[English] 日本語
Yorodumi
- PDB-6h0f: Structure of DDB1-CRBN-pomalidomide complex bound to IKZF1(ZF2) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6h0f
TitleStructure of DDB1-CRBN-pomalidomide complex bound to IKZF1(ZF2)
Components
  • DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1
  • DNA-binding protein Ikaros
  • Protein cereblon
KeywordsSIGNALING PROTEIN / E3 ubiquitin ligase / drug mediated protein-interaction / targeted protein degradation
Function / homology
Function and homology information


negative regulation of monoatomic ion transmembrane transport / lymphocyte differentiation / positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding ...negative regulation of monoatomic ion transmembrane transport / lymphocyte differentiation / positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / NOTCH3 Intracellular Domain Regulates Transcription / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / locomotory exploration behavior / negative regulation of reproductive process / negative regulation of developmental process / cullin family protein binding / mesoderm development / positive regulation of Wnt signaling pathway / viral release from host cell / ectopic germ cell programmed cell death / positive regulation of viral genome replication / negative regulation of protein-containing complex assembly / pericentric heterochromatin / positive regulation of gluconeogenesis / erythrocyte differentiation / proteasomal protein catabolic process / Recognition of DNA damage by PCNA-containing replication complex / nucleotide-excision repair / positive regulation of protein-containing complex assembly / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / regulation of circadian rhythm / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Wnt signaling pathway / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / positive regulation of protein catabolic process / cellular response to UV / rhythmic process / protein-macromolecule adaptor activity / site of double-strand break / Neddylation / chromatin organization / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / Potential therapeutics for SARS / transmembrane transporter binding / damaged DNA binding / chromosome, telomeric region / protein ubiquitination / cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / DNA repair / negative regulation of DNA-templated transcription / apoptotic process / DNA damage response / protein-containing complex binding / nucleolus / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / perinuclear region of cytoplasm / protein-containing complex / DNA binding / extracellular space / extracellular exosome / nucleoplasm / membrane / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / CULT domain / CULT domain profile. / Lon protease, N-terminal domain superfamily / Lon N-terminal domain profile. / Lon protease, N-terminal domain / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) / Cleavage/polyadenylation specificity factor, A subunit, N-terminal ...Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / CULT domain / CULT domain profile. / Lon protease, N-terminal domain superfamily / Lon N-terminal domain profile. / Lon protease, N-terminal domain / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / Mono-functional DNA-alkylating methyl methanesulfonate N-term / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / CPSF A subunit region / PUA-like superfamily / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
S-Pomalidomide / DNA-binding protein Ikaros / DNA damage-binding protein 1 / Protein cereblon
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsPetzold, G. / Bunker, R.D. / Thoma, N.H.
Funding support3items
OrganizationGrant numberCountry
European UnionHorizon 2020 No. 666068
European Molecular Biology OrganizationAdvanced Fellowship aALTF 761-2016
European UnionHuman Frontier Science Program Long-Term Fellowship LT000210/2014
CitationJournal: Science / Year: 2018
Title: Defining the human C2H2 zinc finger degrome targeted by thalidomide analogs through CRBN.
Authors: Sievers, Q.L. / Petzold, G. / Bunker, R.D. / Renneville, A. / Slabicki, M. / Liddicoat, B.J. / Abdulrahman, W. / Mikkelsen, T. / Ebert, B.L. / Thoma, N.H.
History
DepositionJul 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.0Apr 17, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range / struct_site_gen
Item: _atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id ..._atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_mutation / _entity_name_com.entity_id / _entity_name_com.name / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_db_isoform / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id / _struct_site_gen.label_seq_id
Revision 2.1Oct 30, 2019Group: Data collection / Database references / Category: citation / Item: _citation.page_first
Revision 2.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1
B: Protein cereblon
C: DNA-binding protein Ikaros
D: DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1
E: Protein cereblon
F: DNA-binding protein Ikaros
G: DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1
H: Protein cereblon
I: DNA-binding protein Ikaros
J: DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1
K: Protein cereblon
L: DNA-binding protein Ikaros
hetero molecules


Theoretical massNumber of molelcules
Total (without water)597,39124
Polymers595,77412
Non-polymers1,61612
Water57632
1
A: DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1
B: Protein cereblon
C: DNA-binding protein Ikaros
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,3486
Polymers148,9443
Non-polymers4043
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1
E: Protein cereblon
F: DNA-binding protein Ikaros
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,3486
Polymers148,9443
Non-polymers4043
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1
H: Protein cereblon
I: DNA-binding protein Ikaros
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,3486
Polymers148,9443
Non-polymers4043
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1
K: Protein cereblon
L: DNA-binding protein Ikaros
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,3486
Polymers148,9443
Non-polymers4043
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)161.450, 177.860, 242.470
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 2 types, 8 molecules ADGJBEHK

#1: Protein
DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1


Mass: 95773.695 Da / Num. of mol.: 4
Mutation: Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 ...Mutation: Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDB1, XAP1 / Production host: Trichoplusia ni cypovirus 15 / References: UniProt: Q16531*PLUS
#2: Protein
Protein cereblon


Mass: 48976.117 Da / Num. of mol.: 4 / Mutation: N-terminally truncated (1-40 aa deleted)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRBN, AD-006 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96SW2

-
Protein/peptide , 1 types, 4 molecules CFIL

#3: Protein/peptide
DNA-binding protein Ikaros / Ikaros family zinc finger protein 1 / Lymphoid transcription factor LyF-1


Mass: 4193.796 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IKZF1, IK1, IKAROS, LYF1, ZNFN1A1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q13422

-
Non-polymers , 3 types, 44 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: Zn
#5: Chemical
ChemComp-Y70 / S-Pomalidomide


Mass: 273.244 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C13H11N3O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 3.09 Å3/Da / Density % sol: 60.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: Protein solution: 350 uM IKZF1-ZF2, 70 uM DDB1/CRBN, 80 uM pomalidomide in 50 mM HEPES pH 7.4, 200 mM NaCl, 0.25 mM TCEP Crystallisation solution: (Morpheus HT condition) 100 mM Morpheus ...Details: Protein solution: 350 uM IKZF1-ZF2, 70 uM DDB1/CRBN, 80 uM pomalidomide in 50 mM HEPES pH 7.4, 200 mM NaCl, 0.25 mM TCEP Crystallisation solution: (Morpheus HT condition) 100 mM Morpheus buffer system 1 pH 6.5, 10% (v/v) Morpheus NPS solution, 15% (v/v) ethylene glycol and 9.5% (w/v) poly(ethylene glycol) 5000 monomethyl ether.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jan 30, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.25→39.85 Å / Num. obs: 104192 / % possible obs: 94.4 % / Redundancy: 31.3 % / Biso Wilson estimate: 81.08 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.345 / Rpim(I) all: 0.061 / Rrim(I) all: 0.351 / Net I/σ(I): 11.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3.25-3.3111.32.74327060.340.8222.8750.1
17.8-39.8534.30.0670010.010.06191.3

-
Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FQD

5fqd


Resolution: 3.25→39.85 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.895 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.463
RfactorNum. reflection% reflectionSelection details
Rfree0.234 5080 4.95 %RANDOM
Rwork0.212 ---
obs0.213 102694 93.2 %-
Displacement parametersBiso max: 299.98 Å2 / Biso mean: 97.73 Å2 / Biso min: 3.36 Å2
Baniso -1Baniso -2Baniso -3
1-1.0014 Å20 Å20 Å2
2---3.0394 Å20 Å2
3---2.038 Å2
Refine analyzeLuzzati coordinate error obs: 0.47 Å
Refinement stepCycle: final / Resolution: 3.25→39.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms38854 0 88 32 38974
Biso mean--56.59 30.71 -
Num. residues----4940
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d17319SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes12596HARMONIC5
X-RAY DIFFRACTIONt_it78328HARMONIC20
X-RAY DIFFRACTIONt_nbd5SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion5202SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance3557HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact82513SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d78328HARMONIC20.015
X-RAY DIFFRACTIONt_angle_deg141672HARMONIC20.97
X-RAY DIFFRACTIONt_omega_torsion2.48
X-RAY DIFFRACTIONt_other_torsion17.6
LS refinement shellResolution: 3.25→3.31 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3037 90 4.38 %
Rwork0.2624 1964 -
all0.2641 2054 -
obs--38.03 %
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)
10.1635-0.13360.0181.13470.20350.5562-0.02440.11390.0414-0.01120.0652-0.12710.01180.0457-0.04080.0817-0.00340.02920.20010.0828-0.002413.9797-28.223-54.2709
20.39660.4989-0.49620.585-0.49260.20680.01340.1171-0.0195-0.0812-0.04850.0254-0.0060.05120.03510.153-0.01610.01520.11960.09120.1196-5.7274-51.5603-27.6442
32.7803-3.4187-1.53543.2622-0.88240-0.00370.0190.01520.01470.095-0.00950.0443-0.0775-0.09130.1832-0.09030.0584-0.04030.01130.2245-32.4624-70.3082-13.6961
40.8021-0.219-0.17411.2786-0.17790.74620.01980.03610.1825-0.3354-0.1271-0.22770.1663-0.00470.10730.13930.00540.15020.17540.2899-0.109178.718910.1285-57.2613
50.07720.1538-0.22170.34060.202900.00660.06480.0359-0.1484-0.06030.01520.04510.04750.05370.1541-0.0114-0.0270.15070.16370.157368.9435-16.8637-28.5067
62.0387-1.2382-0.38151.9461-1.30361.517-0.0197-0.0394-0.08040.02110.00370.02790.04830.09710.0160.3252-0.0088-0.04510.01440.08190.071748.6621-40.2321-10.8266
70.26390.1473-0.26270.73890.02451.33430.0690.2347-0.15370.22520.0097-0.0666-0.3557-0.4431-0.07870.06970.3227-0.06830.09270.10450.111128.011834.7156-8.5864
80.374-0.7140.02830.7302-0.41180.1034-0.03350.08230.15980.0211-0.05560.0077-0.0285-0.00690.0890.12010.0344-0.0936-0.00520.03920.284846.73710.52192.7125
91.6841-1.2994-1.95861.9459-0.62130.83810.005-0.00350.0798-0.0155-0.0512-0.02140.0632-0.00360.04620.19050.0345-0.03780.06880.06590.149873.2726-19.989614.0799
100.31620.1218-0.30310.570.12480.93910.06550.13190.10340.0777-0.11080.1156-0.033-0.09010.04530.00560.04260.022-0.04980.04560.3294-38.25127.3485-13.91
110.1799-0.61380.16931.0003-0.3600.03050.01640.14770.1513-0.13320.08340.00230.08260.10270.23-0.03160.11-0.0340.04280.2156-28.2775-29.55210.0009
121.0648-1.2674-1.70122.1692-0.50412.5454-0.0081-0.1881-0.1493-0.0223-0.10340.0407-0.02490.01330.11150.29390.02980.0382-0.00230.09620.1116-7.9415-54.40315.3052
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 1140
2X-RAY DIFFRACTION2{ B|* }B69 - 442
3X-RAY DIFFRACTION3{ C|* }C138 - 169
4X-RAY DIFFRACTION4{ D|* }D1 - 1140
5X-RAY DIFFRACTION5{ E|* }E69 - 442
6X-RAY DIFFRACTION6{ F|* }F138 - 169
7X-RAY DIFFRACTION7{ G|* }G1 - 1140
8X-RAY DIFFRACTION8{ H|* }H69 - 442
9X-RAY DIFFRACTION9{ I|* }I138 - 169
10X-RAY DIFFRACTION10{ J|* }J-10 - 1140
11X-RAY DIFFRACTION11{ K|* }K69 - 442
12X-RAY DIFFRACTION12{ L|* }L138 - 169

+
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