[English] 日本語
Yorodumi
- PDB-5ok6: Ubiquitin specific protease 11 USP11 - peptide F complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ok6
TitleUbiquitin specific protease 11 USP11 - peptide F complex
Components
  • ALA-GLU-GLY-GLU-PHE-TYR-LYS-LEU-LYS-ILE-ARG-THR-PRO-AAR
  • Ubiquitin carboxyl-terminal hydrolase 11
KeywordsPROTEIN BINDING / peptide ligand complex / ubiquitin / protease
Function / homology
Function and homology information


Association of TriC/CCT with target proteins during biosynthesis / protein deubiquitination / transcription corepressor binding / chromosome / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Ub-specific processing proteases / cysteine-type endopeptidase activity / proteolysis / nucleoplasm ...Association of TriC/CCT with target proteins during biosynthesis / protein deubiquitination / transcription corepressor binding / chromosome / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Ub-specific processing proteases / cysteine-type endopeptidase activity / proteolysis / nucleoplasm / nucleus / cytosol
Similarity search - Function
DUSP-like / DUSP-like / 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 ...DUSP-like / DUSP-like / 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 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. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Papain-like cysteine peptidase superfamily / Ubiquitin-like (UB roll) / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase 11
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsSpiliotopoulos, A. / Dreveny, I.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/H012656/1 United Kingdom
Citation
Journal: J.Biol.Chem. / Year: 2019
Title: Discovery of peptide ligands targeting a specific ubiquitin-like domain-binding site in the deubiquitinase USP11.
Authors: Spiliotopoulos, A. / Blokpoel Ferreras, L. / Densham, R.M. / Caulton, S.G. / Maddison, B.C. / Morris, J.R. / Dixon, J.E. / Gough, K.C. / Dreveny, I.
#1: Journal: Biochemistry / Year: 2014
Title: Structure and catalytic regulatory function of ubiquitin specific protease 11 N-terminal and ubiquitin-like domains.
Authors: Harper, S. / Gratton, H.E. / Cornaciu, I. / Oberer, M. / Scott, D.J. / Emsley, J. / Dreveny, I.
History
DepositionJul 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 25, 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Ubiquitin carboxyl-terminal hydrolase 11
B: Ubiquitin carboxyl-terminal hydrolase 11
C: ALA-GLU-GLY-GLU-PHE-TYR-LYS-LEU-LYS-ILE-ARG-THR-PRO-AAR
D: ALA-GLU-GLY-GLU-PHE-TYR-LYS-LEU-LYS-ILE-ARG-THR-PRO-AAR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2487
Polymers57,0324
Non-polymers2163
Water11,692649
1
A: Ubiquitin carboxyl-terminal hydrolase 11
D: ALA-GLU-GLY-GLU-PHE-TYR-LYS-LEU-LYS-ILE-ARG-THR-PRO-AAR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6083
Polymers28,5162
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-8 kcal/mol
Surface area13430 Å2
MethodPISA
2
B: Ubiquitin carboxyl-terminal hydrolase 11
C: ALA-GLU-GLY-GLU-PHE-TYR-LYS-LEU-LYS-ILE-ARG-THR-PRO-AAR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6404
Polymers28,5162
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-9 kcal/mol
Surface area13120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.770, 45.510, 100.610
Angle α, β, γ (deg.)90.000, 102.680, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain C and (resid 3 through 11 or resid 13 through 14))
21(chain D and (resid 3 through 11 or resid 13 through 14))
12(chain A and (resid 32 through 36 or resid 38...
22(chain B and (resid 32 through 36 or resid 38...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLYGLYARGARG(chain C and (resid 3 through 11 or resid 13 through 14))CC3 - 113 - 11
121PROPROAARAAR(chain C and (resid 3 through 11 or resid 13 through 14))CC13 - 1413 - 14
211GLYGLYARGARG(chain D and (resid 3 through 11 or resid 13 through 14))DD3 - 113 - 11
221PROPROAARAAR(chain D and (resid 3 through 11 or resid 13 through 14))DD13 - 1413 - 14
112LEULEUASPASP(chain A and (resid 32 through 36 or resid 38...AA32 - 3610 - 14
122GLNGLNGLYGLY(chain A and (resid 32 through 36 or resid 38...AA38 - 4816 - 26
132GLUGLULEULEU(chain A and (resid 32 through 36 or resid 38...AA50 - 6128 - 39
142LYSLYSLYSLYS(chain A and (resid 32 through 36 or resid 38...AA6442
152TRPTRPTRPTRP(chain A and (resid 32 through 36 or resid 38...AA6644
162LYSLYSTRPTRP(chain A and (resid 32 through 36 or resid 38...AA68 - 7046 - 48
172ALAALAASPASP(chain A and (resid 32 through 36 or resid 38...AA72 - 7850 - 56
182ASPASPGLYGLY(chain A and (resid 32 through 36 or resid 38...AA80 - 8658 - 64
192ILEILELYSLYS(chain A and (resid 32 through 36 or resid 38...AA88 - 10366 - 81
1102GLYGLYGLYGLY(chain A and (resid 32 through 36 or resid 38...AA105 - 10983 - 87
1112ASPASPVALVAL(chain A and (resid 32 through 36 or resid 38...AA111 - 12489 - 102
1122TRPTRPPROPRO(chain A and (resid 32 through 36 or resid 38...AA126 - 134104 - 112
1132ILEILEVALVAL(chain A and (resid 32 through 36 or resid 38...AA136 - 159114 - 137
1142HISHISVALVAL(chain A and (resid 32 through 36 or resid 38...AA161 - 170139 - 148
1152PHEPHEGLUGLU(chain A and (resid 32 through 36 or resid 38...AA172 - 195150 - 173
1162THRTHRTHRTHR(chain A and (resid 32 through 36 or resid 38...AA197 - 214175 - 192
1172ILEILEGLUGLU(chain A and (resid 32 through 36 or resid 38...AA216 - 246194 - 224
212LEULEUASPASP(chain B and (resid 32 through 36 or resid 38...BB32 - 3610 - 14
222GLNGLNGLYGLY(chain B and (resid 32 through 36 or resid 38...BB38 - 4816 - 26
232GLUGLULEULEU(chain B and (resid 32 through 36 or resid 38...BB50 - 6128 - 39
242LYSLYSLYSLYS(chain B and (resid 32 through 36 or resid 38...BB6442
252TRPTRPTRPTRP(chain B and (resid 32 through 36 or resid 38...BB6644
262LYSLYSTRPTRP(chain B and (resid 32 through 36 or resid 38...BB68 - 7046 - 48
272ALAALAASPASP(chain B and (resid 32 through 36 or resid 38...BB72 - 7850 - 56
282ASPASPGLYGLY(chain B and (resid 32 through 36 or resid 38...BB80 - 8658 - 64
292ILEILELYSLYS(chain B and (resid 32 through 36 or resid 38...BB88 - 10366 - 81
2102GLYGLYGLYGLY(chain B and (resid 32 through 36 or resid 38...BB105 - 10983 - 87
2112ASPASPVALVAL(chain B and (resid 32 through 36 or resid 38...BB111 - 12489 - 102
2122TRPTRPPROPRO(chain B and (resid 32 through 36 or resid 38...BB126 - 134104 - 112
2132ILEILEVALVAL(chain B and (resid 32 through 36 or resid 38...BB136 - 159114 - 137
2142HISHISVALVAL(chain B and (resid 32 through 36 or resid 38...BB161 - 170139 - 148
2152PHEPHEGLUGLU(chain B and (resid 32 through 36 or resid 38...BB172 - 195150 - 173
2162THRTHRTHRTHR(chain B and (resid 32 through 36 or resid 38...BB197 - 214175 - 192
2172ILEILEGLUGLU(chain B and (resid 32 through 36 or resid 38...BB216 - 246194 - 224

NCS ensembles :
ID
1
2

-
Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 11 / Ubiquitin specific peptidase 11 / isoform CRA_b


Mass: 26804.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP11, hCG_17279 / Production host: Escherichia coli (E. coli) / References: UniProt: G5E9A6, UniProt: P51784*PLUS
#2: Protein/peptide ALA-GLU-GLY-GLU-PHE-TYR-LYS-LEU-LYS-ILE-ARG-THR-PRO-AAR


Mass: 1711.016 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 649 / 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: 2.58 Å3/Da / Density % sol: 52.25 %
Crystal growTemperature: 283.15 K / Method: vapor diffusion, sitting drop / Details: 0.01M tri-sodium citrate, 16% PEG6000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 5, 2013
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.3→49.01 Å / Num. obs: 140611 / % possible obs: 98.3 % / Redundancy: 4.1 % / Biso Wilson estimate: 13.76 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.028 / Rrim(I) all: 0.058 / Net I/σ(I): 16 / Num. measured all: 578764 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1 / Redundancy: 4.1 %

Resolution (Å)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
1.3-1.330.6240.7620.3450.71696.6
5.81-49.010.0290.9980.0160.03398.5

-
Processing

Software
NameVersionClassification
Aimless0.1.29data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MEL

4mel


Resolution: 1.3→49.007 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.51
RfactorNum. reflection% reflection
Rfree0.1779 7056 5.02 %
Rwork0.1571 --
obs0.1582 140596 98.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 100.41 Å2 / Biso mean: 20.2142 Å2 / Biso min: 7.79 Å2
Refinement stepCycle: final / Resolution: 1.3→49.007 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3795 0 14 649 4458
Biso mean--18.32 32.44 -
Num. residues----462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0154140
X-RAY DIFFRACTIONf_angle_d1.3465659
X-RAY DIFFRACTIONf_chiral_restr0.102586
X-RAY DIFFRACTIONf_plane_restr0.011749
X-RAY DIFFRACTIONf_dihedral_angle_d19.2231551
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11C102X-RAY DIFFRACTION6.185TORSIONAL
12D102X-RAY DIFFRACTION6.185TORSIONAL
21A1775X-RAY DIFFRACTION6.185TORSIONAL
22B1775X-RAY DIFFRACTION6.185TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3-1.31480.26912520.25894356460897
1.3148-1.33020.25692260.24824317454396
1.3302-1.34650.25232370.24154352458997
1.3465-1.36350.25452040.22954414461898
1.3635-1.38150.21862200.22014396461696
1.3815-1.40040.24292310.21084372460398
1.4004-1.42040.24691990.214399459896
1.4204-1.44160.22452390.20814363460298
1.4416-1.46410.222390.20334395463497
1.4641-1.48810.22362700.1984353462398
1.4881-1.51380.20792170.18174413463096
1.5138-1.54130.19032510.17294340459198
1.5413-1.5710.20562370.16684379461696
1.571-1.6030.17262190.15564446466598
1.603-1.63790.17762370.14764345458297
1.6379-1.6760.15832260.15414498472498
1.676-1.71790.18212280.15254387461598
1.7179-1.76440.17012670.14814479474699
1.7644-1.81630.17532310.15145094740100
1.8163-1.87490.18372400.14964499473999
1.8749-1.94190.18092380.14744491472999
1.9419-2.01970.16362270.144345314758100
2.0197-2.11160.1562420.141945354777100
2.1116-2.22290.16382460.139545034749100
2.2229-2.36220.17472280.146545544782100
2.3622-2.54460.16362300.15445484778100
2.5446-2.80060.16662370.155345374774100
2.8006-3.20580.17472150.154446224837100
3.2058-4.03870.17842410.145345694810100
4.0387-49.04180.15932820.14764638492099
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)
14.9388-0.53611.80776.2618-0.37317.47930.135-0.4436-0.50630.3383-0.02480.13310.57190.307-0.04260.18650.0604-0.00390.22190.03220.132180.0033-4.074545.1528
26.02590.03554.52891.61240.93777.2969-0.10190.318-0.21430.03290.0898-0.05080.46150.5694-0.01420.22480.04170.03680.1346-0.02410.111377.7372-3.524128.0258
33.34840.4053.48240.78771.47777.8723-0.1158-0.01440.23-0.0376-0.0771-0.0536-0.23080.22110.17010.11250.00380.00880.10420.01890.060472.74775.763340.2672
41.2068-0.31660.87090.3762-0.56452.7453-0.0218-0.1749-0.03440.06520.02160.0523-0.0473-0.0654-0.00470.10370.00490.01040.0883-0.00060.068667.46753.970840.5257
53.551-0.1062-0.53832.94080.09516.1553-0.15740.1343-0.1327-0.2237-0.03010.00350.2002-0.08320.13460.10090.01590.00030.05410.00570.076665.3042-0.13828.7327
63.74350.95441.97960.68980.42761.37770.0128-0.1141-0.050.04420.02220.0170.0996-0.1-0.0330.144-0.0094-0.00370.07220.01510.053348.3598-1.869915.7963
72.09460.04080.16072.3822-0.34652.6083-0.00240.0144-0.1025-0.11480.00710.03450.1944-0.10360.01440.1181-0.0136-0.02270.08230.00460.0543.3322-1.60727.1099
84.6901-0.23872.42130.6736-1.39194.41440.02740.32720.0572-0.0259-0.0666-0.0640.00290.35770.04390.142-0.02450.00350.0880.00920.081854.41383.48277.7783
92.71081.68451.11694.46351.51092.50710.01850.17890.0391-0.31550.02360.32110.0904-0.1557-0.07580.1223-0.0051-0.0210.09510.00690.095439.15770.72532.1924
106.36780.8756-3.04338.53980.09872.2269-0.0193-0.36890.52850.29520.23310.072-0.2173-0.0675-0.22830.15480.0273-0.00670.2034-0.03190.129582.3712-14.472816.328
116.7862-2.3974-0.94338.08960.52517.00760.1351-0.06380.3562-0.05390.0963-0.749-0.05240.9164-0.21760.22950.0146-0.00920.236-0.0620.181772.8634-15.11129.0767
124.9454-0.4033-3.82560.17710.15483.0949-0.1662-0.1137-0.1781-0.0060.02740.00890.08280.20220.11250.14750.00560.00380.1029-0.00730.069175.6061-22.512112.7659
132.92171.6877-0.63942.9027-0.6681.2892-0.04580.14160.0891-0.19450.08690.17620.0229-0.0151-0.02840.12520.0135-0.00310.0686-0.02220.073563.6912-21.597116.3195
143.6434-0.0156-0.93870.10640.00490.2304-0.0576-0.10450.00090.00690.036-0.0151-0.0285-0.0480.0210.15280.01540.00020.0746-0.01380.089254.8509-18.792824.6654
153.0210.156-0.21.1656-0.20232.508-0.03020.02750.0487-0.00850.05230.0256-0.0288-0.0014-0.0190.1110.01830.01760.08670.00220.054339.0963-14.855428.9585
165.33670.7314-0.330.8604-1.22412.2505-0.0435-0.5573-0.25120.1096-0.0725-0.10230.12360.24260.08770.17690.04930.02170.18370.04790.111942.3673-21.543737.0062
173.0301-2.2471-1.62524.380.80913.1997-0.05880.0648-0.23510.1243-0.00920.48360.0731-0.5220.03590.11170.00460.00510.2051-0.00240.107626.974-17.423733.0716
182.7239-3.76233.37477.8585-6.15035.01290.05480.2067-0.2439-0.3527-0.17770.01460.2-0.36130.17490.1584-0.0322-0.00810.2393-0.03350.138924.416-22.13924.1639
197.4465-5.19145.50046.9836-4.15494.2145-0.058-0.8269-0.38290.32990.34170.11210.897-0.7676-0.25510.3102-0.04560.02410.26220.04390.192730.1912-28.936836.5851
206.841-0.98723.80858.4717-2.81552.7382-0.3427-0.78280.26490.60040.24650.5214-0.432-0.73270.07930.21540.0647-0.01880.1828-0.00680.167934.24727.61717.18
219.13142.2915-4.91047.1041.17087.17090.20480.59010.2444-0.52210.0293-0.3959-0.7073-0.0677-0.19930.25290.0104-0.02910.13780.0330.187544.941511.91571.4213
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 29 through 43 )A29 - 43
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 57 )A44 - 57
3X-RAY DIFFRACTION3chain 'A' and (resid 58 through 74 )A58 - 74
4X-RAY DIFFRACTION4chain 'A' and (resid 75 through 127 )A75 - 127
5X-RAY DIFFRACTION5chain 'A' and (resid 128 through 150 )A128 - 150
6X-RAY DIFFRACTION6chain 'A' and (resid 151 through 188 )A151 - 188
7X-RAY DIFFRACTION7chain 'A' and (resid 189 through 207 )A189 - 207
8X-RAY DIFFRACTION8chain 'A' and (resid 208 through 226 )A208 - 226
9X-RAY DIFFRACTION9chain 'A' and (resid 227 through 247 )A227 - 247
10X-RAY DIFFRACTION10chain 'B' and (resid 31 through 43 )B31 - 43
11X-RAY DIFFRACTION11chain 'B' and (resid 44 through 57 )B44 - 57
12X-RAY DIFFRACTION12chain 'B' and (resid 58 through 90 )B58 - 90
13X-RAY DIFFRACTION13chain 'B' and (resid 91 through 127 )B91 - 127
14X-RAY DIFFRACTION14chain 'B' and (resid 128 through 162 )B128 - 162
15X-RAY DIFFRACTION15chain 'B' and (resid 163 through 207 )B163 - 207
16X-RAY DIFFRACTION16chain 'B' and (resid 208 through 226 )B208 - 226
17X-RAY DIFFRACTION17chain 'B' and (resid 227 through 247 )B227 - 247
18X-RAY DIFFRACTION18chain 'C' and (resid 1 through 7 )C1 - 7
19X-RAY DIFFRACTION19chain 'C' and (resid 8 through 13 )C8 - 13
20X-RAY DIFFRACTION20chain 'D' and (resid 3 through 7 )D3 - 7
21X-RAY DIFFRACTION21chain 'D' and (resid 8 through 13 )D8 - 13

+
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