[English] 日本語
Yorodumi
- PDB-3b08: Crystal structure of the mouse HOIL1-L-NZF in complex with linear... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3b08
TitleCrystal structure of the mouse HOIL1-L-NZF in complex with linear di-ubiquitin
Components
  • Polyubiquitin-C
  • RanBP-type and C3HC4-type zinc finger-containing protein 1
KeywordsSIGNALING PROTEIN/METAL BINDING PROTEIN / protein complex / SIGNALING PROTEIN-METAL BINDING PROTEIN complex
Function / homology
Function and homology information


TNFR1-induced proapoptotic signaling / TNFR1-induced NF-kappa-B signaling pathway / protein linear polyubiquitination / Regulation of TNFR1 signaling / LUBAC complex / RBR-type E3 ubiquitin transferase / negative regulation of necroptotic process / ubiquitin ligase activator activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of extrinsic apoptotic signaling pathway ...TNFR1-induced proapoptotic signaling / TNFR1-induced NF-kappa-B signaling pathway / protein linear polyubiquitination / Regulation of TNFR1 signaling / LUBAC complex / RBR-type E3 ubiquitin transferase / negative regulation of necroptotic process / ubiquitin ligase activator activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of extrinsic apoptotic signaling pathway / 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 / 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 / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / 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 / Regulation of FZD by ubiquitination / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / InlB-mediated entry of Listeria monocytogenes into host cell / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Josephin domain DUBs / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / ubiquitin binding / Gap-filling DNA repair synthesis and ligation in GG-NER / tumor necrosis factor-mediated signaling pathway / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / 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 / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / activated TAK1 mediates p38 MAPK activation / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / Negative regulators of DDX58/IFIH1 signaling / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Deactivation of the beta-catenin transactivating complex / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Negative regulation of FGFR3 signaling / Fanconi Anemia Pathway / Peroxisomal protein import / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Negative regulation of FGFR2 signaling / Stabilization of p53 / Negative regulation of FGFR4 signaling / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR1 signaling
Similarity search - Function
: / : / : / LUBAC thetering domain / : / Zn-finger domain of Sec23/24 / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / TRIAD supradomain / TRIAD supradomain profile. ...: / : / : / LUBAC thetering domain / : / Zn-finger domain of Sec23/24 / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / TRIAD supradomain / TRIAD supradomain profile. / Zinc finger domain / Zinc finger RanBP2 type profile. / Zinc finger, RanBP2-type superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ring finger / Zinc finger RING-type profile. / SH3 type barrels. / Zinc finger, RING-type / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Roll / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
trehalose / Polyubiquitin-C / RanBP-type and C3HC4-type zinc finger-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.701 Å
AuthorsSato, Y. / Fujita, H. / Yoshikawa, A. / Yamashita, M. / Yamagata, A. / Kaiser, S.E. / Iwai, K. / Fukai, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Specific recognition of linear ubiquitin chains by the Npl4 zinc finger (NZF) domain of the HOIL-1L subunit of the linear ubiquitin chain assembly complex
Authors: Sato, Y. / Fujita, H. / Yoshikawa, A. / Yamashita, M. / Yamagata, A. / Kaiser, S.E. / Iwai, K. / Fukai, S.
History
DepositionJun 7, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
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.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Polyubiquitin-C
B: RanBP-type and C3HC4-type zinc finger-containing protein 1
D: Polyubiquitin-C
E: RanBP-type and C3HC4-type zinc finger-containing protein 1
G: Polyubiquitin-C
H: RanBP-type and C3HC4-type zinc finger-containing protein 1
J: Polyubiquitin-C
K: RanBP-type and C3HC4-type zinc finger-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,59714
Polymers97,6518
Non-polymers9466
Water14,952830
1
A: Polyubiquitin-C
B: RanBP-type and C3HC4-type zinc finger-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4783
Polymers24,4132
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-11 kcal/mol
Surface area12200 Å2
MethodPISA
2
D: Polyubiquitin-C
E: RanBP-type and C3HC4-type zinc finger-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4783
Polymers24,4132
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-11 kcal/mol
Surface area12340 Å2
MethodPISA
3
G: Polyubiquitin-C
H: RanBP-type and C3HC4-type zinc finger-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8214
Polymers24,4132
Non-polymers4082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-13 kcal/mol
Surface area11720 Å2
MethodPISA
4
J: Polyubiquitin-C
K: RanBP-type and C3HC4-type zinc finger-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8214
Polymers24,4132
Non-polymers4082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-16 kcal/mol
Surface area11790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.938, 104.938, 170.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein
Polyubiquitin-C / Ubiquitin


Mass: 17135.654 Da / Num. of mol.: 4 / Fragment: linear di ubiquitin, UNP residues 1-152
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P0CG48
#2: Protein
RanBP-type and C3HC4-type zinc finger-containing protein 1 / Heme-oxidized IRP2 ubiquitin ligase 1 homolog / HOIL-1 / UbcM4-interacting protein 28 / Ubiquitin- ...Heme-oxidized IRP2 ubiquitin ligase 1 homolog / HOIL-1 / UbcM4-interacting protein 28 / Ubiquitin-conjugating enzyme 7-interacting protein 3


Mass: 7277.155 Da / Num. of mol.: 4 / Fragment: UNP residues 192-250
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rbck1, Rbck, Ubce7ip3, Uip28 / Plasmid: pCold GST / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q9WUB0
#3: Polysaccharide alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose / trehalose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: trehalose
DescriptorTypeProgram
DGlcpa1-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 830 / 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: 2.4 Å3/Da / Density % sol: 48.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.3M tri-sodium citrate, 90mM HEPES-NaOH buffer, 100mM potassium sodium tartrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1.2826 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 17, 2010 / Details: mirros
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2826 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 125184 / Num. obs: 125184 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 16.57 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 36.2
Reflection shellResolution: 1.6→1.62 Å / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.75 / % possible all: 89.8

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.7.1_743refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3a9j

3a9j


Resolution: 1.701→46.93 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.931 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8866 / SU ML: 0.42 / σ(F): 2.1 / Phase error: 18.66 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2112 5102 5 %
Rwork0.1735 --
obs0.1754 101984 97.47 %
all-125184 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.057 Å2 / ksol: 0.401 e/Å3
Displacement parametersBiso max: 107.41 Å2 / Biso mean: 24.7385 Å2 / Biso min: 6.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.301 Å2-0 Å20 Å2
2--0.301 Å20 Å2
3----0.6019 Å2
Refinement stepCycle: LAST / Resolution: 1.701→46.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6649 0 50 830 7529
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076816
X-RAY DIFFRACTIONf_angle_d1.0799199
X-RAY DIFFRACTIONf_dihedral_angle_d14.3452725
X-RAY DIFFRACTIONf_chiral_restr0.0771048
X-RAY DIFFRACTIONf_plane_restr0.0051202
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7012-1.72050.26011770.20552967314491
1.7205-1.74080.26171490.2053046319593
1.7408-1.7620.26121420.20733068321093
1.762-1.78430.25761650.19353066323194
1.7843-1.80780.22111610.17493108326994
1.8078-1.83250.21941660.18083104327095
1.8325-1.85870.25931670.17753108327595
1.8587-1.88650.20131580.16993159331796
1.8865-1.91590.231570.17043156331396
1.9159-1.94740.20371770.1623181335897
1.9474-1.98090.2081610.1663228338998
1.9809-2.0170.23251760.16713204338098
2.017-2.05580.20281560.16433258341499
2.0558-2.09770.21771730.16683231340499
2.0977-2.14330.19811550.16463270342599
2.1433-2.19320.20951730.16493263343699
2.1932-2.2480.20341810.16583231341298
2.248-2.30880.20441630.16433235339899
2.3088-2.37670.241910.17233282347399
2.3767-2.45350.22251800.18232703450100
2.4535-2.54110.2111670.18693290345799
2.5411-2.64290.24121730.188233123485100
2.6429-2.76310.24811760.193433253501100
2.7631-2.90880.22931810.185833113492100
2.9088-3.0910.20111920.171333233515100
3.091-3.32960.21461960.167433153511100
3.3296-3.66460.16741670.154733673534100
3.6646-4.19460.17431860.14843380356699
4.1946-5.28360.1771840.16193301348596
5.2836-46.94750.25641520.21193523367596
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)
10.8232-0.7628-0.78841.83491.48591.67830.00860.01510.0503-0.06180.0149-0.0143-0.03210.0525-0.02180.10540.0223-0.00190.09290.03790.108329.458244.242430.8375
21.51380.68060.06081.98791.17423.58950.06020.16290.038-0.1655-0.01690.16180.0561-0.2017-0.03960.11590.0234-0.01660.08650.03020.136617.397433.889128.2409
31.0303-0.7881-0.73222.1011.52311.924-0.0035-0.004-0.0092-0.0452-0.00780.0115-0.03380.06270.010.09020.0043-0.00910.07380.04360.101381.93396.449831.5992
41.67410.2599-0.06721.54841.03393.15110.0290.1017-0.0114-0.189-0.05130.13670.1619-0.25570.0240.1196-0.0033-0.01890.06640.01860.115569.579986.41428.6768
51.3749-0.39730.77751.1704-0.91761.8209-0.0188-0.0462-0.1065-0.05930.00210.04440.0981-0.12140.0180.12720.01960.03170.0634-0.03310.096323.51516.046934.8732
61.53060.3484-0.20221.1702-0.09741.3664-0.02960.35730.0159-0.4074-0.0749-0.11310.14240.0987-0.01190.14370.04980.04190.0590.02610.036934.69915.505229.1013
71.4657-0.8521.13991.5123-1.35122.54570.0118-0.039-0.0605-0.0266-0.0080.07550.0995-0.0954-0.01290.1123-0.00630.01460.0707-0.02010.111575.255157.934834.7442
81.74380.5102-0.09621.42170.00462.329-0.01080.2365-0.0782-0.27160.0512-0.1418-0.04020.0085-0.02210.10850.0260.02610.06150.00050.064486.146567.036829.0096
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA1 - 151
2X-RAY DIFFRACTION2chain BB191 - 248
3X-RAY DIFFRACTION3chain DD1 - 151
4X-RAY DIFFRACTION4chain EE191 - 249
5X-RAY DIFFRACTION5chain GG1 - 150
6X-RAY DIFFRACTION6chain HH191 - 249
7X-RAY DIFFRACTION7chain JJ1 - 149
8X-RAY DIFFRACTION8chain KK190 - 248

+
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