone lysines / p53 binding / Senescence-Associated Secretory Phenotype (SASP) / nuclear speck / chromatin / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Histone-lysine N-methyltransferase EHMT2 / Histone-lysine N-methyltransferase EHMT1/EHMT2 / : / Histone-lysine N-methyltransferase EHMT1/EHMT2, Cys-rich region / Pre-SET motif / Pre-SET domain / Pre-SET domain profile. / N-terminal to some SET domains / Beta-clip-like / SET domain ...Histone-lysine N-methyltransferase EHMT2 / Histone-lysine N-methyltransferase EHMT1/EHMT2 / : / Histone-lysine N-methyltransferase EHMT1/EHMT2, Cys-rich region / Pre-SET motif / Pre-SET domain / Pre-SET domain profile. / N-terminal to some SET domains / Beta-clip-like / SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / Ankyrin repeat / Beta Complex / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Chem-9HG / S-ADENOSYLMETHIONINE / Histone-lysine N-methyltransferase EHMT2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsBabault, N. / Xiong, Y. / Liu, J. / Jin, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM103893 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM122749 United States
CitationJournal: Bioorg. Med. Chem. / Year: 2017
Title: Structure-activity relationship studies of G9a-like protein (GLP) inhibitors.
Authors: Xiong, Y. / Li, F. / Babault, N. / Wu, H. / Dong, A. / Zeng, H. / Chen, X. / Arrowsmith, C.H. / Brown, P.J. / Liu, J. / Vedadi, M. / Jin, J.
History
DepositionMay 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histone-lysine N-methyltransferase EHMT2
B: Histone-lysine N-methyltransferase EHMT2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,56114
Polymers63,4422
Non-polymers2,11912
Water6,089338
1
A: Histone-lysine N-methyltransferase EHMT2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7817
Polymers31,7211
Non-polymers1,0606
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone-lysine N-methyltransferase EHMT2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7817
Polymers31,7211
Non-polymers1,0606
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-8 kcal/mol
Surface area25640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.491, 78.691, 72.610
Angle α, β, γ (deg.)90.000, 91.350, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 919 through 1090 or resid 1095 through 1190))
21(chain B and resid 919 through 1190)

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU

Dom-IDComponent-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASP(chain A and (resid 919 through 1090 or resid 1095 through 1190))AA919 - 10904 - 175
12ALAALA(chain A and (resid 919 through 1090 or resid 1095 through 1190))AA1095 - 1190180 - 275
21ALAALA(chain B and resid 919 through 1190)BB919 - 11904 - 275

-
Components

#1: Protein Histone-lysine N-methyltransferase EHMT2 / Euchromatic histone-lysine N-methyltransferase 2 / HLA-B-associated transcript 8 / Histone H3-K9 ...Euchromatic histone-lysine N-methyltransferase 2 / HLA-B-associated transcript 8 / Histone H3-K9 methyltransferase 3 / H3-K9-HMTase 3 / Lysine N-methyltransferase 1C / Protein G9a


Mass: 31720.930 Da / Num. of mol.: 2 / Fragment: G9a catalytic SET-domain (913-1193)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EHMT2, BAT8, C6orf30, G9A, KMT1C, NG36 / Plasmid: pET28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) codon plus RIL
References: UniProt: Q96KQ7, Transferases; Transferring one-carbon groups; Methyltransferases, histone-lysine N-methyltransferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Chemical ChemComp-9HG / N~2~-cyclopentyl-6,7-dimethoxy-N~2~-methyl-N~4~-(1-methylpiperidin-4-yl)quinazoline-2,4-diamine


Mass: 399.530 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H33N5O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 2.54 Å3/Da / Density % sol: 51.64 %
Crystal growTemperature: 290 K / Method: vapor diffusion / pH: 6.5
Details: 20 % PEG3350, 10% glycerol, 0.2 M Sodium fluoride, Bis-Tris propane pH6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.6→72.589 Å / Num. all: 82905 / Num. obs: 82905 / % possible obs: 99 % / Redundancy: 3.5 % / Biso Wilson estimate: 24.78 Å2 / Rpim(I) all: 0.03 / Rrim(I) all: 0.057 / Rsym value: 0.048 / Net I/av σ(I): 7.6 / Net I/σ(I): 10 / Num. measured all: 293095
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
1.6-1.693.60.4691.60.2880.5520.46999.3
1.69-1.793.60.2832.40.1750.3340.28399.2
1.79-1.913.30.17340.110.2060.17398.3
1.91-2.073.50.1235.10.0760.1450.12399.3
2.07-2.263.70.0936.20.0570.110.09399.7
2.26-2.533.50.078.40.0430.0820.0799
2.53-2.923.30.05311.20.0330.0630.05397.9
2.92-3.583.80.04213.80.0250.0490.04299.7
3.58-5.063.50.03416.80.0210.040.03499.1
5.06-72.5893.60.03516.30.0210.0410.03597.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TUY

5tuy


Resolution: 1.6→45.882 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.24
RfactorNum. reflection% reflection
Rfree0.1906 4118 4.98 %
Rwork0.1675 --
obs0.1686 82711 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 109.13 Å2 / Biso mean: 38.6584 Å2 / Biso min: 17.61 Å2
Refinement stepCycle: final / Resolution: 1.6→45.882 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4353 0 120 338 4811
Biso mean--32.19 39.01 -
Num. residues----540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064565
X-RAY DIFFRACTIONf_angle_d1.1046177
X-RAY DIFFRACTIONf_chiral_restr0.065656
X-RAY DIFFRACTIONf_plane_restr0.006800
X-RAY DIFFRACTIONf_dihedral_angle_d14.7492743
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2608X-RAY DIFFRACTION7.565TORSIONAL
12B2608X-RAY DIFFRACTION7.565TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.61880.28031400.2832735287599
1.6188-1.63860.28521340.25712667280199
1.6386-1.65930.27591410.25162712285399
1.6593-1.68110.26841450.24042664280999
1.6811-1.70420.25961310.22772709284099
1.7042-1.72850.21161580.21192698285699
1.7285-1.75430.24121750.20372667284299
1.7543-1.78170.21381630.18662658282199
1.7817-1.81090.21891950.18212678287399
1.8109-1.84220.22881610.18532637279898
1.8422-1.87570.19381650.18392661282698
1.8757-1.91180.23941220.17592705282797
1.9118-1.95080.22071310.1752672280398
1.9508-1.99320.18511400.175227092849100
1.9932-2.03960.20111290.174527592888100
2.0396-2.09060.21221320.174427572889100
2.0906-2.14710.20661500.181227212871100
2.1471-2.21030.22111150.176327372852100
2.2103-2.28160.19811180.17382754287299
2.2816-2.36310.22261340.18142728286299
2.3631-2.45780.24621080.18252778288699
2.4578-2.56960.21241390.18412677281698
2.5696-2.70510.21111300.18052683281397
2.7051-2.87450.20411590.17912652281198
2.8745-3.09640.20991460.17692747289399
3.0964-3.40790.18291110.170727712882100
3.4079-3.90090.16741290.151127772906100
3.9009-4.91380.14281490.1252747289699
4.9138-45.90080.15591680.14642733290198
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)
12.243-0.4095-0.55251.23160.33591.40110.05590.1175-0.0715-0.0989-0.0094-0.0772-0.0052-0.0878-0.02130.2227-0.0316-0.02070.1622-0.00850.183228.1475-1.7915-6.7506
22.8451-0.6063-1.43013.31430.62923.40450.19290.10690.447-0.22880.0888-0.4841-0.43220.0991-0.21750.2808-0.0430.03610.1743-0.01960.328835.68110.3536-5.6088
32.6374-0.6537-0.86471.46520.12251.64620.08340.3603-0.0487-0.2768-0.0243-0.0176-0.0227-0.1363-0.04830.2509-0.0376-0.01110.20660.00640.171127.12282.0209-12.7902
42.73010.1373-1.50432.2294-1.04235.55850.15940.90930.3256-0.5760.0619-0.2559-0.21870.0024-0.21640.4509-0.0220.16380.47250.05550.383742.9268.3177-25.7243
55.68790.5953-2.73732.9266-0.86415.769-0.19450.4312-0.6529-0.21870.23220.38430.2891-0.6376-0.03960.2616-0.0443-0.02130.3325-0.00050.42073.6845-8.699912.3376
67.57493.8592-2.95544.851-2.39383.3388-0.04920.4753-0.0502-0.01380.27290.38290.035-0.4749-0.21040.17020.0009-0.01340.29070.06760.27441.30990.858614.6359
73.8952-0.6093-0.49542.07050.02191.0268-0.1853-0.39070.07270.19440.1937-0.2155-0.12970.1807-0.00630.2505-0.029-0.00230.2938-0.0020.235932.15816.371315.5273
85.7661.3578-1.19334.0440.22125.7516-0.1121-1.2139-0.48171.0232-0.0849-0.732-0.34741.08580.15210.4910.0634-0.06490.7630.10250.458130.2988-4.439227.7425
94.3688-0.5797-1.87893.3960.53624.9775-0.0677-0.522-0.01360.5762-0.0115-0.06580.08420.05030.09090.2737-0.0144-0.02120.37650.03710.21728.91940.685722.3489
104.64010.4937-0.60681.1059-0.33151.0625-0.077-0.0547-0.57630.0980.07260.12940.0979-0.07340.03470.23-0.00280.00990.230.08610.32111.6647-7.960622.171
113.581-0.925-1.39827.2334-0.23693.66920.0831-0.3750.42680.41480.22860.0193-0.6296-0.0855-0.28280.28470.01740.04490.25930.02410.254510.341212.345322.1894
123.51420.7474-1.11271.1533-0.37611.50910.0134-0.27660.08930.12390.05040.0417-0.0762-0.021-0.06910.22970.01890.01270.24630.04850.215414.00245.028622.8451
134.3738-1.5731-0.67923.26120.40562.9713-0.0936-0.7246-0.36810.55670.15590.3086-0.06580.0403-0.06550.27920.00510.0880.42660.11870.25677.23740.147132.3775
141.702-0.23910.84271.89221.09314.59050.2208-0.31090.30380.365-0.09590.1756-0.18710.0925-0.12160.48750.02270.18580.64020.07490.4166-1.29316.006442.953
153.1868-3.3043-3.46025.14192.40155.4367-0.2006-0.39440.08760.13270.2741-0.57050.36260.47440.0230.2608-0.0338-0.01480.1934-0.03070.309139.148-10.8896-0.3449
164.6322-3.1897-2.99083.62822.23472.3213-0.2715-0.29860.18970.15710.4017-0.66140.0810.4606-0.17180.2802-0.0172-0.04420.2624-0.06010.380543.4422-4.3445-1.6487
172.6827-0.2871-0.75682.0410.30461.82030.02650.25940.0117-0.0675-0.00470.12120.0138-0.3502-0.03570.2430.0027-0.00860.27560.0480.240512.89158.6646-0.0692
183.5884-0.8233-1.84112.30280.84634.49820.16620.8461-0.0392-0.4407-0.19180.2396-0.0141-0.7130.0370.3008-0.0131-0.07140.45890.01390.257512.77181.5962-12.6795
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 1022 through 1079 )B0
2X-RAY DIFFRACTION2chain 'B' and (resid 1080 through 1110 )B0
3X-RAY DIFFRACTION3chain 'B' and (resid 1111 through 1155 )B0
4X-RAY DIFFRACTION4chain 'B' and (resid 1156 through 1190 )B0
5X-RAY DIFFRACTION5chain 'A' and (resid 919 through 938 )A919 - 938
6X-RAY DIFFRACTION6chain 'A' and (resid 939 through 958 )A939 - 958
7X-RAY DIFFRACTION7chain 'A' and (resid 959 through 985 )A959 - 985
8X-RAY DIFFRACTION8chain 'A' and (resid 986 through 1005 )A986 - 1005
9X-RAY DIFFRACTION9chain 'A' and (resid 1006 through 1025 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 1026 through 1062 )A0
11X-RAY DIFFRACTION11chain 'A' and (resid 1063 through 1096 )A0
12X-RAY DIFFRACTION12chain 'A' and (resid 1097 through 1140 )A0
13X-RAY DIFFRACTION13chain 'A' and (resid 1141 through 1162 )A0
14X-RAY DIFFRACTION14chain 'A' and (resid 1163 through 1190 )A0
15X-RAY DIFFRACTION15chain 'B' and (resid 916 through 935 )B916 - 935
16X-RAY DIFFRACTION16chain 'B' and (resid 936 through 954 )B936 - 954
17X-RAY DIFFRACTION17chain 'B' and (resid 955 through 985 )B955 - 985
18X-RAY DIFFRACTION18chain 'B' and (resid 986 through 1021 )B986 - 1021

+
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