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- PDB-2c2v: Crystal structure of the CHIP-UBC13-UEV1a complex -

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Basic information

Entry
Database: PDB / ID: 2c2v
TitleCrystal structure of the CHIP-UBC13-UEV1a complex
Components
  • STIP1 homology and U box-containing protein 1
  • Ubiquitin-conjugating enzyme E2 N
  • Ubiquitin-conjugating enzyme E2 variant 1
KeywordsCHAPERONE / HEAT-SHOCK PROTEIN COMPLEX / E3 LIGASE / UBIQUITINYLATION / TPR / HEAT-SHOCK PROTEIN
Function / homology
Function and homology information


positive regulation of chaperone-mediated protein complex assembly / Downregulation of TGF-beta receptor signaling / regulation of glucocorticoid metabolic process / : / UBC13-UEV1A complex / UBC13-MMS2 complex / Downregulation of ERBB2 signaling / Regulation of TNFR1 signaling / Regulation of necroptotic cell death / Regulation of PTEN stability and activity ...positive regulation of chaperone-mediated protein complex assembly / Downregulation of TGF-beta receptor signaling / regulation of glucocorticoid metabolic process / : / UBC13-UEV1A complex / UBC13-MMS2 complex / Downregulation of ERBB2 signaling / Regulation of TNFR1 signaling / Regulation of necroptotic cell death / Regulation of PTEN stability and activity / Regulation of RUNX2 expression and activity / ubiquitin conjugating enzyme complex / positive regulation of ERAD pathway / ubiquitin-protein transferase activator activity / DNA double-strand break processing / positive regulation of mitophagy / positive regulation of smooth muscle cell apoptotic process / positive regulation of protein K63-linked ubiquitination / nuclear inclusion body / Antigen processing: Ubiquitination & Proteasome degradation / misfolded protein binding / protein folding chaperone complex / cellular response to misfolded protein / postreplication repair / positive regulation of ubiquitin-protein transferase activity / positive regulation of double-strand break repair / ubiquitin-ubiquitin ligase activity / E2 ubiquitin-conjugating enzyme / positive regulation of intracellular signal transduction / chaperone-mediated autophagy / protein quality control for misfolded or incompletely synthesized proteins / TPR domain binding / ubiquitin conjugating enzyme activity / SMAD binding / protein monoubiquitination / protein K63-linked ubiquitination / negative regulation of smooth muscle cell apoptotic process / positive regulation of proteolysis / antiviral innate immune response / R-SMAD binding / protein maturation / regulation of DNA repair / protein autoubiquitination / ubiquitin ligase complex / : / endoplasmic reticulum unfolded protein response / negative regulation of TORC1 signaling / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Hsp70 protein binding / positive regulation of DNA repair / heat shock protein binding / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / negative regulation of protein binding / ubiquitin binding / positive regulation of protein ubiquitination / G protein-coupled receptor binding / activated TAK1 mediates p38 MAPK activation / response to ischemia / Nonhomologous End-Joining (NHEJ) / double-strand break repair via homologous recombination / negative regulation of transforming growth factor beta receptor signaling pathway / Hsp90 protein binding / TAK1-dependent IKK and NF-kappa-B activation / RING-type E3 ubiquitin transferase / NOD1/2 Signaling Pathway / regulation of protein stability / G2/M DNA damage checkpoint / ISG15 antiviral mechanism / CLEC7A (Dectin-1) signaling / Z disc / Formation of Incision Complex in GG-NER / kinase binding / Aggrephagy / FCERI mediated NF-kB activation / Interleukin-1 signaling / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / MAPK cascade / protein-macromolecule adaptor activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / protein folding / Downstream TCR signaling / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / cellular response to heat / positive regulation of NF-kappaB transcription factor activity / Processing of DNA double-strand break ends / T cell receptor signaling pathway / ubiquitin-dependent protein catabolic process / cellular response to hypoxia / protein-folding chaperone binding / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / cell differentiation
Similarity search - Function
CHIP, N-terminal tetratricopeptide repeat domain / CHIP/LubX , U box domain / CHIP N-terminal tetratricopeptide repeat domain / U-box domain / Anaphase-promoting complex, cyclosome, subunit 3 / U-box domain profile. / Modified RING finger domain / U-box domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme ...CHIP, N-terminal tetratricopeptide repeat domain / CHIP/LubX , U box domain / CHIP N-terminal tetratricopeptide repeat domain / U-box domain / Anaphase-promoting complex, cyclosome, subunit 3 / U-box domain profile. / Modified RING finger domain / U-box domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Zinc finger, RING/FYVE/PHD-type / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 N / Ubiquitin-conjugating enzyme E2 variant 1 / E3 ubiquitin-protein ligase CHIP
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsZhang, M. / Roe, S.M. / Pearl, L.H.
CitationJournal: Mol. Cell / Year: 2005
Title: Chaperoned ubiquitylation--crystal structures of the CHIP U box E3 ubiquitin ligase and a CHIP-Ubc13-Uev1a complex.
Authors: Zhang, M. / Windheim, M. / Roe, S.M. / Peggie, M. / Cohen, P. / Prodromou, C. / Pearl, L.H.
History
DepositionSep 30, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jun 13, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity.pdbx_description / _entity.pdbx_ec / _entity_name_com.name / _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_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type
Revision 1.3Mar 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Ubiquitin-conjugating enzyme E2 N
C: Ubiquitin-conjugating enzyme E2 variant 1
E: Ubiquitin-conjugating enzyme E2 N
F: Ubiquitin-conjugating enzyme E2 variant 1
H: Ubiquitin-conjugating enzyme E2 N
I: Ubiquitin-conjugating enzyme E2 variant 1
K: Ubiquitin-conjugating enzyme E2 N
L: Ubiquitin-conjugating enzyme E2 variant 1
S: STIP1 homology and U box-containing protein 1
T: STIP1 homology and U box-containing protein 1
U: STIP1 homology and U box-containing protein 1
V: STIP1 homology and U box-containing protein 1


Theoretical massNumber of molelcules
Total (without water)169,48212
Polymers169,48212
Non-polymers00
Water63135
1
B: Ubiquitin-conjugating enzyme E2 N
C: Ubiquitin-conjugating enzyme E2 variant 1
H: Ubiquitin-conjugating enzyme E2 N
I: Ubiquitin-conjugating enzyme E2 variant 1
S: STIP1 homology and U box-containing protein 1
T: STIP1 homology and U box-containing protein 1


Theoretical massNumber of molelcules
Total (without water)84,7416
Polymers84,7416
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
E: Ubiquitin-conjugating enzyme E2 N
F: Ubiquitin-conjugating enzyme E2 variant 1
K: Ubiquitin-conjugating enzyme E2 N
L: Ubiquitin-conjugating enzyme E2 variant 1
U: STIP1 homology and U box-containing protein 1
V: STIP1 homology and U box-containing protein 1


Theoretical massNumber of molelcules
Total (without water)84,7416
Polymers84,7416
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)180.310, 69.991, 204.477
Angle α, β, γ (deg.)90.00, 106.95, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11S
21T
31U
41V
12B
22H
32E
42K
13C
23I
33F
43L

NCS domain segments:

Refine code: 4

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111TYRTYRPHEPHESI231 - 2945 - 68
211TYRTYRPHEPHETJ231 - 2945 - 68
311TYRTYRPHEPHEUK231 - 2945 - 68
411TYRTYRPHEPHEVL231 - 2945 - 68
112ARGARGGLUGLUBA11 - 339 - 31
212ARGARGGLUGLUHE11 - 339 - 31
312ARGARGGLUGLUEC11 - 339 - 31
412ARGARGGLUGLUKG11 - 339 - 31
122ALAALALEULEUBA36 - 9534 - 93
222ALAALALEULEUHE36 - 9534 - 93
322ALAALALEULEUEC36 - 9534 - 93
422ALAALALEULEUKG36 - 9534 - 93
132TRPTRPPROPROBA99 - 12197 - 119
232TRPTRPPROPROHE99 - 12197 - 119
332TRPTRPPROPROEC99 - 12197 - 119
432TRPTRPPROPROKG99 - 12197 - 119
142ALAALAASNASNBA140 - 155138 - 153
242ALAALAASNASNHE140 - 155138 - 153
342ALAALAASNASNEC140 - 155138 - 153
442ALAALAASNASNKG140 - 155138 - 153
113VALVALGLNGLNCB38 - 526 - 20
213VALVALGLNGLNIF38 - 526 - 20
313VALVALGLNGLNFD38 - 526 - 20
413VALVALGLNGLNLH38 - 526 - 20
123TRPTRPPROPROCB62 - 12930 - 97
223TRPTRPPROPROIF62 - 12930 - 97
323TRPTRPPROPROFD62 - 12930 - 97
423TRPTRPPROPROLH62 - 12930 - 97
133VALVALGLNGLNCB134 - 165102 - 133
233VALVALGLNGLNIF134 - 165102 - 133
333VALVALGLNGLNFD134 - 165102 - 133
433VALVALGLNGLNLH134 - 165102 - 133

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
Ubiquitin-conjugating enzyme E2 N / Bendless-like ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme N / Ubc13 / UbcH13 / ...Bendless-like ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme N / Ubc13 / UbcH13 / Ubiquitin carrier protein N / Ubiquitin-protein ligase N


Mass: 17241.779 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2N, BLU / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P61088, E2 ubiquitin-conjugating enzyme
#2: Protein
Ubiquitin-conjugating enzyme E2 variant 1 / UEV-1 / CROC-1 / TRAF6-regulated IKK activator 1 beta Uev1A


Mass: 16095.452 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2V1, CROC1, UBE2V, UEV1, P/OKcl.19 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q13404
#3: Protein
STIP1 homology and U box-containing protein 1 / Carboxy terminus of Hsp70-interacting protein / E3 ubiquitin-protein ligase CHIP / RING-type E3 ...Carboxy terminus of Hsp70-interacting protein / E3 ubiquitin-protein ligase CHIP / RING-type E3 ubiquitin transferase CHIP


Mass: 9033.194 Da / Num. of mol.: 4 / Fragment: C-TEMINAL DOMAIN, RESIDUES 227-304
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Stub1, Chip / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q9WUD1, RING-type E3 ubiquitin transferase
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.9 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: MCHIP(166-304), UBC13 AND UEV1A WERE COMBINED IN A 1:1:1 MOLAR RATIO, INCUBATED FOR 30 MIN, AND CONCENTRATED TO 10 MG/ML BY ULTRAFILTRATION. CRYSTALS WERE GROWN BY VAPOUR DIFFUSION AT 20C ...Details: MCHIP(166-304), UBC13 AND UEV1A WERE COMBINED IN A 1:1:1 MOLAR RATIO, INCUBATED FOR 30 MIN, AND CONCENTRATED TO 10 MG/ML BY ULTRAFILTRATION. CRYSTALS WERE GROWN BY VAPOUR DIFFUSION AT 20C AGAINST 20% (W/V) PEG2000 MME, 100 MM TRIS-HCL (PH 7.0).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.934
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 13, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.9→60 Å / Num. obs: 154327 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.8
Reflection shellResolution: 2.9→3.05 Å / Redundancy: 3 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.1 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JAT
Resolution: 2.9→196.12 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.875 / SU B: 42.875 / SU ML: 0.368 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.275 / ESU R Free: 0.432 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.297 2621 5 %RANDOM
Rwork0.214 ---
obs0.218 49474 95.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 4.56 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.9→196.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11601 0 0 35 11636
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0660.02211866
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg4.8421.98316107
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.3251439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.99724.346543
X-RAY DIFFRACTIONr_dihedral_angle_3_deg26.605152085
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.971588
X-RAY DIFFRACTIONr_chiral_restr0.3130.21762
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.029056
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3560.26915
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3920.28029
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2670.2611
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3430.293
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4510.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.991.57758
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.395211903
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.70935050
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0964.54204
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
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
11S517medium positional0.570.5
12T517medium positional0.570.5
13U517medium positional0.590.5
14V517medium positional0.70.5
21B973medium positional0.450.5
22H973medium positional0.570.5
23E973medium positional0.520.5
24K973medium positional0.540.5
31C938medium positional0.510.5
32I938medium positional0.610.5
33F938medium positional0.510.5
34L938medium positional0.60.5
11S517medium thermal1.652
12T517medium thermal1.752
13U517medium thermal1.342
14V517medium thermal2.392
21B973medium thermal1.132
22H973medium thermal1.172
23E973medium thermal1.032
24K973medium thermal1.32
31C938medium thermal1.262
32I938medium thermal0.92
33F938medium thermal0.942
34L938medium thermal1.032
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.442 199
Rwork0.386 3611
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.84361.27221.04151.99291.43321.5394-0.06040.1573-0.1462-0.11470.1357-0.0015-0.0226-0.0291-0.07530.17420.08230.2420.2598-0.0826-0.1329-23.224-54.56-11.253
20.3719-0.1705-1.33390.31440.67154.79890.1154-0.16540.1090.07370.0727-0.0483-0.09280.3781-0.18810.15730.00160.17450.2272-0.0535-0.0228-12.450.9585.314
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B3 - 156
2X-RAY DIFFRACTION1C33 - 174
3X-RAY DIFFRACTION1S227 - 300
4X-RAY DIFFRACTION1H6 - 156
5X-RAY DIFFRACTION1I36 - 174
6X-RAY DIFFRACTION1T227 - 300
7X-RAY DIFFRACTION2E6 - 156
8X-RAY DIFFRACTION2F36 - 174
9X-RAY DIFFRACTION2U227 - 298
10X-RAY DIFFRACTION2K3 - 156
11X-RAY DIFFRACTION2L36 - 174
12X-RAY DIFFRACTION2V229 - 298

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