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- PDB-6u3j: Structure of the 2-oxoadipate dehydrogenase DHTKD1 -

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Basic information

Entry
Database: PDB / ID: 6u3j
TitleStructure of the 2-oxoadipate dehydrogenase DHTKD1
Components2-oxoglutarate dehydrogenase E1 component DHKTD1, mitochondrial
KeywordsOXIDOREDUCTASE / lysine metabolism mitochondrial dehydrogenase
Function / homology
Function and homology information


Oxidoreductases; Acting on the aldehyde or oxo group of donors; With a disulfide as acceptor / oxoglutarate dehydrogenase (succinyl-transferring) activity / oxoglutarate dehydrogenase complex / Glyoxylate metabolism and glycine degradation / thiamine pyrophosphate binding / hematopoietic progenitor cell differentiation / tricarboxylic acid cycle / generation of precursor metabolites and energy / glycolytic process / mitochondrial matrix ...Oxidoreductases; Acting on the aldehyde or oxo group of donors; With a disulfide as acceptor / oxoglutarate dehydrogenase (succinyl-transferring) activity / oxoglutarate dehydrogenase complex / Glyoxylate metabolism and glycine degradation / thiamine pyrophosphate binding / hematopoietic progenitor cell differentiation / tricarboxylic acid cycle / generation of precursor metabolites and energy / glycolytic process / mitochondrial matrix / mitochondrion / cytosol
Similarity search - Function
Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal / Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal domain superfamily / 2-oxoglutarate dehydrogenase C-terminal / 2-oxoglutarate dehydrogenase E1 component / Dehydrogenase, E1 component / Dehydrogenase E1 component / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain / Transketolase, pyrimidine binding domain / Thiamin diphosphate-binding fold
Similarity search - Domain/homology
THIAMINE DIPHOSPHATE / 2-oxoadipate dehydrogenase complex component E1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsKhamrui, S. / Lazarus, M.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM124838 United States
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: Inhibition and Crystal Structure of the Human DHTKD1-Thiamin Diphosphate Complex.
Authors: Leandro, J. / Khamrui, S. / Wang, H. / Suebsuwong, C. / Nemeria, N.S. / Huynh, K. / Moustakim, M. / Secor, C. / Wang, M. / Dodatko, T. / Stauffer, B. / Wilson, C.G. / Yu, C. / Arkin, M.R. / ...Authors: Leandro, J. / Khamrui, S. / Wang, H. / Suebsuwong, C. / Nemeria, N.S. / Huynh, K. / Moustakim, M. / Secor, C. / Wang, M. / Dodatko, T. / Stauffer, B. / Wilson, C.G. / Yu, C. / Arkin, M.R. / Jordan, F. / Sanchez, R. / DeVita, R.J. / Lazarus, M.B. / Houten, S.M.
History
DepositionAug 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.2Sep 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 11, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2-oxoglutarate dehydrogenase E1 component DHKTD1, mitochondrial
B: 2-oxoglutarate dehydrogenase E1 component DHKTD1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,6007
Polymers203,6762
Non-polymers9245
Water17,330962
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12490 Å2
ΔGint-67 kcal/mol
Surface area57800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)332.314, 72.612, 79.675
Angle α, β, γ (deg.)90.000, 91.870, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 2 or resseq 29:35 or resseq 51:63 or resseq 65:919))
21(chain B and (resseq 2 or resseq 29:35 or resseq 51:63 or resseq 65:919))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resseq 2 or resseq 29:35 or resseq 51:63 or resseq 65:919))A2
121(chain A and (resseq 2 or resseq 29:35 or resseq 51:63 or resseq 65:919))A29 - 35
131(chain A and (resseq 2 or resseq 29:35 or resseq 51:63 or resseq 65:919))A51 - 63
141(chain A and (resseq 2 or resseq 29:35 or resseq 51:63 or resseq 65:919))A65 - 919
211(chain B and (resseq 2 or resseq 29:35 or resseq 51:63 or resseq 65:919))B2
221(chain B and (resseq 2 or resseq 29:35 or resseq 51:63 or resseq 65:919))B29 - 35
231(chain B and (resseq 2 or resseq 29:35 or resseq 51:63 or resseq 65:919))B51 - 63
241(chain B and (resseq 2 or resseq 29:35 or resseq 51:63 or resseq 65:919))B65 - 919

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Components

#1: Protein 2-oxoglutarate dehydrogenase E1 component DHKTD1, mitochondrial / Dehydrogenase E1 and transketolase domain-containing protein 1


Mass: 101838.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DHTKD1, KIAA1630 / Production host: Escherichia coli (E. coli)
References: UniProt: Q96HY7, oxoglutarate dehydrogenase (succinyl-transferring)
#2: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 962 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.49 %
Description: Data were collected from two crystals and two datasets were scaled together
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Magnesium Acetate, 0.1 M MOPS, 12% PEG 8000, 10% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92013 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92013 Å / Relative weight: 1
ReflectionResolution: 2.25→49.01 Å / Num. obs: 90407 / % possible obs: 99.9 % / Redundancy: 8.3 % / Biso Wilson estimate: 30.76 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.239 / Rpim(I) all: 0.087 / Rrim(I) all: 0.255 / Net I/σ(I): 7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.25-2.295.21.1782295943900.5040.5651.3111.498.6
12.32-49.018.40.10649895960.9890.0380.11316.798.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.15 Å166.03 Å
Translation2.15 Å166.03 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.10.1_2155refinement
MOSFLMdata reduction
Aimless0.7.2data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZHQ
Resolution: 2.25→49.01 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.93
RfactorNum. reflection% reflection
Rfree0.2409 4590 5.08 %
Rwork0.209 --
obs0.2107 90328 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 162.57 Å2 / Biso mean: 41.509 Å2 / Biso min: 12.04 Å2
Refinement stepCycle: final / Resolution: 2.25→49.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13744 0 55 962 14761
Biso mean--37.25 41.36 -
Num. residues----1752
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00214158
X-RAY DIFFRACTIONf_angle_d0.50419196
X-RAY DIFFRACTIONf_chiral_restr0.0412086
X-RAY DIFFRACTIONf_plane_restr0.0042496
X-RAY DIFFRACTIONf_dihedral_angle_d13.1358446
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A6892X-RAY DIFFRACTIONPOSITIONAL0.008
12B6892X-RAY DIFFRACTIONPOSITIONAL0.008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.25-2.27560.3431580.28712866100
2.2756-2.30240.32041450.27842809100
2.3024-2.33040.28741570.26762854100
2.3304-2.35990.28611580.25932801100
2.3599-2.3910.28661660.24832850100
2.391-2.42370.28321530.24172844100
2.4237-2.45840.27951210.24392829100
2.4584-2.49510.28591450.2462911100
2.4951-2.5340.29011190.24692808100
2.534-2.57560.31511580.23992919100
2.5756-2.620.25011470.23842782100
2.62-2.66760.26471830.22142831100
2.6676-2.71890.25481660.22132819100
2.7189-2.77440.26741660.2132835100
2.7744-2.83470.24531480.20742871100
2.8347-2.90070.22841400.21162869100
2.9007-2.97320.30441360.20492851100
2.9732-3.05360.24141750.20832819100
3.0536-3.14340.22721340.20972880100
3.1434-3.24490.21611490.20222863100
3.2449-3.36080.22731730.20312843100
3.3608-3.49540.24191330.19042870100
3.4954-3.65440.21081700.18742855100
3.6544-3.8470.20181710.17422862100
3.847-4.08790.19421520.17532837100
4.0879-4.40330.2211690.17792867100
4.4033-4.84610.19221790.17712875100
4.8461-5.54650.25091200.20382898100
5.5465-6.98480.26771580.23342912100
6.9848-490.24221410.2209300899
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.16191.25-0.57740.84560.39380.90090.1701-0.3871-0.20720.0490.0679-0.05250.12330.4036-0.1440.26220.06040.04260.2220.00630.2757150.4331-5.056116.0344
24.7198-2.9024-0.26222.022-0.78427.5623-0.33880.50820.4885-0.1096-0.0806-0.4086-1.12991.09520.35990.7652-0.18260.08351.03470.21120.8289148.98071.8774-2.9862
39.7051-0.9097-0.52197.31571.32934.2027-0.0027-0.37910.03130.20110.1539-1.08170.09071.2638-0.25740.35380.02120.06790.6443-0.07170.2637166.2878-2.14710.5058
42.41260.3774-0.47361.33750.04242.0039-0.0502-0.1969-0.1363-0.14540.0127-0.27330.16690.5758-0.02690.20410.01040.07620.2702-0.01850.2456154.7584-6.645911.4765
51.54760.1096-0.44121.2660.14392.0099-0.09180.5072-0.2851-0.2816-0.0648-0.07820.3615-0.23980.1270.3334-0.01520.07950.3031-0.09510.267133.7007-19.21940.4508
66.9997-2.5913-0.6694.34832.27052.84630.20070.596-0.7590.1816-0.40480.79570.2302-0.4250.2880.6473-0.24130.03250.7446-0.27260.5803110.1475-22.2097-1.3579
71.86080.0955-0.48261.13670.20651.8761-0.03940.3001-0.0431-0.24930.00980.00330.0171-0.07650.02840.229-0.0040.04460.1474-0.02280.1839131.9342-11.44778.3568
85.73490.0508-1.31522.1474-0.03842.582-0.2711.0294-0.674-0.37490.0441-0.00090.5786-0.07770.12510.6636-0.06740.05060.8254-0.31580.4549129.2485-26.4999-14.9695
93.5671-0.3687-2.50085.6345-0.35792.6683-0.34430.6039-0.5581-0.00150.8122-0.21080.72780.09-0.28430.7863-0.34360.07740.9083-0.27810.8606110.4701-29.1477-1.6957
108.49980.3366-1.50123.42720.68692.6772-0.35890.2661-0.92670.29790.3475-0.32510.6646-0.20470.09310.6456-0.05580.02730.4107-0.03580.5076105.663-25.68419.0002
112.9798-0.24180.59780.7935-0.06632.42950.0497-0.7939-0.09080.39210.0298-0.1381-0.0002-0.0156-0.07930.519-0.04420.06260.44680.06580.3041111.7514-16.770651.0909
121.5104-0.1-0.41021.4103-0.19831.3114-0.0102-0.29080.00450.27920.0504-0.0104-0.0364-0.0017-0.01890.2865-0.03480.02680.25060.01440.1692113.7186-12.327342.1207
133.8447-0.2671-0.06923.25190.22684.5835-0.275-0.5597-0.38160.60820.2156-0.33920.1889-0.0845-0.00580.410.0375-0.00060.3040.0780.2858122.861-20.793544.9133
141.0326-0.0965-0.320.8457-0.1181.1787-0.0002-0.0911-0.02240.13120.05750.19250.0583-0.3374-0.0270.2073-0.04190.0680.24670.01660.2326101.0361-8.03231.3641
152.41210.21860.20852.24730.03821.8176-0.0141-0.13690.09850.1942-0.03420.7298-0.0056-0.51850.03810.21570.02340.06670.40310.00760.333187.77573.229830.1987
163.1842-0.94360.70921.62460.28780.54680.14050.41680.1961-0.16050.0242-0.1196-0.07110.5619-0.130.1917-0.07210.03620.2176-0.01870.2217150.22119.646522.7822
176.43681.9849-0.8744.37560.76418.5974-0.1844-0.65320.14870.0491-0.06460.01880.86770.610.26040.8195-0.06580.01730.95710.12840.8289147.47992.716941.6587
189.31250.78510.54646.76371.65633.70210.14020.2020.2911-0.01470.1016-1.0697-0.07111.1292-0.26420.3850.0333-0.01240.6796-0.05570.3691165.66216.720129.365
192.7237-0.43740.73021.50460.26342.4056-0.01960.19130.08190.12810.0172-0.1531-0.1830.5278-0.0160.2253-0.0050.01150.2590.01440.213154.229611.231427.6182
201.5839-0.23410.41911.31140.17971.9073-0.1126-0.56680.33120.2256-0.03490.0007-0.305-0.28060.12960.33820.0065-0.01350.2871-0.08590.2456132.489923.830737.1966
217.85472.30211.51624.54352.30693.05650.0528-0.49680.5397-0.0097-0.56211.1985-0.7212-1.28140.61770.56240.23920.02930.7967-0.26480.5979108.871226.846337.4119
221.6206-0.17960.46491.28270.15431.9516-0.0308-0.28910.04980.29260.00560.0197-0.0913-0.0870.02010.23180.00220.02120.1382-0.02350.1904131.251816.058929.1908
235.5926-0.28231.31782.1904-0.25632.5686-0.1717-1.04570.72040.6627-0.09010.1314-0.6145-0.16830.07920.70090.04650.02810.6995-0.2790.4611127.01531.117752.281
243.04031.33641.97365.1629-0.50381.6917-0.508-0.74790.7554-0.01460.6379-0.3043-0.5390.2014-0.07690.96710.5789-0.01871.0451-0.32450.9901109.17833.784237.7702
253.3188-0.27820.31675.3778-1.17951.2221-0.8705-0.13921.1388-0.47750.7736-0.1414-1.0706-0.02680.01420.9465-0.0564-0.0060.4081-0.11740.8487112.541631.91817.2335
262.98880.0871-0.32221.30750.35393.0810.11170.8419-0.1238-0.4995-0.1096-0.0489-0.0931-0.22670.02140.42350.0448-0.04240.40130.06390.2948112.095822.1695-11.3166
271.78170.37510.4041.5563-0.25081.6721-0.02980.3459-0.0091-0.40230.0701-0.07020.0590.08150.00680.3280.01890.01990.30250.01870.208115.35716.9531-5.7256
284.07440.43760.11192.86560.16414.8436-0.33290.73250.2397-0.59160.0273-0.5118-0.29590.08740.02520.4459-0.05920.06610.35930.11570.2844124.67625.4089-7.8957
291.10340.33460.26110.8474-0.08151.27170.00040.13930.0485-0.15230.03870.2003-0.0749-0.3016-0.02050.19830.0474-0.01460.22880.00170.2276101.97312.67374.1511
302.774-0.4461-0.62113.14290.18661.86750.01620.2699-0.0119-0.2534-0.06620.60770.0174-0.56-0.0080.1868-0.0315-0.04470.40950.02130.319188.65161.42634.4198
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 29:76)A29 - 76
2X-RAY DIFFRACTION2(chain A and resid 77:85)A77 - 85
3X-RAY DIFFRACTION3(chain A and resid 86:112)A86 - 112
4X-RAY DIFFRACTION4(chain A and resid 113:145)A113 - 145
5X-RAY DIFFRACTION5(chain A and resid 146:235)A146 - 235
6X-RAY DIFFRACTION6(chain A and resid 236:256)A236 - 256
7X-RAY DIFFRACTION7(chain A and resid 257:471)A257 - 471
8X-RAY DIFFRACTION8(chain A and resid 472:493)A472 - 493
9X-RAY DIFFRACTION9(chain A and resid 494:504)A494 - 504
10X-RAY DIFFRACTION10(chain A and resid 505:519)A505 - 519
11X-RAY DIFFRACTION11(chain A and resid 520:565)A520 - 565
12X-RAY DIFFRACTION12(chain A and resid 566:612)A566 - 612
13X-RAY DIFFRACTION13(chain A and resid 613:628)A613 - 628
14X-RAY DIFFRACTION14(chain A and resid 629:843)A629 - 843
15X-RAY DIFFRACTION15(chain A and resid 844:919)A844 - 919
16X-RAY DIFFRACTION16(chain B and resid 29:76)B29 - 76
17X-RAY DIFFRACTION17(chain B and resid 77:85)B77 - 85
18X-RAY DIFFRACTION18(chain B and resid 86:112)B86 - 112
19X-RAY DIFFRACTION19(chain B and resid 113:145)B113 - 145
20X-RAY DIFFRACTION20(chain B and resid 146:235)B146 - 235
21X-RAY DIFFRACTION21(chain B and resid 236:256)B236 - 256
22X-RAY DIFFRACTION22(chain B and resid 257:471)B257 - 471
23X-RAY DIFFRACTION23(chain B and resid 472:493)B472 - 493
24X-RAY DIFFRACTION24(chain B and resid 494:504)B494 - 504
25X-RAY DIFFRACTION25(chain B and resid 505:512)B505 - 512
26X-RAY DIFFRACTION26(chain B and resid 513:565)B513 - 565
27X-RAY DIFFRACTION27(chain B and resid 566:612)B566 - 612
28X-RAY DIFFRACTION28(chain B and resid 613:628)B613 - 628
29X-RAY DIFFRACTION29(chain B and resid 629:843)B629 - 843
30X-RAY DIFFRACTION30(chain B and resid 844:919)B844 - 919

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