[English] 日本語
Yorodumi
- PDB-6crn: Structure of the USP15 deubiquitinase domain in complex with a hi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6crn
TitleStructure of the USP15 deubiquitinase domain in complex with a high-affinity first-generation Ubv
Components
  • Ubiquitin carboxyl-terminal hydrolase 15
  • Ubiquitin variant 15.2
KeywordsSIGNALING PROTEIN / deubiuqitination / Ubv / high-affinity / inhibition
Function / homology
Function and homology information


negative regulation of antifungal innate immune response / regulation of intrinsic apoptotic signaling pathway in response to osmotic stress by p53 class mediator / protein K27-linked deubiquitination / positive regulation of RIG-I signaling pathway / regulation of RNA metabolic process / monoubiquitinated protein deubiquitination / ubiquitin-modified histone reader activity / transforming growth factor beta receptor binding / deubiquitinase activity / K48-linked deubiquitinase activity ...negative regulation of antifungal innate immune response / regulation of intrinsic apoptotic signaling pathway in response to osmotic stress by p53 class mediator / protein K27-linked deubiquitination / positive regulation of RIG-I signaling pathway / regulation of RNA metabolic process / monoubiquitinated protein deubiquitination / ubiquitin-modified histone reader activity / transforming growth factor beta receptor binding / deubiquitinase activity / K48-linked deubiquitinase activity / transcription elongation-coupled chromatin remodeling / SMAD binding / protein deubiquitination / BMP signaling pathway / transforming growth factor beta receptor signaling pathway / Downregulation of TGF-beta receptor signaling / negative regulation of transforming growth factor beta receptor signaling pathway / UCH proteinases / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Ub-specific processing proteases / nuclear body / cysteine-type endopeptidase activity / mitochondrion / proteolysis / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ubiquitin-like domain, USP-type / Ubiquitin-like domain / Peptidase C19, ubiquitin-specific peptidase, DUSP domain / DUSP-like superfamily / DUSP domain / DUSP domain profile. / Domain in ubiquitin-specific proteases. / Ubiquitin carboxyl-terminal hydrolase, C-terminal / Ubiquitin-specific protease C-terminal / : ...Ubiquitin-like domain, USP-type / Ubiquitin-like domain / Peptidase C19, ubiquitin-specific peptidase, DUSP domain / DUSP-like superfamily / DUSP domain / DUSP domain profile. / Domain in ubiquitin-specific proteases. / Ubiquitin carboxyl-terminal hydrolase, C-terminal / Ubiquitin-specific protease C-terminal / : / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Cysteine proteinases / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Ubiquitin-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase 15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSinger, A.U. / Teyra, J. / Boehmelt, G. / Lenter, M. / Sicheri, F. / Sidhu, S.S.
CitationJournal: Structure / Year: 2019
Title: Structural and Functional Characterization of Ubiquitin Variant Inhibitors of USP15.
Authors: Teyra, J. / Singer, A.U. / Schmitges, F.W. / Jaynes, P. / Kit Leng Lui, S. / Polyak, M.J. / Fodil, N. / Krieger, J.R. / Tong, J. / Schwerdtfeger, C. / Brasher, B.B. / Ceccarelli, D.F.J. / ...Authors: Teyra, J. / Singer, A.U. / Schmitges, F.W. / Jaynes, P. / Kit Leng Lui, S. / Polyak, M.J. / Fodil, N. / Krieger, J.R. / Tong, J. / Schwerdtfeger, C. / Brasher, B.B. / Ceccarelli, D.F.J. / Moffat, J. / Sicheri, F. / Moran, M.F. / Gros, P. / Eichhorn, P.J.A. / Lenter, M. / Boehmelt, G. / Sidhu, S.S.
History
DepositionMar 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation / citation_author
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 1.2Apr 17, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Oct 4, 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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 15
B: Ubiquitin carboxyl-terminal hydrolase 15
C: Ubiquitin carboxyl-terminal hydrolase 15
D: Ubiquitin carboxyl-terminal hydrolase 15
E: Ubiquitin variant 15.2
F: Ubiquitin variant 15.2
G: Ubiquitin variant 15.2
H: Ubiquitin variant 15.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,39712
Polymers200,1358
Non-polymers2624
Water5,711317
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.770, 98.942, 122.043
Angle α, β, γ (deg.)66.49, 88.31, 78.10
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Ubiquitin carboxyl-terminal hydrolase 15 / Deubiquitinating enzyme 15 / Ubiquitin thioesterase 15 / Ubiquitin-specific-processing protease 15 ...Deubiquitinating enzyme 15 / Ubiquitin thioesterase 15 / Ubiquitin-specific-processing protease 15 / Unph-2 / Unph4


Mass: 40959.340 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP15, KIAA0529 / Plasmid: pHH0103
Details (production host): N-terminal GST with a His tag and a TEV cleavage site
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y4E8, ubiquitinyl hydrolase 1
#2: Protein
Ubiquitin variant 15.2 / Ubv 15.2


Mass: 9074.376 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: This is a Ubv (ubiquitin variant) selected by phage display to bind the USP15 USP domain with high affinity
Source: (gene. exp.) Homo sapiens (human) / Gene: Ubb / Plasmid: modified pET53
Details (production host): N-terminal His tag, TEV cleavage site
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.32 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 24% PDG3350, 200 mM Potassium Citrate tribasic, 100 mM MES 6.5, cryoprotected in 21% PEG3350, 100 mM Potassium Citrate tribasic, 100 mM MES 6.5, 25% glycerol

-
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: Oct 15, 2016 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.11→111.72 Å / Num. obs: 92086 / % possible obs: 91.2 % / Redundancy: 2.1 % / CC1/2: 0.993 / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.6
Reflection shellResolution: 2.11→2.14 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.815 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 612 / CC1/2: 0.419 / % possible all: 63.5

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 2Y6E and a SwissModeller model of the 15.13 Ubvc

2y6e


Resolution: 2.5→111.72 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 25.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2355 2878 5.12 %
Rwork0.188 --
obs0.1904 56174 92.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→111.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13091 0 4 317 13412
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813451
X-RAY DIFFRACTIONf_angle_d1.25318217
X-RAY DIFFRACTIONf_dihedral_angle_d8.94110113
X-RAY DIFFRACTIONf_chiral_restr0.0791978
X-RAY DIFFRACTIONf_plane_restr0.0072358
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)
10.20860.0396-0.05170.2087-0.10090.3124-0.0198-0.1114-0.06610.1660.00620.0432-0.0166-0.0205-00.15050.01710.00230.20080.06180.114377.34-161.8295-10.8572
20.17230.13420.29290.17580.08970.0552-0.3661-0.0807-0.206-0.27270.2911-0.3421-0.1993-0.176-00.06650.0443-0.10860.17910.02780.077174.1554-151.6502-25.3594
30.18840.28280.00550.23410.12260.15690.0398-0.0125-0.0962-0.0487-0.0577-0.05470.0352-0.0432-00.1205-0.00880.02090.1757-0.01850.207792.2587-184.5464-51.255
40.03-0.1153-0.19550.3-0.08570.33480.0961-0.13740.1246-0.0729-0.12130.0286-0.1488-0.0459-00.20080.0258-0.01730.12840.02190.180495.3748-165.0343-55.5362
5-0.0283-0.046-0.02490.0811-0.02710.05180.0720.10460.113-0.1662-0.32330.0079-0.01320.006-00.1230.0003-0.06290.1744-0.10.292291.4101-106.9936-66.5225
60.041-0.0744-0.07950.1351-0.01110.07450.09890.04820.2815-0.0277-0.3159-0.07770.17660.082500.1703-0.0571-0.01130.1329-0.09460.238892.9553-108.7043-56.9097
7-0.1130.00680.0941-0.0595-0.12660.1027-0.03860.969-0.34190.2256-0.75990.39060.3852-0.4326-00.3379-0.27670.1423-0.36340.06170.195193.8341-128.8158-47.3313
80.02750.0469-0.00880.04610.0640.0271-0.08560.50130.4995-0.1176-0.5588-0.46430.71910.240800.1077-0.122-0.10810.1181-0.26880.032696.2921-125.6322-68.9821
90.006-0.01120.0027-0.00420.00310.00750.0251-0.04090.0694-0.00260.05710.0335-0.1392-0.126600.19330.0631-0.04380.3034-0.0050.320567.3843-117.404-94.7592
100.0165-0.0911-0.01320.0661-0.05230.06590.1957-0.00790.0486-0.2955-0.18760.0657-0.1526-0.283500.19380.0935-0.10830.04560.5642-0.923574.6715-126.7211-102.5272
110.00220.0013-0.0080.0050.01030.0046-0.01620.22110.0239-0.04680.0525-0.14450.11330.0164-00.380.09050.06330.21850.00480.164789.8362-148.9249-102.221
12-0.0180.0058-0.06870.00140.0079-0.0417-0.21330.13230.09820.0486-0.37620.16040.3157-0.013500.2737-0.25320.4689-0.24780.4759-0.427676.6781-148.1158-88.6287
130.00320.00890.00240.0089-0.00430.0038-0.0482-0.0155-0.00060.0749-0.10390.0344-0.05440.003700.498-0.06980.46330.5749-0.55930.446472.4757-161.9224-96.1636
140.0192-0.0151-0.00710.0921-0.07910.0173-0.0934-0.0196-0.08230.14160.09350.01370.1316-0.0098-00.16390.00140.01830.19260.01830.15771.833-141.7351-85.0688
150.0242-0.04150.01620.09020.04310.0946-0.12840.05690.03060.09060.1075-0.05540.0622-0.108300.07950.0195-0.010.1898-0.0090.147873.3847-128.7381-83.9617
160.0026-0.0042-0.0009-0.00180.00180.001-0.0423-0.05070.01590.0562-0.0607-0.02770.006-0.0194-00.6045-0.1025-0.09150.37450.05910.304196.2208-116.5001-28.5096
170.0004-0.00020.00040.0031-0.00120.00110.0030.00230.0036-0.00490.00750.0005-0.00340.010900.99350.066-0.05240.94460.24481.0817111.9438-118.6802-31.9919
18-0.0017-0.0033-0.0019-0.0022-0.00490.0042-0.0313-0.0734-0.05250.0006-0.1486-0.035-0.0199-0.063600.5535-0.0494-0.08110.455-0.00290.386496.4227-111.7546-28.1896
190.00260.0046-00.00390.0019-0.0008-0.036-0.0683-0.0477-0.028-0.0773-0.0149-0.0487-0.004-00.6422-0.1186-0.11160.38140.01610.4431103.0655-106.6213-28.6832
200.0010.0012-0.00060.0011-0.00020.0012-0.0081-0.0098-0.008-0.0176-0.0067-0.0062-0.0020.019900.617-0.1334-0.12890.42430.15420.7443110.3749-103.6375-32.5267
21-0.00170.00280.00020.0022-0.00090.003-0.03680.01270.00410.0372-0.0525-0.0338-0.03470.0202-00.5862-0.17630.04460.37520.09650.4498102.0076-111.8291-41.0332
220.0039-0.00160.00590.00190.00640.0118-0.00730.05510.01120.0935-0.08540.02790.0914-0.0600.546-0.0763-0.05770.28110.05730.375193.4377-110.7305-37.1148
230.0035-0.0003-0.0030.00050.0021-0.00060.02250.00320.0080.00180.0191-0.03210.00240.0513-00.4794-0.2291-0.05970.4551-0.04580.5262104.9914-114.941-36.574
24-0.0004-0.00280.00330.0068-0.0032-0.0013-0.0312-0.012-0.0235-0.0652-0.0974-0.08640.06220.026300.52010.05260.03860.2470.09930.3713102.8088-175.0527-82.4514
25-0.0023-0.00140.00330.00070.0055-0.00860.02140.09360.0509-0.0219-0.01690.00440.1441-0.1798-00.73570.09680.05480.3903-0.00360.48396.65-180.792-84.2462
26-0.0016-0.0027-0.00150.00240.00120.00160.0250.03350.00570.03110.0224-0.04880.05820.021700.83310.18120.28820.26290.1260.2593103.3962-185.9432-83.7652
27-0.0008-0.00370.00330.0023-0.00160.0026-0.1233-0.1197-0.023-0.0154-0.1197-0.1275-0.0248-0.065700.69770.29880.14890.38360.18970.5307105.1661-183.7488-74.4695
28-0.0021-0.0006-0.00820.00440.0080.0074-0.0137-0.1116-0.0285-0.0841-0.08280.0285-0.0923-0.059700.46220.08680.03550.22860.04490.18793.5139-181.3098-75.6602
290.00010.00050.00310.00130.00310.00130.04620.0111-0.03010.03080.0344-0.06040.0076-0.007800.68660.0819-0.08960.40930.11160.5245106.8445-179.7235-74.8834
300.00370.0002-0.001-0.00090.00160.00180.0232-0.0202-0.0207-0.04020.04970.01160.0356-0.028-00.7712-0.1254-0.0110.7104-0.15710.841274.3599-159.7803-111.3448
310.0019-0.00760.00210.0387-0.01460.0074-0.004-0.01240.0046-0.00160.00610.00610.00810.011101.0503-0.0461-0.13581.1979-0.03481.125660.0158-160.1687-106.1245
32-0.00130.0032-0.00270.00460.00630.00260.04910.035-0.03150.0243-0.01430.00380.0117-0.0006-01.0621-0.096-0.03570.689-0.0610.754974.8349-157.9481-115.8956
33-0.00030.00060.0050.0001-0.0010.0022-0.07320.0587-0.00540.0018-0.04120.0291-0.0052-0.009200.9414-0.0817-0.28970.7928-0.25690.714667.6268-155.8303-120.3505
340.00070.00030.00170.01340.0008-0.00020.02110.0066-0.0024-0.01010.01450.01260.0016-0.0168-01.4555-0.0804-0.26641.4095-0.00851.477960.6047-152.2594-119.6148
35-0.0001-0.00260.0020.00150.0009-0.00110.01290.0050.00990.02280.0090.02870.0013-0.0044-01.00310.3212-0.17170.814-0.19650.941869.3867-147.0351-107.8215
360.0014-0.00180.0120.00530.0077-0.0014-0.01270.02570.02210.00670.00380.07710.0394-0.0301-00.74870.09870.01360.4578-0.08920.520574.5716-150.6972-111.1926
370.001-0.0014-0.001-0.00130.00340.0015-0.00340.01490.00280.00010.01220.0036-0.0121-0.0366-00.8480.10570.11220.8734-0.23880.707974.8136-132.7942-0.7452
380.0043-0.00330.0009-0.00040.0068-0.00030.04890.0070.01270.01860.07080.0141-0.014-0.02200.9490.18580.15810.8172-0.18880.889768.5452-132.1681-0.1223
390.00960.0042-0.00210.0056-0.00180.0014-0.01320.01470.01550.0044-0.0081-0.0077-0.0127-0.004800.98290.16330.09420.8942-0.2650.685479.3625-139.60667.1959
40-0.0006-0.0003-0.0028-0.0014-0.00190.00120.0445-0.0240.0425-0.00160.05460.0444-0.0043-0.0065-00.96590.39180.25890.9961-0.27780.836365.9158-137.988.037
41-0.00040.0011-0.0005-0.00020.00060.00060.009-0.02060.0129-0.0357-0.0076-0.00440.0002-0.004500.793-0.00180.10570.9627-0.20340.903769.769-145.251-4.8093
420.0045-0.0037-0.00630.00150.00740.00870.0516-0.10460.0531-0.0434-0.02120.0099-0.0553-0.0613-00.6279-0.00460.10640.4954-0.06240.633477.444-142.59850.0389
430.0004-0.00060.00010.00150.0004-0.0022-0.00340.00650.009-0.0032-0.0084-0.0047-0.01-0.0182-00.6396-0.02850.10650.7235-0.10530.942264.4262-139.9266-3.1556
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 280 through 429 )
2X-RAY DIFFRACTION2chain 'A' and (resid 430 through 626 )
3X-RAY DIFFRACTION3chain 'B' and (resid 277 through 414 )
4X-RAY DIFFRACTION4chain 'B' and (resid 415 through 623 )
5X-RAY DIFFRACTION5chain 'C' and (resid 277 through 336 )
6X-RAY DIFFRACTION6chain 'C' and (resid 337 through 414 )
7X-RAY DIFFRACTION7chain 'C' and (resid 415 through 526 )
8X-RAY DIFFRACTION8chain 'C' and (resid 527 through 623 )
9X-RAY DIFFRACTION9chain 'D' and (resid 280 through 299 )
10X-RAY DIFFRACTION10chain 'D' and (resid 300 through 396 )
11X-RAY DIFFRACTION11chain 'D' and (resid 397 through 429 )
12X-RAY DIFFRACTION12chain 'D' and (resid 430 through 485 )
13X-RAY DIFFRACTION13chain 'D' and (resid 486 through 508 )
14X-RAY DIFFRACTION14chain 'D' and (resid 509 through 554 )
15X-RAY DIFFRACTION15chain 'D' and (resid 555 through 626 )
16X-RAY DIFFRACTION16chain 'E' and (resid -2 through 6 )
17X-RAY DIFFRACTION17chain 'E' and (resid 7 through 11 )
18X-RAY DIFFRACTION18chain 'E' and (resid 12 through 22 )
19X-RAY DIFFRACTION19chain 'E' and (resid 23 through 34 )
20X-RAY DIFFRACTION20chain 'E' and (resid 35 through 40 )
21X-RAY DIFFRACTION21chain 'E' and (resid 41 through 49 )
22X-RAY DIFFRACTION22chain 'E' and (resid 50 through 64 )
23X-RAY DIFFRACTION23chain 'E' and (resid 65 through 71 )
24X-RAY DIFFRACTION24chain 'F' and (resid -1 through 11 )
25X-RAY DIFFRACTION25chain 'F' and (resid 12 through 22 )
26X-RAY DIFFRACTION26chain 'F' and (resid 23 through 34 )
27X-RAY DIFFRACTION27chain 'F' and (resid 35 through 50 )
28X-RAY DIFFRACTION28chain 'F' and (resid 51 through 65 )
29X-RAY DIFFRACTION29chain 'F' and (resid 66 through 72 )
30X-RAY DIFFRACTION30chain 'G' and (resid -1 through 6 )
31X-RAY DIFFRACTION31chain 'G' and (resid 7 through 11 )
32X-RAY DIFFRACTION32chain 'G' and (resid 12 through 22 )
33X-RAY DIFFRACTION33chain 'G' and (resid 23 through 34 )
34X-RAY DIFFRACTION34chain 'G' and (resid 35 through 41 )
35X-RAY DIFFRACTION35chain 'G' and (resid 42 through 50 )
36X-RAY DIFFRACTION36chain 'G' and (resid 51 through 70 )
37X-RAY DIFFRACTION37chain 'H' and (resid -1 through 6 )
38X-RAY DIFFRACTION38chain 'H' and (resid 7 through 17 )
39X-RAY DIFFRACTION39chain 'H' and (resid 18 through 22 )
40X-RAY DIFFRACTION40chain 'H' and (resid 23 through 39 )
41X-RAY DIFFRACTION41chain 'H' and (resid 42 through 50 )
42X-RAY DIFFRACTION42chain 'H' and (resid 51 through 65 )
43X-RAY DIFFRACTION43chain 'H' and (resid 66 through 72 )

+
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