[English] 日本語
Yorodumi
- PDB-6vaf: Structure of mono-ubiquitinated FANCD2 bound to non-ubiquitinated... -

+
Open data


ID or keywords:

Loading...

-
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 / double-strand break repair involved in meiotic recombination / homologous chromosome pairing at meiosis / 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 / double-strand break repair involved in meiotic recombination / homologous chromosome pairing at meiosis / 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 / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / PINK1-PRKN Mediated Mitophagy / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / Regulation of PTEN localization / NRIF signals cell death from the nucleus / 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 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / positive regulation of protein ubiquitination / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / NOTCH3 Activation and Transmission of Signal to the Nucleus / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / TP53 Regulates Transcription of DNA Repair Genes / response to gamma radiation / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Hh mutants are degraded by ERAD / Negative regulation of FGFR3 signaling / Degradation of AXIN / Peroxisomal protein import / Recognition of DNA damage by PCNA-containing replication complex
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

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-21139
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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)

-
Experimental details

-
Experiment

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

-
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

-
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)

-
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

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

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)
10.0442-0.04080.04110.05-0.04160.0452-0.3033-0.15190.21130.24050.0093-0.3537-0.1898-0.19870.29413.37710.1127-0.15723.51390.08543.596872.58331.77519.513
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

+
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://pdbjlc1.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