[English] 日本語
Yorodumi
- PDB-3prm: Structural analysis of a viral OTU domain protease from the Crime... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3prm
TitleStructural analysis of a viral OTU domain protease from the Crimean-Congo Hemorrhagic Fever virus in complex with human ubiquitin
Components
  • Polyubiquitin-B (Fragment)
  • RNA-directed RNA polymerase L
KeywordsHYDROLASE/HYDROLASE / ubiquitin hydrolase / deubiquitinase / hydrolase / cysteine protease / viral protein / HYDROLASE-HYDROLASE complex
Function / homology
Function and homology information


RNA-templated viral transcription / negative stranded viral RNA replication / protein deubiquitination / endoplasmic reticulum unfolded protein response / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway ...RNA-templated viral transcription / negative stranded viral RNA replication / protein deubiquitination / endoplasmic reticulum unfolded protein response / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Glycogen synthesis / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / Regulation of FZD by ubiquitination / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / VLDLR internalisation and degradation / Downregulation of ERBB4 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / NF-kB is activated and signals survival / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Pexophagy / Regulation of PTEN localization / Regulation of BACH1 activity / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / InlB-mediated entry of Listeria monocytogenes into host cell / Regulation of activated PAK-2p34 by proteasome mediated degradation / Josephin domain DUBs / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / Asymmetric localization of PCP proteins / NIK-->noncanonical NF-kB signaling / Regulation of NF-kappa B signaling / Ubiquitin-dependent degradation of Cyclin D / activated TAK1 mediates p38 MAPK activation / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Regulation of signaling by CBL / Vpu mediated degradation of CD4 / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / Assembly of the pre-replicative complex / Degradation of DVL / Deactivation of the beta-catenin transactivating complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Iron uptake and transport / Negative regulation of FGFR2 signaling / Negative regulation of FGFR3 signaling / Hh mutants are degraded by ERAD / Peroxisomal protein import / Degradation of AXIN / Recognition of DNA damage by PCNA-containing replication complex / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / Stabilization of p53 / Regulation of TNFR1 signaling / EGFR downregulation / Termination of translesion DNA synthesis / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Hedgehog ligand biogenesis / Negative regulation of FGFR4 signaling
Similarity search - Function
RNA-directed RNA polymerase, nairovirus / : / Cathepsin B; Chain A - #80 / OTU-like cysteine protease / RNA-directed RNA polymerase L, N-terminal / L protein N-terminus / OTU domain / OTU domain profile. / RNA-dependent RNA polymerase, bunyaviral / Bunyavirus RNA dependent RNA polymerase ...RNA-directed RNA polymerase, nairovirus / : / Cathepsin B; Chain A - #80 / OTU-like cysteine protease / RNA-directed RNA polymerase L, N-terminal / L protein N-terminus / OTU domain / OTU domain profile. / RNA-dependent RNA polymerase, bunyaviral / Bunyavirus RNA dependent RNA polymerase / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile. / Cathepsin B; Chain A / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Papain-like cysteine peptidase superfamily / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Ubiquitin B / Polyubiquitin-C / RNA-directed RNA polymerase L / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesCrimean-Congo hemorrhagic fever virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsCapodagli, G.C. / McKercher, M.A. / Baker, E.A. / Masters, E.M. / Brunzelle, J.S. / Pegan, S.D.
CitationJournal: J.Virol. / Year: 2011
Title: Structural analysis of a viral ovarian tumor domain protease from the crimean-congo hemorrhagic Fever virus in complex with covalently bonded ubiquitin.
Authors: Capodagli, G.C. / McKercher, M.A. / Baker, E.A. / Masters, E.M. / Brunzelle, J.S. / Pegan, S.D.
History
DepositionNov 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Feb 22, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_2 / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_mod_residue.details / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_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 / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA-directed RNA polymerase L
B: Polyubiquitin-B (Fragment)
C: RNA-directed RNA polymerase L
D: Polyubiquitin-B (Fragment)


Theoretical massNumber of molelcules
Total (without water)58,4284
Polymers58,4284
Non-polymers00
Water3,963220
1
A: RNA-directed RNA polymerase L
B: Polyubiquitin-B (Fragment)


Theoretical massNumber of molelcules
Total (without water)29,2142
Polymers29,2142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-11 kcal/mol
Surface area11410 Å2
MethodPISA
2
C: RNA-directed RNA polymerase L
D: Polyubiquitin-B (Fragment)


Theoretical massNumber of molelcules
Total (without water)29,2142
Polymers29,2142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-11 kcal/mol
Surface area11400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.462, 65.651, 133.133
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein RNA-directed RNA polymerase L / Protein L / Large structural protein / Replicase / Transcriptase


Mass: 20574.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crimean-Congo hemorrhagic fever virus / Strain: IbAr10200 / Plasmid: pET11A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q6TQR6, UniProt: Q6TFZ7*PLUS, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, Hydrolases; Acting on ester bonds, RNA-directed RNA polymerase
#2: Protein Polyubiquitin-B (Fragment)


Mass: 8639.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Plasmid: pTYB2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus / References: UniProt: J3QS39, UniProt: P0CG48*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.27 Å3/Da / Density % sol: 45.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 22-26% PEG 8000, 0.1 M Na cacodylate, 0.2 M Mg acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 31, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.3→66.57 Å / Num. all: 24243 / Num. obs: 23928 / % possible obs: 98.7 % / Rmerge(I) obs: 0.072
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 0.322 / % possible all: 100

-
Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→29.48 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.903 / WRfactor Rfree: 0.2624 / WRfactor Rwork: 0.1961 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8116 / SU B: 16.219 / SU ML: 0.183 / SU R Cruickshank DPI: 0.4011 / SU Rfree: 0.2697 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.401 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2672 1212 5.1 %RANDOM
Rwork0.2043 ---
obs0.2076 23872 98.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 91.87 Å2 / Biso mean: 34.7658 Å2 / Biso min: 12.79 Å2
Baniso -1Baniso -2Baniso -3
1-3.84 Å2-0 Å2-0 Å2
2---2.21 Å20 Å2
3----1.64 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3788 0 8 220 4016
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224040
X-RAY DIFFRACTIONr_angle_refined_deg1.6421.9585487
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6685505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.35724.264197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.32215722
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1811528
X-RAY DIFFRACTIONr_chiral_restr0.110.2607
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213094
X-RAY DIFFRACTIONr_mcbond_it0.7571.52455
X-RAY DIFFRACTIONr_mcangle_it1.3623996
X-RAY DIFFRACTIONr_scbond_it2.69931585
X-RAY DIFFRACTIONr_scangle_it4.0964.51490
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 85 -
Rwork0.229 1633 -
all-1718 -
obs--97.06 %
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)
16.76985.90351.96822.77546.38915.64680.1703-0.05340.78790.2104-0.34110.8566-0.6434-0.32220.17080.14160.01510.0170.24740.01450.2307-23.41841.38450.3297
20.2074-0.4920.65832.2658-0.72162.7767-0.08280.01010.05390.1393-0.0459-0.1189-0.28840.05960.12870.04770.00590.01720.07870.00360.0969-11.3857-4.31017.3346
30.2212-0.8984-0.27633.87441.17820.3599-0.2143-0.0929-0.01011.07650.14050.12570.32350.05260.07380.36290.02460.04260.3837-0.03980.191-9.8555-11.520622.3155
43.6244-0.12280.14125.3843-1.41170.4813-0.08990.0731-0.304-0.1470.2140.44080.1728-0.1748-0.12410.2431-0.10450.01790.19290.02240.1938-16.2061-25.64568.345
50.113-0.47250.12375.2962-1.55410.4655-0.0213-0.1162-0.1057-0.11360.01060.05810.07660.01730.01070.23420.05450.0340.25260.09350.2221-8.4853-21.586710.2072
610.70423.9227-4.07938.5766-2.9726.7045-0.0475-0.207-0.14360.1641-0.1045-0.03340.04650.1450.1520.0330.0325-0.03450.0554-0.05690.0775-15.9921-6.05864.7627
75.0767-2.47940.21215.1070.70262.8716-0.10830.0090.08390.00390.047-0.0107-0.2060.00970.06130.06910.0002-0.01710.04250.00860.0302-10.9518-3.79078.8478
814.2562-23.2443-8.359740.03947.415222.9567-0.4497-0.033-0.41550.94380.52020.8072-0.2465-1.3062-0.07050.27410.0371-0.03270.3542-0.03760.3733-18.25849.869113.2771
94.96880.5867-0.38466.27562.65775.0920.08610.2579-0.0178-0.27730.1744-0.0257-0.18410.0246-0.26050.1242-0.02010.00010.09180.03280.1122-14.5069-10.3864-17.9751
106.5080.3435-2.64774.77943.6714.1293-0.24360.2457-0.11280.27690.3229-0.11390.33490.1754-0.07920.22120.0562-0.02240.1487-0.06880.2132-12.0023-23.0597-18.4695
112.99830.06710.71770.57871.18775.12110.1261-0.0033-0.3538-0.0133-0.0009-0.22860.30830.1305-0.12520.09060.01480.01820.0810.00880.2038-14.8483-19.7641-11.9412
125.7680.37075.13571.65031.26158.9362-0.28710.44120.3201-0.3601-0.08610.0874-0.29010.08560.37320.1228-0.01450.0220.09090.01670.1074-16.0933-14.4275-10.9594
134.5373-3.81480.722214.964810.612210.82750.67920.1592-0.44520.0637-0.96510.69710.6703-0.84630.28590.4629-0.00680.01240.39330.07790.4167-22.3901-0.3612-19.8159
140.19370.4047-0.44093.5063-0.7873.2356-0.17490.0678-0.0119-0.11670.0749-0.17070.34360.10160.10.1951-0.0503-0.04260.1650.00610.1353-12.63587.976-22.0066
155.34440.9881-4.16766.41295.890310.5515-0.42050.81350.0511-0.38590.4492-0.00130.0461-0.0265-0.02860.2869-0.0070.08640.52440.05160.1478-7.495514.2519-37.0612
1623.9579-7.5537-14.50182.90166.063813.09380.02271.06811.1657-0.2727-0.0545-0.1607-0.7132-0.10620.03180.4532-0.1510.04660.23170.06360.2572-9.783923.5292-37.2957
173.2617-1.04341.50364.0898-3.975711.9048-0.1547-0.34210.4177-0.02990.0180.2337-0.4402-0.80360.13670.19370.0330.02090.21520.00030.2125-17.942729.4521-24.5193
188.1327-3.27-3.02833.9733.70658.54410.1110.27770.2441-0.3839-0.1345-0.4645-0.23880.05530.02350.2283-0.05240.04050.162-0.00920.2427-8.248932.7884-27.2584
192.78050.985-0.51765.0637-0.77824.4936-0.12780.162-0.0324-0.39760.1037-0.1010.3498-0.07650.02410.1579-0.01770.0470.1266-0.03160.1274-13.445113.2896-24.5165
203.6449-0.2771-1.55949.979-0.73431.00410.0775-0.0111-0.3261-0.0128-0.153-0.16540.284-0.16420.07550.5468-0.065-0.01920.29850.09780.1497-9.03565.1504-26.8555
217.296-2.21970.67678.9308-2.34950.6215-0.2361-0.15390.06830.40230.29260.2538-0.0879-0.0819-0.05650.2162-0.02740.00820.07450.01590.1814-16.534816.1395-0.0751
221.0492-2.3242-0.200718.97910.53930.1033-0.044-0.13530.15980.32730.07670.30120.08870.0821-0.03270.16140.0115-0.02120.1371-0.00680.2031-14.084720.80621.8745
234.47290.3464-0.80513.09750.53185.53820.08890.13670.4209-0.04530.0471-0.1406-0.30350.1652-0.1360.1301-0.0043-0.00430.1077-0.01820.1473-13.762424.7608-5.1837
246.9611.2022-6.08572.6798-1.079.8867-0.2762-0.254-0.1890.11670.12140.11720.40390.04490.15490.11130.0044-0.04940.05430.00360.1849-16.043419.4493-7.0752
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 11
2X-RAY DIFFRACTION2A12 - 46
3X-RAY DIFFRACTION3A47 - 62
4X-RAY DIFFRACTION4A63 - 87
5X-RAY DIFFRACTION5A88 - 109
6X-RAY DIFFRACTION6A110 - 137
7X-RAY DIFFRACTION7A138 - 157
8X-RAY DIFFRACTION8A158 - 162
9X-RAY DIFFRACTION9B1 - 17
10X-RAY DIFFRACTION10B18 - 29
11X-RAY DIFFRACTION11B30 - 60
12X-RAY DIFFRACTION12B61 - 75
13X-RAY DIFFRACTION13C2 - 8
14X-RAY DIFFRACTION14C9 - 39
15X-RAY DIFFRACTION15C40 - 57
16X-RAY DIFFRACTION16C58 - 66
17X-RAY DIFFRACTION17C67 - 81
18X-RAY DIFFRACTION18C82 - 95
19X-RAY DIFFRACTION19C96 - 145
20X-RAY DIFFRACTION20C146 - 162
21X-RAY DIFFRACTION21D1 - 8
22X-RAY DIFFRACTION22D9 - 23
23X-RAY DIFFRACTION23D24 - 60
24X-RAY DIFFRACTION24D61 - 75

+
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