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- PDB-6vaf: Structure of mono-ubiquitinated FANCD2 bound to non-ubiquitinated... -

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Basic information

Entry
Database: PDB / ID: 6vaf
TitleStructure of mono-ubiquitinated FANCD2 bound to non-ubiquitinated FANCI and to DNA
Components
  • (DNA (29-MER)) x 2
  • Fanconi anemia group D2 protein
  • Fanconi anemia, complementation group I
  • Ubiquitin
KeywordsDNA BINDING PROTEIN/DNA / DNA clamp / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


regulation of CD40 signaling pathway / regulation of regulatory T cell differentiation / homologous chromosome pairing at meiosis / double-strand break repair involved in meiotic recombination / gamete generation / neuronal stem cell population maintenance / brain morphogenesis / DNA repair complex / mitotic intra-S DNA damage checkpoint signaling / interstrand cross-link repair ...regulation of CD40 signaling pathway / regulation of regulatory T cell differentiation / homologous chromosome pairing at meiosis / double-strand break repair involved in meiotic recombination / gamete generation / neuronal stem cell population maintenance / brain morphogenesis / DNA repair complex / mitotic intra-S DNA damage checkpoint signaling / interstrand cross-link repair / DNA polymerase binding / condensed chromosome / 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) / positive regulation of protein ubiquitination / response to gamma radiation / 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 / TP53 Regulates Transcription of DNA Repair Genes / 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
Similarity search - Function
Fanconi anemia group I protein / FANCI solenoid 1 cap / FANCI solenoid 1 domain / FANCI helical domain 1 / FANCI helical domain 2 / FANCI solenoid 3 domain / FANCI solenoid 4 domain / FANCI solenoid 2 domain / FANCI solenoid 1 cap / FANCI solenoid 1 ...Fanconi anemia group I protein / FANCI solenoid 1 cap / FANCI solenoid 1 domain / FANCI helical domain 1 / FANCI helical domain 2 / FANCI solenoid 3 domain / FANCI solenoid 4 domain / FANCI solenoid 2 domain / FANCI solenoid 1 cap / FANCI solenoid 1 / FANCI solenoid 2 / FANCI solenoid 3 / FANCI solenoid 4 / FANCI helical domain 1 / FANCI helical domain 2 / Fanconi anaemia protein FANCD2 / Fanconi anaemia protein FancD2 nuclease / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Fanconi anemia, complementation group I / Polyubiquitin-C / Fanconi anemia group D2 protein / Fanconi anemia group I protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsPavletich, N.P.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nature / Year: 2020
Title: DNA clamp function of the monoubiquitinated Fanconi anaemia ID complex.
Authors: Renjing Wang / Shengliu Wang / Ankita Dhar / Christopher Peralta / Nikola P Pavletich /
Abstract: The ID complex, involving the proteins FANCI and FANCD2, is required for the repair of DNA interstrand crosslinks (ICL) and related lesions. These proteins are mutated in Fanconi anaemia, a disease ...The ID complex, involving the proteins FANCI and FANCD2, is required for the repair of DNA interstrand crosslinks (ICL) and related lesions. These proteins are mutated in Fanconi anaemia, a disease in which patients are predisposed to cancer. The Fanconi anaemia pathway of ICL repair is activated when a replication fork stalls at an ICL; this triggers monoubiquitination of the ID complex, in which one ubiquitin molecule is conjugated to each of FANCI and FANCD2. Monoubiquitination of ID is essential for ICL repair by excision, translesion synthesis and homologous recombination; however, its function remains unknown. Here we report a cryo-electron microscopy structure of the monoubiquitinated human ID complex bound to DNA, and reveal that it forms a closed ring that encircles the DNA. By comparison with the structure of the non-ubiquitinated ID complex bound to ICL DNA-which we also report here-we show that monoubiquitination triggers a complete rearrangement of the open, trough-like ID structure through the ubiquitin of one protomer binding to the other protomer in a reciprocal fashion. These structures-together with biochemical data-indicate that the monoubiquitinated ID complex loses its preference for ICL and related branched DNA structures, and becomes a sliding DNA clamp that can coordinate the subsequent repair reactions. Our findings also reveal how monoubiquitination in general can induce an alternative protein structure with a new function.
History
DepositionDec 17, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-21139
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Fanconi anemia, complementation group I
B: Fanconi anemia group D2 protein
D: Ubiquitin
S: DNA (29-MER)
T: DNA (29-MER)


Theoretical massNumber of molelcules
Total (without water)340,2905
Polymers340,2905
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Fanconi anemia, complementation group I


Mass: 149566.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FANCI / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: B7ZMF2, UniProt: Q9NVI1*PLUS
#2: Protein Fanconi anemia group D2 protein / Protein FACD2


Mass: 164314.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FANCD2, FACD / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9BXW9
#3: Protein Ubiquitin


Mass: 8576.831 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48
#4: DNA chain DNA (29-MER)


Mass: 8951.746 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#5: DNA chain DNA (29-MER)


Mass: 8880.711 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Mono-ubiquitinated FANCD2 bound to non-ubiquitinated FANCI and to DNA
Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 51 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: REFMAC / Version: 5.8.0257 / Classification: refinement
EM software
IDNameVersionCategory
4CTFFIND4CTF correction
7Omodel fitting
9RELION3initial Euler assignment
13REFMAC5model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 57993 / Symmetry type: POINT
Atomic model buildingB value: 195 / Protocol: OTHER / Space: RECIPROCAL / Target criteria: R-factor
Atomic model buildingPDB-ID: 3S4W
Accession code: 3S4W / Source name: PDB / Type: experimental model
RefinementResolution: 3.9→30 Å / Cor.coef. Fo:Fc: 0.89 / SU B: 104.283 / SU ML: 0.592 / ESU R: 1.756
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.32812 --
obs0.32812 93203 99.78 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 169.92 Å2
Baniso -1Baniso -2Baniso -3
1--1.84 Å2-1.1 Å2-2.1 Å2
2---0.03 Å21.93 Å2
3---1.87 Å2
Refinement stepCycle: 1 / Total: 20566
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0090.01321110
ELECTRON MICROSCOPYr_bond_other_d0.0130.01719671
ELECTRON MICROSCOPYr_angle_refined_deg1.6591.59528652
ELECTRON MICROSCOPYr_angle_other_deg1.5251.61745798
ELECTRON MICROSCOPYr_dihedral_angle_1_deg8.4575.1052716
ELECTRON MICROSCOPYr_dihedral_angle_2_deg37.07723.558936
ELECTRON MICROSCOPYr_dihedral_angle_3_deg16.262153769
ELECTRON MICROSCOPYr_dihedral_angle_4_deg18.0631588
ELECTRON MICROSCOPYr_chiral_restr0.1570.2062843
ELECTRON MICROSCOPYr_gen_planes_refined0.0070.0221987
ELECTRON MICROSCOPYr_gen_planes_other0.0040.024092
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it3.2092.8759694
ELECTRON MICROSCOPYr_mcbond_other3.2092.8759692
ELECTRON MICROSCOPYr_mcangle_it5.7314.312079
ELECTRON MICROSCOPYr_mcangle_other5.7314.312079
ELECTRON MICROSCOPYr_scbond_it3.0712.98211416
ELECTRON MICROSCOPYr_scbond_other3.0712.98311415
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other5.5044.39116573
ELECTRON MICROSCOPYr_long_range_B_refined10.62956.23155873
ELECTRON MICROSCOPYr_long_range_B_other10.62956.2355874
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.9→4 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.457 6697 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: ELECTRON MICROSCOPY

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)
10.0442-0.04080.04110.05-0.04160.0452-0.3033-0.15190.21130.24050.0093-0.3537-0.1898-0.19870.29413.37710.1127-0.15723.51390.08543.596872.58331.77519.513
22.4013-4.03252.77127.1316-4.87453.3392-0.0926-0.6883-0.2915-0.40090.12610.17470.2558-0.2033-0.03353.99630.4179-0.0473.87970.14934.385481.88748.1526.294
35.4163-0.19561.4598.08190.09346.53310.36390.7691-0.8752-1.0741-0.0185-1.16970.51020.3407-0.34531.6651-0.00960.09271.713-0.0141.91678.63173.19534.645
419.42656.9066-0.417415.12813.22362.4869-0.37271.1431-0.0011-0.1206-0.0606-0.26360.569-0.21120.43340.790.0940.13010.48520.04320.824877.06692.77345.789
58.9828-6.1505-5.4113.08465.45484.8553-0.0446-0.0532-0.48290.4974-0.28472.0370.3595-0.74720.32930.6459-0.07420.23530.8847-0.14631.495553.193110.22657.655
63.40880.5348-2.38568.54392.22433.04540.5816-0.58350.78831.0687-0.46710.625-0.7175-0.4653-0.11461.67660.1610.56931.7976-0.26022.11653.955140.3370.409
78.31686.07451.711514.0778-2.59312.02950.3111-1.031.21871.3666-0.5859-0.2428-0.12911.03060.27481.39720.23630.72181.408-0.63811.838167.69144.11667.043
812.1352-1.3567-0.244616.7806-0.75059.28040.22590.76561.02620.0791-0.0353-0.379-1.31670.6885-0.19060.464-00.51210.6844-0.17051.238574.902137.61151.284
99.2884-6.9117-3.293610.9656-3.38338.64990.50250.75821.5146-0.5962-0.6518-0.8732-0.72610.26390.14920.9680.23590.24021.07730.34371.805495.005129.18244.826
1010.69741.40912.466914.95353.63749.98260.29871.27941.0528-0.9502-0.3443-0.9603-0.69890.45020.04550.37790.18150.37030.51370.46771.1513108.657110.8450.121
1112.45644.1913.055720.54655.93614.4199-0.04931.0776-0.5467-0.44780.195-1.3050.40131.7809-0.14560.290.24110.13840.53090.35780.8455112.4799.65254.391
1210.25982.12984.857710.62853.535312.39240.1346-0.47280.28320.554-0.3742-1.2462-0.54380.97260.23960.5443-0.0709-0.01560.43690.56441.1796116.28595.33769.126
130.2387-0.2707-0.91040.50191.51714.68440.1547-0.2199-0.23120.3067-0.2178-0.08320.71-0.21630.06312.97660.08140.19323.94950.16674.007123.613122.55275.701
1412.45-2.29812.93342.3112-1.67751.4002-0.8924-0.0605-0.31580.55310.82410.1335-0.2801-0.48250.06822.7371-0.07730.14312.5842-0.17672.428541.618113.71290.468
153.5458-3.1322-0.75652.80350.68720.21530.0547-0.565-0.11970.10440.24440.00920.19870.1483-0.29912.8173-0.005-0.1862.63990.0342.569557.01299.66891.137
162.43372.39790.05385.74442.63052.82780.30890.20380.78490.9664-0.04010.35990.11-0.2232-0.26892.41340.0537-0.1911.85090.28862.329463.82883.6978.103
174.7831-1.4563-0.735912.36583.05453.51740.4460.66540.1078-0.318-0.17181.1511-0.0123-0.1748-0.27411.648-0.0223-0.51311.89870.15081.679463.21353.43459.978
184.3664-1.52940.00124.327-0.95174.1917-0.24960.8103-0.8089-0.7602-0.1539-0.32850.79930.32670.40352.0636-0.2319-0.52031.9339-0.21972.185586.76928.08261.807
1913.5912-2.65111.68288.765-2.530213.41560.2688-0.61520.2414-0.0201-0.2184-0.4995-0.2293-0.0042-0.05041.4966-0.4888-0.63590.8511-0.10431.517590.96942.47776.202
205.863-0.59570.2486.5747-1.64076.9687-0.1565-1.3036-0.9081.3673-0.3320.49490.06930.00840.48841.7294-0.5658-0.35861.41990.12621.499597.89749.13590.39
213.5173-1.67690.801912.5432-1.97746.66870.4334-0.6497-0.00861.2614-0.153-1.41180.71830.6519-0.28031.3132-0.5104-0.4851.05370.37491.371114.97766.50984.229
226.12040.61821.837910.50951.93158.7497-0.0293-1.5415-0.09921.2805-0.2002-0.4991-0.68080.81030.22951.1028-0.1374-0.40641.17160.45091.4024115.46787.86484.27
235.3047-0.1006-0.58945.84981.27140.84990.16521.2851-0.1619-0.6490.16241.42040.3464-0.9975-0.32762.4528-0.3741-0.53243.1231-0.09812.746256.05868.53431.936
241.99043.45181.910131.861910.685.39371.845-0.5610.3523-1.3603-3.5504-1.5942-0.077-1.49681.70542.7190.0319-0.02993.18840.25123.042391.148113.73472.038
254.2652-0.3192-4.56935.93245.903111.2343-0.23962.66770.00453.0551-0.2108-1.32492.7581-2.23750.45043.0299-0.2412-0.29533.35830.623.7167102.49370.08458.953
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1ELECTRON MICROSCOPY1A1 - 81
2ELECTRON MICROSCOPY2A82 - 169
3ELECTRON MICROSCOPY3A170 - 305
4ELECTRON MICROSCOPY4A306 - 399
5ELECTRON MICROSCOPY5A408 - 617
6ELECTRON MICROSCOPY6A618 - 743
7ELECTRON MICROSCOPY7A744 - 800
8ELECTRON MICROSCOPY8A801 - 934
9ELECTRON MICROSCOPY9A949 - 1039
10ELECTRON MICROSCOPY10A1040 - 1154
11ELECTRON MICROSCOPY11A1155 - 1221
12ELECTRON MICROSCOPY12A1233 - 1297
13ELECTRON MICROSCOPY12B1339 - 1400
14ELECTRON MICROSCOPY13B45 - 187
15ELECTRON MICROSCOPY14B188 - 254
16ELECTRON MICROSCOPY15B255 - 311
17ELECTRON MICROSCOPY16B337 - 465
18ELECTRON MICROSCOPY17B466 - 645
19ELECTRON MICROSCOPY18B646 - 841
20ELECTRON MICROSCOPY19B916 - 1020
21ELECTRON MICROSCOPY20B1021 - 1145
22ELECTRON MICROSCOPY21B1150 - 1250
23ELECTRON MICROSCOPY22B1251 - 1338
24ELECTRON MICROSCOPY23D1 - 76
25ELECTRON MICROSCOPY24S1 - 18
26ELECTRON MICROSCOPY24T41 - 58
27ELECTRON MICROSCOPY25T30 - 40
28ELECTRON MICROSCOPY25S19 - 29

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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

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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

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