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- PDB-3i3t: Crystal structure of covalent ubiquitin-USP21 complex -

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Basic information

Entry
Database: PDB / ID: 3i3t
TitleCrystal structure of covalent ubiquitin-USP21 complex
Components
  • Ubiquitin carboxyl-terminal hydrolase 21
  • Ubiquitin
KeywordsHYDROLASE / ubiquitin-specific protease activity / Ubiquitin biology / Structural Genomics Consortium / SGC / Activator / Chromatin regulator / Nucleus / Protease / Thiol protease / Transcription / Transcription regulation / Ubl conjugation pathway / Isopeptide bond / Phosphoprotein
Function / homology
Function and homology information


: / : / deNEDDylase activity / protein modification process => GO:0036211 / TNFR1-induced proapoptotic signaling / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency ...: / : / deNEDDylase activity / protein modification process => GO:0036211 / TNFR1-induced proapoptotic signaling / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / cysteine-type peptidase activity / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / transcription initiation-coupled chromatin remodeling / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Constitutive Signaling by NOTCH1 HD Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of FZD by ubiquitination / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of PTEN localization / Translesion synthesis by POLK / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / cytosolic ribosome / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Recognition of DNA damage by PCNA-containing replication complex / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants are degraded by ERAD / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling
Similarity search - Function
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 / Ribosomal L40e family ...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 / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Papain-like cysteine peptidase superfamily / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ETHANAMINE / Ubiquitin-ribosomal protein eL40 fusion protein / Ubiquitin-60S ribosomal protein L40 / Ubiquitin carboxyl-terminal hydrolase 21
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsNeculai, D. / Avvakumov, G.V. / Walker, J.R. / Xue, S. / Butler-Cole, C. / Weigelt, J. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Bochkarev, A. ...Neculai, D. / Avvakumov, G.V. / Walker, J.R. / Xue, S. / Butler-Cole, C. / Weigelt, J. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: Science / Year: 2013
Title: A strategy for modulation of enzymes in the ubiquitin system.
Authors: Ernst, A. / Avvakumov, G. / Tong, J. / Fan, Y. / Zhao, Y. / Alberts, P. / Persaud, A. / Walker, J.R. / Neculai, A.M. / Neculai, D. / Vorobyov, A. / Garg, P. / Beatty, L. / Chan, P.K. / ...Authors: Ernst, A. / Avvakumov, G. / Tong, J. / Fan, Y. / Zhao, Y. / Alberts, P. / Persaud, A. / Walker, J.R. / Neculai, A.M. / Neculai, D. / Vorobyov, A. / Garg, P. / Beatty, L. / Chan, P.K. / Juang, Y.C. / Landry, M.C. / Yeh, C. / Zeqiraj, E. / Karamboulas, K. / Allali-Hassani, A. / Vedadi, M. / Tyers, M. / Moffat, J. / Sicheri, F. / Pelletier, L. / Durocher, D. / Raught, B. / Rotin, D. / Yang, J. / Moran, M.F. / Dhe-Paganon, S. / Sidhu, S.S.
History
DepositionJun 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 27, 2013Group: Database references
Revision 1.3Sep 6, 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 / struct_conn / struct_conn_type / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_type.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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 21
C: Ubiquitin carboxyl-terminal hydrolase 21
E: Ubiquitin carboxyl-terminal hydrolase 21
G: Ubiquitin carboxyl-terminal hydrolase 21
B: Ubiquitin
D: Ubiquitin
F: Ubiquitin
H: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,94416
Polymers194,5028
Non-polymers4428
Water2,180121
1
A: Ubiquitin carboxyl-terminal hydrolase 21
B: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7364
Polymers48,6252
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-8.4 kcal/mol
Surface area17090 Å2
MethodPISA
2
C: Ubiquitin carboxyl-terminal hydrolase 21
D: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7364
Polymers48,6252
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-8.4 kcal/mol
Surface area17500 Å2
MethodPISA
3
E: Ubiquitin carboxyl-terminal hydrolase 21
F: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7364
Polymers48,6252
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-9.8 kcal/mol
Surface area17470 Å2
MethodPISA
4
G: Ubiquitin carboxyl-terminal hydrolase 21
H: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7364
Polymers48,6252
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-8.5 kcal/mol
Surface area17070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.428, 83.663, 118.792
Angle α, β, γ (deg.)88.71, 75.73, 85.11
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
41G
12B
22D
32F
42H

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111HISHISVALVALAA211 - 2493 - 41
211HISHISVALVALCB211 - 2493 - 41
311HISHISVALVALEC211 - 2493 - 41
411HISHISVALVALGD211 - 2493 - 41
121GLNGLNARGARGAA256 - 32048 - 112
221GLNGLNARGARGCB256 - 32048 - 112
321GLNGLNARGARGEC256 - 32048 - 112
421GLNGLNARGARGGD256 - 32048 - 112
131LEULEULYSLYSAA349 - 406141 - 198
231LEULEULYSLYSCB349 - 406141 - 198
331LEULEULYSLYSEC349 - 406141 - 198
431LEULEULYSLYSGD349 - 406141 - 198
141VALVALSERSERAA414 - 494206 - 286
241VALVALSERSERCB414 - 494206 - 286
341VALVALSERSEREC414 - 494206 - 286
441VALVALSERSERGD414 - 494206 - 286
151SERSERMETMETAA499 - 558291 - 350
251SERSERMETMETCB499 - 558291 - 350
351SERSERMETMETEC499 - 558291 - 350
451SERSERMETMETGD499 - 558291 - 350
112METMETGLYGLYBE1 - 751 - 75
212METMETGLYGLYDF1 - 751 - 75
312METMETGLYGLYFG1 - 751 - 75
412METMETGLYGLYHH1 - 751 - 75

NCS ensembles :
ID
1
2

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Components

#1: Protein
Ubiquitin carboxyl-terminal hydrolase 21 / Ubiquitin thioesterase 21 / Ubiquitin-specific-processing protease 21 / Deubiquitinating enzyme 21


Mass: 40105.652 Da / Num. of mol.: 4 / Fragment: Catalytic domain: UNP residues 209-563
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PP1490, USP21, USP23 / Plasmid: pET28aLIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9UK80, EC: 3.1.2.15
#2: Protein
Ubiquitin /


Mass: 8519.778 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS27A, UBA52, UBA80, UBB, UBC, UBCEP1, UBCEP2, UBQ / Plasmid: pET28aLIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P62988, UniProt: P62987*PLUS
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-NEH / ETHANAMINE / Ethylamine


Mass: 45.084 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H7N
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O

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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: 2.88 Å3/Da / Density % sol: 57.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 13% PEG 3350, 0.1 M Bis-Tris, 0.1 M Ammonium sulfate, 5 mM TCEP, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97949 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 19, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.54
11-H, -K, -H+L20.46
ReflectionResolution: 2.59→83.37 Å / Num. all: 65088 / Num. obs: 65088 / % possible obs: 96.3 % / Observed criterion σ(I): 0 / Redundancy: 2.54 % / Rmerge(I) obs: 0.08 / Rsym value: 0.083 / Net I/σ(I): 9.81
Reflection shellResolution: 2.59→2.61 Å / Redundancy: 2.56 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 2.08 / Rsym value: 0.529 / % possible all: 95.6

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
REFMAC5.5.0088refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IBI

2ibi


Resolution: 2.59→83.37 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.914 / SU B: 6.519 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21801 3293 5.1 %RANDOM
Rwork0.18614 ---
obs0.18777 61793 95.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.685 Å2
Baniso -1Baniso -2Baniso -3
1--14.9 Å25.35 Å24.35 Å2
2--13.28 Å2-24 Å2
3---1.62 Å2
Refinement stepCycle: LAST / Resolution: 2.59→83.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12293 0 16 121 12430
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.02212578
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9981.96316924
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.46651511
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.51323.237621
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.173152273
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.74915121
X-RAY DIFFRACTIONr_chiral_restr0.1310.21872
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219451
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9781.57618
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.9212282
X-RAY DIFFRACTIONr_scbond_it2.85734960
X-RAY DIFFRACTIONr_scangle_it4.8524.54641
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2425tight positional0.090.05
11C2425tight positional0.080.05
11E2425tight positional0.090.05
11G2425tight positional0.070.05
22B597tight positional0.070.05
22D597tight positional0.120.05
22F597tight positional0.070.05
22H597tight positional0.070.05
11A2425tight thermal0.180.5
11C2425tight thermal0.180.5
11E2425tight thermal0.190.5
11G2425tight thermal0.180.5
22B597tight thermal0.170.5
22D597tight thermal0.180.5
22F597tight thermal0.160.5
22H597tight thermal0.160.5
LS refinement shellResolution: 2.59→2.652 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 219 -
Rwork0.235 4277 -
obs--89.38 %

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