[English] 日本語
Yorodumi
- PDB-6st3: HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with 4-hydroxy-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6st3
TitleHIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with 4-hydroxy-N-(4-phenoxybenzyl)-2-(1H-pyrazol-1-yl)pyrimidine-5-carboxamide
ComponentsEgl nine homolog 1
KeywordsOXIDOREDUCTASE / NON-HEME DIOXYGENASE / IRON / 2-OXOGLUTARATE / HYPOXIA-INDUCIBLE FACTOR / HIF / HIF PROLYL HYDROXYLASE DOMAIN 2 / PHD2 / EGLN1 / OXYGENASE / HYPOXIA / DNA-BINDING / METAL-BINDING / TRANSCRIPTION / HELIX-LOOP-HELIX-BETA / DSBH / FACIAL TRIAD / CYTOPLASM / TRANSCRIPTION/EPIGENETIC REGULATION / SIGNALING / DEVELOPMENT / CELL STRUCTURE / BETA-HYDROXYLATION / TRANSCRIPTION ACTIVATOR/INHIBITOR / UBL CONJUGATION / POLYMORPHISM / VITAMIN C / ZINC-FINGER / FAMILIAL ERYTHROCYTOSIS / BREAST CANCER / TRANSCRIPTION COMPLEX
Function / homology
Function and homology information


peptidyl-proline 4-dioxygenase activity / hypoxia-inducible factor-proline dioxygenase activity / hypoxia-inducible factor-proline dioxygenase / negative regulation of hypoxia-inducible factor-1alpha signaling pathway / peptidyl-proline dioxygenase activity / regulation protein catabolic process at postsynapse / intracellular oxygen homeostasis / regulation of modification of postsynaptic structure / labyrinthine layer development / 2-oxoglutarate-dependent dioxygenase activity ...peptidyl-proline 4-dioxygenase activity / hypoxia-inducible factor-proline dioxygenase activity / hypoxia-inducible factor-proline dioxygenase / negative regulation of hypoxia-inducible factor-1alpha signaling pathway / peptidyl-proline dioxygenase activity / regulation protein catabolic process at postsynapse / intracellular oxygen homeostasis / regulation of modification of postsynaptic structure / labyrinthine layer development / 2-oxoglutarate-dependent dioxygenase activity / heart trabecula formation / cardiac muscle tissue morphogenesis / L-ascorbic acid binding / response to nitric oxide / ventricular septum morphogenesis / enzyme inhibitor activity / regulation of angiogenesis / regulation of neuron apoptotic process / ferrous iron binding / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / cellular response to hypoxia / intracellular iron ion homeostasis / response to hypoxia / postsynaptic density / intracellular membrane-bounded organelle / glutamatergic synapse / enzyme binding / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / Prolyl 4-hydroxylase alpha subunit, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / MYND finger / Zinc finger MYND-type signature. / Zinc finger, MYND-type / Zinc finger MYND-type profile. / q2cbj1_9rhob like domain ...: / Prolyl 4-hydroxylase alpha subunit, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / MYND finger / Zinc finger MYND-type signature. / Zinc finger, MYND-type / Zinc finger MYND-type profile. / q2cbj1_9rhob like domain / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
FORMIC ACID / Chem-LUW / : / Egl nine homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.426 Å
AuthorsChowdhury, R. / Holt-Martyn, J.P. / Schofield, C.J.
Citation
Journal: Chemmedchem / Year: 2020
Title: Structure-Activity Relationship and Crystallographic Studies on 4-Hydroxypyrimidine HIF Prolyl Hydroxylase Domain Inhibitors.
Authors: Holt-Martyn, J.P. / Chowdhury, R. / Tumber, A. / Yeh, T.L. / Abboud, M.I. / Lippl, K. / Lohans, C.T. / Langley, G.W. / Figg Jr., W. / McDonough, M.A. / Pugh, C.W. / Ratcliffe, P.J. / Schofield, C.J.
#1: Journal: ACS Chem. Biol. / Year: 2013
Title: Selective small molecule probes for the hypoxia inducible factor (HIF) prolyl hydroxylases.
Authors: Chowdhury, R. / Candela-Lena, J.I. / Chan, M.C. / Greenald, D.J. / Yeoh, K.K. / Tian, Y.M. / McDonough, M.A. / Tumber, A. / Rose, N.R. / Conejo-Garcia, A. / Demetriades, M. / Mathavan, S. / ...Authors: Chowdhury, R. / Candela-Lena, J.I. / Chan, M.C. / Greenald, D.J. / Yeoh, K.K. / Tian, Y.M. / McDonough, M.A. / Tumber, A. / Rose, N.R. / Conejo-Garcia, A. / Demetriades, M. / Mathavan, S. / Kawamura, A. / Lee, M.K. / van Eeden, F. / Pugh, C.W. / Ratcliffe, P.J. / Schofield, C.J.
History
DepositionSep 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Egl nine homolog 1
B: Egl nine homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0508
Polymers52,0732
Non-polymers9776
Water2,342130
1
A: Egl nine homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5254
Polymers26,0371
Non-polymers4883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Egl nine homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5254
Polymers26,0371
Non-polymers4883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.870, 80.580, 83.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 187 through 215 or (resid 216...
21(chain B and (resid 187 or (resid 188 and (name...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 187 through 215 or (resid 216...A187 - 215
121(chain A and (resid 187 through 215 or (resid 216...A216
131(chain A and (resid 187 through 215 or (resid 216...A189 - 405
141(chain A and (resid 187 through 215 or (resid 216...A189 - 405
151(chain A and (resid 187 through 215 or (resid 216...A189 - 405
161(chain A and (resid 187 through 215 or (resid 216...A189 - 405
171(chain A and (resid 187 through 215 or (resid 216...A189 - 405
211(chain B and (resid 187 or (resid 188 and (name...B187
221(chain B and (resid 187 or (resid 188 and (name...B188
231(chain B and (resid 187 or (resid 188 and (name...B188 - 406
241(chain B and (resid 187 or (resid 188 and (name...B188 - 406
251(chain B and (resid 187 or (resid 188 and (name...B188 - 406
261(chain B and (resid 187 or (resid 188 and (name...B188 - 406

-
Components

#1: Protein Egl nine homolog 1 / Hypoxia-inducible factor prolyl hydroxylase 2 / HPH-2 / Prolyl hydroxylase domain-containing ...Hypoxia-inducible factor prolyl hydroxylase 2 / HPH-2 / Prolyl hydroxylase domain-containing protein 2 / PHD2 / SM-20


Mass: 26036.582 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: FRAGMENT: CATALYTIC DOMAIN (aa 181-407) / Source: (gene. exp.) Homo sapiens (human) / Gene: EGLN1, C1orf12, PNAS-118, PNAS-137 / Plasmid: PET28A(+) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9GZT9, hypoxia-inducible factor-proline dioxygenase
#2: Chemical ChemComp-LUW / 4-oxidanyl-~{N}-[(4-phenoxyphenyl)methyl]-2-pyrazol-1-yl-pyrimidine-5-carboxamide


Mass: 387.391 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H17N5O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2 M Ammonium acetate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 30% PEG 4000, Sitting drop (300 nl), protein-to-well ratio, 1:2, 293K

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 21, 2015 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.426→83.92 Å / Num. obs: 19127 / % possible obs: 99.3 % / Redundancy: 3.8 % / Biso Wilson estimate: 35.8 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.089 / Rrim(I) all: 0.182 / Net I/σ(I): 6.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.43-2.523.80.9741.519780.5480.5861.20699.5
9.08-83.923.50.054240.990.0330.06498.5

-
Processing

Software
NameVersionClassification
Aimless0.7.3data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BQX

4bqx


Resolution: 2.426→58.123 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.53
RfactorNum. reflection% reflection
Rfree0.2173 946 4.96 %
Rwork0.1924 --
obs0.1936 19083 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: 46.4 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 153.19 Å2 / Biso mean: 49.777 Å2 / Biso min: 20.62 Å2
Refinement stepCycle: final / Resolution: 2.426→58.123 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3202 0 102 130 3434
Biso mean--48.15 46.68 -
Num. residues----419
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1815X-RAY DIFFRACTION6.233TORSIONAL
12B1815X-RAY DIFFRACTION6.233TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.426-2.55370.36371240.3021253499
2.5537-2.71370.25751370.2682257699
2.7137-2.92320.2311270.2278254298
2.9232-3.21740.22571580.2092254999
3.2174-3.68290.20581230.1685260399
3.6829-4.63980.20241340.1516262599
4.6398-58.1230.18651430.1792270898
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)
10.0909-0.09430.13880.1340.01870.321-0.45720.28570.4978-0.06670.3736-0.0645-0.7124-0.1520.00040.7145-0.0684-0.07580.459-0.16390.677510.920346.876423.9922
20.1661-0.0120.08380.1542-0.21230.1331-0.54380.40230.9332-0.42040.08880.3232-0.4025-0.6331-0.00490.5447-0.0489-0.13040.37930.01220.58338.965339.842117.6651
30.27920.1322-0.03761.17610.30870.44740.16240.70180.1199-1.8313-0.251-0.45650.02680.2275-0.00730.4499-0.0010.04930.4588-0.01280.413818.322224.09869.2826
40.6288-0.7432-0.20440.7252-0.96341.25850.0965-0.5448-0.70190.4088-0.1127-0.11350.5649-0.0420.02450.3992-0.00680.04540.39260.01020.468914.713416.233922.0423
51.7170.2359-1.27580.358-0.5583.2612-0.4113-0.10490.2715-0.2863-0.012-0.5291-0.39690.5695-0.84970.446-0.0663-0.16260.3664-0.03030.550220.528735.550722.3582
60.49570.20160.23350.07510.00470.27990.131-0.89670.90310.3364-0.03630.7429-0.561-0.32990.2680.7083-0.0407-0.10350.6783-0.15410.630613.017941.001435.4431
70.3044-0.69750.50710.5597-0.14710.1706-0.01720.27010.0480.21-0.0306-0.03780.42030.6274-0.00120.3212-0.05510.03270.28160.00970.340711.117622.360920.4757
80.06180.24290.39350.1798-0.01920.2018-0.2315-0.13250.12020.5403-0.18890.66840.35180.2681-0.00720.39490.02090.03120.4148-0.00570.36740.985624.122328.4998
90.85810.08190.07470.92910.07970.2286-0.54060.04490.2049-0.2861-0.14780.1061-0.45080.1229-0.01550.4072-0.0375-0.03240.3028-0.01870.27428.461830.437417.5239
100.3998-0.207-0.0060.04990.04180.01260.0539-0.02290.3837-0.3193-0.33790.2341-1.2352-0.6699-0.04530.51770.0199-0.05020.3876-0.08860.4302-3.733331.370418.0303
110.7358-0.11610.84150.0617-0.07710.93320.16810.41931.1728-0.9009-0.16331.2037-1.3064-0.1044-0.34520.42960.0079-0.10350.2789-0.1450.55950.684834.534315.293
121.432-0.49370.93870.6505-0.86953.8318-0.4590.1373-0.10770.2879-0.86230.3209-0.35310.5447-0.5610.46160.07110.02460.1812-0.15810.42054.663934.925327.049
130.2262-0.10350.09980.59450.0199-0.01010.0532-0.0824-0.3561-0.1868-0.07370.4834-0.1794-0.0808-0.01110.2657-0.0199-0.07360.3149-0.09680.3874-2.007925.63318.091
140.3152-0.3870.54330.2839-0.41370.2969-0.25050.26060.0280.23110.2558-0.1255-0.66280.4451-0.00060.399-0.0357-0.04570.3166-0.04560.328711.283927.686223.2354
150.64660.0686-0.20750.3069-0.30230.2593-0.01640.4019-0.07720.87690.4861-0.01190.58170.02440.73230.99660.0865-0.27570.7572-0.19480.408912.163328.811644.2272
160.1789-0.21850.16540.28440.02220.52960.0441-0.14290.2460.31110.05340.2169-0.08470.2674-00.3327-0.001-0.03010.4160.00510.251225.44169.19737.751
170.1263-0.1173-0.12440.44310.31210.03390.4907-0.56040.7880.4175-0.18630.3389-0.62440.49700.2846-0.04-0.00230.31210.02910.376922.198713.6276-0.4327
180.78540.22010.85691.29750.38841.01520.47480.85620.8469-0.66610.0968-0.9084-1.22020.55190.15870.438-0.0470.08180.67270.1570.297228.052314.4313-19.7638
190.2467-0.3175-0.01915.6279-1.2171.6104-0.4550.8152-0.3795-0.58140.22330.73660.3156-0.48370.17650.4739-0.02770.03490.5581-0.05260.310121.39392.9577-20.3681
200.8623-0.02470.23170.5324-0.03220.284-0.15170.4352-0.0082-0.017-0.0669-0.0691-0.02420.4268-0.00010.3012-0.01170.02930.45250.01910.378131.42545.3058-5.3068
21-0.0139-0.01810.01840.2181-0.20070.076-0.3446-0.4359-0.23370.77510.21810.00910.43230.32480.00030.41010.0330.02960.3741-0.00740.439723.7634-3.75965.3826
220.24880.23740.27070.1315-0.0128-0.06960.4970.548-0.0711-0.2477-0.4140.15060.07040.49120.00010.3560.0678-0.01090.3897-0.03110.318119.16295.3764-16.0593
230.48320.20070.44670.1992-0.38480.6027-0.04440.1927-0.5042-0.35670.49070.43710.4024-0.38460.04020.3718-0.0554-0.01370.3529-0.09120.40398.83350.6561-9.7944
241.55310.15150.35080.28390.39040.3188-0.19720.35880.13040.17590.18-0.3147-0.1247-0.09510.00540.24350.02790.02170.27730.05710.322819.390711.4639-9.2079
250.46-0.2355-0.24660.6930.74170.413-0.0944-0.09690.10431.0337-0.07570.1494-0.75820.1783-0.00330.38190.0174-0.01340.28150.01250.38437.597613.4009-5.1155
260.3293-0.25160.25910.57170.32490.38280.8506-0.19420.79980.2649-0.30230.2491-0.93020.2037-0.00020.36270.01720.03140.31360.06090.493613.707216.4122-4.5009
271.0212-0.18850.33480.26010.01230.8628-0.19260.0309-0.31830.10070.3433-0.09760.3005-0.14720.00670.3267-0.01150.04970.22930.00630.246915.4074.3318-1.1461
281.14850.8305-0.06510.2921-0.10380.13260.0591-0.01920.3460.47060.09070.0710.0342-0.21550.52140.14750.0114-0.04630.33440.06760.37497.783611.3472-11.1899
290.8436-0.23720.11290.50920.74020.69240.0250.3343-0.14270.16160.01720.4141-0.16630.2573-0.00050.2911-0.011-0.01450.30830.01780.279520.50234.27-10.2966
300.6885-0.1403-0.08640.55480.47460.4921-0.36780.2282-0.07320.3014-0.17230.1130.16950.5549-0.01220.5049-00.08360.31520.03290.358118.9286-15.3316-4.3078
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 188:204)A188 - 204
2X-RAY DIFFRACTION2(chain A and resid 205:215)A205 - 215
3X-RAY DIFFRACTION3(chain A and resid 216:232)A216 - 232
4X-RAY DIFFRACTION4(chain A and resid 233:266)A233 - 266
5X-RAY DIFFRACTION5(chain A and resid 267:283)A267 - 283
6X-RAY DIFFRACTION6(chain A and resid 284:293)A284 - 293
7X-RAY DIFFRACTION7(chain A and resid 294:306)A294 - 306
8X-RAY DIFFRACTION8(chain A and resid 307:320)A307 - 320
9X-RAY DIFFRACTION9(chain A and resid 321:335)A321 - 335
10X-RAY DIFFRACTION10(chain A and resid 336:350)A336 - 350
11X-RAY DIFFRACTION11(chain A and resid 351:361)A351 - 361
12X-RAY DIFFRACTION12(chain A and resid 362:371)A362 - 371
13X-RAY DIFFRACTION13(chain A and resid 372:381)A372 - 381
14X-RAY DIFFRACTION14(chain A and resid 382:392)A382 - 392
15X-RAY DIFFRACTION15(chain A and resid 393:403)A393 - 403
16X-RAY DIFFRACTION16(chain B and resid 188:204)B188 - 204
17X-RAY DIFFRACTION17(chain B and resid 205:215)B205 - 215
18X-RAY DIFFRACTION18(chain B and resid 216:232)B216 - 232
19X-RAY DIFFRACTION19(chain B and resid 233:266)B233 - 266
20X-RAY DIFFRACTION20(chain B and resid 267:283)B267 - 283
21X-RAY DIFFRACTION21(chain B and resid 284:293)B284 - 293
22X-RAY DIFFRACTION22(chain B and resid 294:306)B294 - 306
23X-RAY DIFFRACTION23(chain B and resid 307:320)B307 - 320
24X-RAY DIFFRACTION24(chain B and resid 321:335)B321 - 335
25X-RAY DIFFRACTION25(chain B and resid 336:350)B336 - 350
26X-RAY DIFFRACTION26(chain B and resid 351:361)B351 - 361
27X-RAY DIFFRACTION27(chain B and resid 362:371)B362 - 371
28X-RAY DIFFRACTION28(chain B and resid 372:381)B372 - 381
29X-RAY DIFFRACTION29(chain B and resid 382:392)B382 - 392
30X-RAY DIFFRACTION30(chain B and resid 393:403)B393 - 403

+
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