[English] 日本語
Yorodumi
- PDB-6hfa: Crystal structure of hDM2 in complex with a C-terminal triurea ca... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hfa
TitleCrystal structure of hDM2 in complex with a C-terminal triurea capped peptide chimera foldamer.
Components
  • E3 ubiquitin-protein ligase Mdm2
  • LM266, 1-[(2~{S})-2-azanyl-3-methyl-butyl]urea
KeywordsONCOPROTEIN / PROTEIN FOLDAMER COMPLEX / PROTEIN PROTEIN INTERACTION INHIBITOR / UREA BASED CHIMERA FOLDAMER
Function / homology
Function and homology information


cellular response to vitamin B1 / response to formaldehyde / response to ether / response to water-immersion restraint stress / cellular response to UV-C / fibroblast activation / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / Trafficking of AMPA receptors / receptor serine/threonine kinase binding / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator ...cellular response to vitamin B1 / response to formaldehyde / response to ether / response to water-immersion restraint stress / cellular response to UV-C / fibroblast activation / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / Trafficking of AMPA receptors / receptor serine/threonine kinase binding / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / cellular response to alkaloid / SUMO transferase activity / response to steroid hormone / negative regulation of protein processing / positive regulation of vascular associated smooth muscle cell migration / peroxisome proliferator activated receptor binding / AKT phosphorylates targets in the cytosol / response to iron ion / ligase activity / NEDD8 ligase activity / cellular response to peptide hormone stimulus / : / regulation of protein catabolic process / positive regulation of muscle cell differentiation / cellular response to antibiotic / regulation of postsynaptic neurotransmitter receptor internalization / SUMOylation of ubiquitinylation proteins / Constitutive Signaling by AKT1 E17K in Cancer / negative regulation of DNA damage response, signal transduction by p53 class mediator / SUMOylation of transcription factors / negative regulation of signal transduction by p53 class mediator / cellular response to estrogen stimulus / protein localization to nucleus / protein sumoylation / response to magnesium ion / ribonucleoprotein complex binding / positive regulation of vascular associated smooth muscle cell proliferation / protein autoubiquitination / positive regulation of mitotic cell cycle / NPAS4 regulates expression of target genes / positive regulation of protein export from nucleus / response to cocaine / DNA damage response, signal transduction by p53 class mediator / negative regulation of neuron projection development / ubiquitin binding / establishment of protein localization / Stabilization of p53 / protein destabilization / cellular response to gamma radiation / response to toxic substance / Regulation of RUNX3 expression and activity / Oncogene Induced Senescence / RING-type E3 ubiquitin transferase / Regulation of TP53 Activity through Methylation / cellular response to growth factor stimulus / Degradation of CDH1 / protein polyubiquitination / disordered domain specific binding / ubiquitin-protein transferase activity / p53 binding / cellular response to hydrogen peroxide / endocytic vesicle membrane / Signaling by ALK fusions and activated point mutants / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Regulation of TP53 Degradation / ubiquitin protein ligase activity / protein-containing complex assembly / 5S rRNA binding / ubiquitin-dependent protein catabolic process / Oxidative Stress Induced Senescence / Regulation of TP53 Activity through Phosphorylation / amyloid fibril formation / regulation of cell cycle / cellular response to hypoxia / proteasome-mediated ubiquitin-dependent protein catabolic process / response to antibiotic / postsynaptic density / protein ubiquitination / response to xenobiotic stimulus / Ub-specific processing proteases / apoptotic process / protein domain specific binding / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / positive regulation of gene expression / positive regulation of cell population proliferation / negative regulation of apoptotic process / nucleolus / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / enzyme binding / protein-containing complex / zinc ion binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
E3 ubiquitin-protein ligase Mdm2 / MDM2, modified RING finger, HC subclass / MDM2 / SWIB/MDM2 domain / p53 negative regulator Mdm2/Mdm4 / SWIB/MDM2 domain / SWIB/MDM2 domain / SWIB/MDM2 domain profile. / SWIB/MDM2 domain superfamily / Zn-finger in Ran binding protein and others ...E3 ubiquitin-protein ligase Mdm2 / MDM2, modified RING finger, HC subclass / MDM2 / SWIB/MDM2 domain / p53 negative regulator Mdm2/Mdm4 / SWIB/MDM2 domain / SWIB/MDM2 domain / SWIB/MDM2 domain profile. / SWIB/MDM2 domain superfamily / Zn-finger in Ran binding protein and others / Zinc finger, C3HC4 type (RING finger) / Zinc finger RanBP2 type profile. / Zinc finger, RanBP2-type superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
E3 ubiquitin-protein ligase Mdm2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.79 Å
AuthorsBuratto, J. / Mauran, L. / Goudreau, S. / Fribourg, S. / Guichard, G.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-15-CE07-0010-01 France
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2020
Title: Structural Basis for alpha-Helix Mimicry and Inhibition of Protein-Protein Interactions with Oligourea Foldamers.
Authors: Cussol, L. / Mauran-Ambrosino, L. / Buratto, J. / Belorusova, A.Y. / Neuville, M. / Osz, J. / Fribourg, S. / Fremaux, J. / Dolain, C. / Goudreau, S.R. / Rochel, N. / Guichard, G.
History
DepositionAug 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0May 24, 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_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_rmsd_angle / struct_asym / struct_conn / struct_ref_seq / 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.group_PDB / _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.pdbx_formal_charge / _atom_site.type_symbol / _atom_site_anisotrop.id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_common_name / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / struct_conn / struct_ncs_dom_lim
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_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
Revision 3.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: E3 ubiquitin-protein ligase Mdm2
B: E3 ubiquitin-protein ligase Mdm2
C: LM266, 1-[(2~{S})-2-azanyl-3-methyl-butyl]urea
D: LM266, 1-[(2~{S})-2-azanyl-3-methyl-butyl]urea


Theoretical massNumber of molelcules
Total (without water)25,2534
Polymers25,2534
Non-polymers00
Water1,17165
1
A: E3 ubiquitin-protein ligase Mdm2
D: LM266, 1-[(2~{S})-2-azanyl-3-methyl-butyl]urea


Theoretical massNumber of molelcules
Total (without water)12,6272
Polymers12,6272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-11 kcal/mol
Surface area5660 Å2
MethodPISA
2
B: E3 ubiquitin-protein ligase Mdm2
C: LM266, 1-[(2~{S})-2-azanyl-3-methyl-butyl]urea


Theoretical massNumber of molelcules
Total (without water)12,6272
Polymers12,6272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-9 kcal/mol
Surface area5320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.350, 49.410, 82.130
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11(chain A and (resseq 26:35 or (resid 36 and (name...
21(chain B and (resseq 26:30 or (resid 31 and (name...
12chain C
22chain D

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
111THRTHRLEULEU(chain A and (resseq 26:35 or (resid 36 and (name...AA26 - 3513 - 22
121LYSLYSLYSLYS(chain A and (resseq 26:35 or (resid 36 and (name...AA3623
131GLUGLUASNASN(chain A and (resseq 26:35 or (resid 36 and (name...AA25 - 11112 - 98
141GLUGLUASNASN(chain A and (resseq 26:35 or (resid 36 and (name...AA25 - 11112 - 98
151GLUGLUASNASN(chain A and (resseq 26:35 or (resid 36 and (name...AA25 - 11112 - 98
161GLUGLUASNASN(chain A and (resseq 26:35 or (resid 36 and (name...AA25 - 11112 - 98
171GLUGLUASNASN(chain A and (resseq 26:35 or (resid 36 and (name...AA25 - 11112 - 98
211THRTHRPROPRO(chain B and (resseq 26:30 or (resid 31 and (name...BB26 - 3013 - 17
221LYSLYSLYSLYS(chain B and (resseq 26:30 or (resid 31 and (name...BB3118
231GLUGLUASNASN(chain B and (resseq 26:30 or (resid 31 and (name...BB25 - 11112 - 98
241GLUGLUASNASN(chain B and (resseq 26:30 or (resid 31 and (name...BB25 - 11112 - 98
251GLUGLUASNASN(chain B and (resseq 26:30 or (resid 31 and (name...BB25 - 11112 - 98
261GLUGLUASNASN(chain B and (resseq 26:30 or (resid 31 and (name...BB25 - 11112 - 98
271GLUGLUASNASN(chain B and (resseq 26:30 or (resid 31 and (name...BB25 - 11112 - 98
281GLUGLUASNASN(chain B and (resseq 26:30 or (resid 31 and (name...BB25 - 11112 - 98
291GLUGLUASNASN(chain B and (resseq 26:30 or (resid 31 and (name...BB25 - 11112 - 98
2101GLUGLUASNASN(chain B and (resseq 26:30 or (resid 31 and (name...BB25 - 11112 - 98
112THRTHRURVURVchain CCC17 - 261 - 10
212THRTHRURVURVchain DDD17 - 261 - 10

NCS ensembles :
ID
1
2

-
Components

#1: Protein E3 ubiquitin-protein ligase Mdm2 / Double minute 2 protein / Hdm2 / Oncoprotein Mdm2 / RING-type E3 ubiquitin transferase Mdm2 / p53- ...Double minute 2 protein / Hdm2 / Oncoprotein Mdm2 / RING-type E3 ubiquitin transferase Mdm2 / p53-binding protein Mdm2


Mass: 11397.342 Da / Num. of mol.: 2 / Fragment: residues 17-111
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MDM2 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q00987, RING-type E3 ubiquitin transferase
#2: Protein/peptide LM266, 1-[(2~{S})-2-azanyl-3-methyl-butyl]urea


Mass: 1229.364 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.8 Å3/Da / Density % sol: 31.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 90 mM HEPES, 1.26 M Na Citrate, 10% glycerol. Cryo: +30% Glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9811 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9811 Å / Relative weight: 1
ReflectionResolution: 1.79→44.35 Å / Num. obs: 17433 / % possible obs: 98.6 % / Redundancy: 12.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.044 / Rrim(I) all: 0.155 / Net I/σ(I): 11.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.79-1.8310.41.811470.4720.5511.88889.7
8-44.359.90.0512490.9990.0170.05499.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.6.2data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→42.339 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.09
RfactorNum. reflection% reflection
Rfree0.2384 863 5 %
Rwork0.1908 --
obs0.1931 17262 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 92.35 Å2 / Biso mean: 37.7329 Å2 / Biso min: 18.31 Å2
Refinement stepCycle: final / Resolution: 1.79→42.339 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1562 0 20 65 1647
Biso mean--57.01 47.09 -
Num. residues----192
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061616
X-RAY DIFFRACTIONf_angle_d1.0142181
X-RAY DIFFRACTIONf_chiral_restr0.056250
X-RAY DIFFRACTIONf_plane_restr0.008271
X-RAY DIFFRACTIONf_dihedral_angle_d14.516965
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A698X-RAY DIFFRACTION8.111TORSIONAL
12B698X-RAY DIFFRACTION8.111TORSIONAL
21C58X-RAY DIFFRACTION8.111TORSIONAL
22D58X-RAY DIFFRACTION8.111TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7901-1.90220.36971320.31092510264292
1.9022-2.04910.29051420.24262698284098
2.0491-2.25530.27721420.20792715285799
2.2553-2.58160.2521460.21592761290799
2.5816-3.25240.24691460.19152778292499
3.2524-42.35050.2031550.162929373092100
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)
10.0528-0.10170.15370.439-0.69610.77050.02380.14570.0253-0.0478-0.0986-0.0703-0.0320.0734-0.00010.23670.0088-0.00260.2675-0.01210.258-3.6371.8563-9.8267
20.0106-0.02370.02870.073-0.11850.1919-0.152-0.081-0.1524-0.03610.38770.2582-0.1819-0.23860.00010.24520.01740.01130.28880.02640.285-20.548910.2043-7.664
30.0162-0.0090.00960.04830.03520.0158-0.0204-0.1634-0.42310.22920.18690.06940.41160.53470.00070.33420.08310.00390.2793-0.00560.3586-12.77442.63-0.528
40.21680.14810.08020.2540.38170.5335-0.2276-0.1490.17480.27940.1908-0.0942-0.0597-0.04850.00030.28210.0181-0.0180.3336-0.02280.2497-5.20479.6338-0.2485
50.248-0.04130.20570.80620.42230.44590.3467-0.3101-0.2178-0.2479-0.2338-0.1193-0.31940.086400.3409-0.03520.0410.25780.00290.368-17.517225.7633-28.9787
60.0808-0.04920.06440.1349-0.1920.2169-0.14540.0253-0.0028-0.05360.01320.0359-0.0737-0.25510.00030.29010.0338-0.01680.2786-0.00230.3369-22.820318.1261-24.3653
70.40140.21120.3710.34750.01470.2127-0.0429-0.0016-0.0024-0.16120.12870.12130.1615-0.126-00.2890.0016-0.01230.3112-0.00560.2203-12.69828.1834-22.4658
80.04230.04950.03910.04120.02490.04370.3793-0.2901-0.3077-0.21980.21490.2180.0719-0.1491-0.00020.43-0.0372-0.07390.4038-0.01160.4219-14.70050.8346-29.9967
90.0246-0.0246-0.01430.0340.01540.00950.4566-0.31870.2801-0.6031-0.13180.3299-0.1088-0.35050.00120.4377-0.0371-0.07680.381-0.06480.375-18.9658.1091-33.4223
100.0499-0.01720.03290.0033-0.00930.01080.32070.3905-0.0849-0.6529-0.2316-0.2663-0.17960.007-0.00010.49140.1008-0.00310.377300.3115-7.92065.4001-32.732
110.1647-0.0009-0.26290.1850.1060.35480.12110.25120.0579-0.0625-0.241-0.1724-0.0614-0.0228-00.3395-0.04520.02510.3488-0.00290.3445-12.07218.8047-33.8409
120.02880.0369-0.02170.0697-0.02810.00420.2272-0.2728-0.00220.1925-0.1888-0.40560.18910.3228-0.00050.25330.04560.0110.32470.04450.2911-4.86517.4937-20.9232
130.02120.05160.00730.08640.0104-0.00220.34020.05960.3403-0.26-0.03360.09790.07170.1841-0.00020.20980.0198-0.0090.21230.0010.2334-12.945316.7503-12.948
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 25 through 63 )A25 - 63
2X-RAY DIFFRACTION2chain 'A' and (resid 64 through 80 )A64 - 80
3X-RAY DIFFRACTION3chain 'A' and (resid 81 through 86 )A81 - 86
4X-RAY DIFFRACTION4chain 'A' and (resid 87 through 111 )A87 - 111
5X-RAY DIFFRACTION5chain 'B' and (resid 25 through 31 )B25 - 31
6X-RAY DIFFRACTION6chain 'B' and (resid 32 through 49 )B32 - 49
7X-RAY DIFFRACTION7chain 'B' and (resid 50 through 73 )B50 - 73
8X-RAY DIFFRACTION8chain 'B' and (resid 74 through 80 )B74 - 80
9X-RAY DIFFRACTION9chain 'B' and (resid 81 through 86 )B81 - 86
10X-RAY DIFFRACTION10chain 'B' and (resid 87 through 95 )B87 - 95
11X-RAY DIFFRACTION11chain 'B' and (resid 96 through 111 )B96 - 111
12X-RAY DIFFRACTION12chain 'C' and (resid 17 through 23 )C17 - 23
13X-RAY DIFFRACTION13chain 'D' and (resid 17 through 23 )D17 - 23

+
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