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- PDB-9y3u: Eukaryotic translation initiation factor 2-B (eIF2B) with a trunc... -

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Basic information

Entry
Database: PDB / ID: 9y3u
TitleEukaryotic translation initiation factor 2-B (eIF2B) with a truncation in the beta subunit (inactive state)
Components
  • (Translation initiation factor eIF-2B subunit ...) x 2
  • (Translation initiation factor eIF2B subunit ...) x 3
KeywordsTRANSLATION / Guanine nucleotide exchange factor / GEF / initiation
Function / homology
Function and homology information


eukaryotic translation initiation factor 2B complex / Recycling of eIF2:GDP / astrocyte development / astrocyte differentiation / oligodendrocyte development / regulation of translational initiation / cytoplasmic translational initiation / positive regulation of translational initiation / response to glucose / ovarian follicle development ...eukaryotic translation initiation factor 2B complex / Recycling of eIF2:GDP / astrocyte development / astrocyte differentiation / oligodendrocyte development / regulation of translational initiation / cytoplasmic translational initiation / positive regulation of translational initiation / response to glucose / ovarian follicle development / myelination / translation initiation factor activity / translation initiation factor binding / guanyl-nucleotide exchange factor activity / response to endoplasmic reticulum stress / central nervous system development / hippocampus development / translational initiation / response to peptide hormone / regulation of translation / T cell receptor signaling pathway / response to heat / positive regulation of apoptotic process / GTP binding / ATP binding / membrane / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Translation initiation factor eIF-2B subunit alpha, N-terminal / Translation initiation factor eIF-2B subunit epsilon, N-terminal / Translation initiation factor eIF-2B subunit epsilon, W2 domain / : / : / : / : / : / EIF2B subunit epsilon LbH domain / Initiation factor 2B-related ...Translation initiation factor eIF-2B subunit alpha, N-terminal / Translation initiation factor eIF-2B subunit epsilon, N-terminal / Translation initiation factor eIF-2B subunit epsilon, W2 domain / : / : / : / : / : / EIF2B subunit epsilon LbH domain / Initiation factor 2B-related / Initiation factor 2B-like, C-terminal / Initiation factor 2 subunit family / eIF4-gamma/eIF5/eIF2-epsilon / Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5 / W2 domain / W2 domain profile. / Nucleotidyl transferase domain / Nucleotidyl transferase / NagB/RpiA transferase-like / Trimeric LpxA-like superfamily / Nucleotide-diphospho-sugar transferases / Armadillo-type fold
Similarity search - Domain/homology
PHOSPHATE ION / Translation initiation factor eIF2B subunit beta / Translation initiation factor eIF2B subunit epsilon / Translation initiation factor eIF2B subunit alpha / Translation initiation factor eIF2B subunit gamma / Translation initiation factor eIF2B subunit delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsDalwadi, U. / Croll, T. / Subramanian, A. / Lee, D.J. / Arthur, C. / Walter, P. / Frost, A.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: To Be Published
Title: Allosteric Disordering of eIF2B Regulates the Integrated Stress Response
Authors: Dalwadi, U. / Croll, T. / Subramanian, A. / Lee, D.J. / Arthur, C. / Walter, P. / Frost, A.
History
DepositionSep 2, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Translation initiation factor eIF2B subunit epsilon
B: Translation initiation factor eIF2B subunit epsilon
C: Translation initiation factor eIF2B subunit beta
D: Translation initiation factor eIF2B subunit beta
E: Translation initiation factor eIF-2B subunit delta
F: Translation initiation factor eIF-2B subunit delta
G: Translation initiation factor eIF2B subunit alpha
H: Translation initiation factor eIF2B subunit alpha
I: Translation initiation factor eIF-2B subunit gamma
J: Translation initiation factor eIF-2B subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)465,36614
Polymers465,04510
Non-polymers3214
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Translation initiation factor eIF2B subunit ... , 3 types, 6 molecules ABCDGH

#1: Protein Translation initiation factor eIF2B subunit epsilon / eIF2B GDP-GTP exchange factor subunit epsilon


Mass: 51385.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2B5, EIF2BE / Production host: Escherichia coli (E. coli) / References: UniProt: Q13144
#2: Protein Translation initiation factor eIF2B subunit beta / S20I15 / S20III15 / eIF2B GDP-GTP exchange factor subunit beta


Mass: 39438.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Latch helix replaced with a flexible linker / Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2B2, EIF2BB / Production host: Escherichia coli (E. coli) / References: UniProt: P49770
#4: Protein Translation initiation factor eIF2B subunit alpha / eIF2B GDP-GTP exchange factor subunit alpha


Mass: 33754.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2B1, EIF2BA / Production host: Escherichia coli (E. coli) / References: UniProt: Q14232

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Translation initiation factor eIF-2B subunit ... , 2 types, 4 molecules EFIJ

#3: Protein Translation initiation factor eIF-2B subunit delta / eIF-2B GDP-GTP exchange factor subunit delta


Mass: 57640.168 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2B4, EIF2BD / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UI10
#5: Protein Translation initiation factor eIF-2B subunit gamma / eIF-2B GDP-GTP exchange factor subunit gamma


Mass: 50304.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2B3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NR50

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Non-polymers , 2 types, 4 molecules

#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
Has protein modificationN

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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: Eukaryotic translation initiation factor 2B / Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Molecular weightValue: 0.521758 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
Details: 20 mM HEPES KOH pH 7.4, 200 mM KCl, 5 mM MgCl2, 1 mM TCEP
Buffer component
IDConc.NameFormulaBuffer-ID
120 mM2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid or 4-(2-Hydroxyethyl)piperazine-1-ethanesulfonic acidHEPES1
2200 mMPotassium ChlorideKCl1
35 mMMagnesium ChlorideMgCl21
41 mMtris(2-carboxyethyl)phosphineTCEP1
SpecimenConc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4136
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 10 eV
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6.2particle selection
2EPUimage acquisition
4cryoSPARC4.6.2CTF correction
7ISOLDEmodel fitting
9Servalcatmodel refinement
10cryoSPARC4.6.2initial Euler assignment
11cryoSPARC4.6.2final Euler assignment
12cryoSPARC4.2.1classification
13cryoSPARC4.6.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2125688
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 96151 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Atomic model buildingPDB-ID: 7L7G

7l7g


Accession code: 7L7G / Source name: PDB / Type: experimental model
RefinementResolution: 2.4→2.4 Å / Num. reflection obs: 8270356 / Average fsc work: 0.7024
Displacement parametersBiso mean: 66.66 Å2
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
ELECTRON MICROSCOPYs_bond_nonh_d0.0078286750.0119
ELECTRON MICROSCOPYs_angle_nonh_deg1.6248388511.8239
ELECTRON MICROSCOPYs_dihedral_angle_1_deg7.286935935
ELECTRON MICROSCOPYs_dihedral_angle_2_deg4.07518665
ELECTRON MICROSCOPYs_dihedral_angle_3_deg11.1046775910
ELECTRON MICROSCOPYs_dihedral_angle_6_deg14.5993141210
ELECTRON MICROSCOPYs_chiral_restr0.068345500.1309
ELECTRON MICROSCOPYs_planes0.0056396640.02
ELECTRON MICROSCOPYs_nbd0.2089420250.2
ELECTRON MICROSCOPYs_nbtor0.2254513820.2
ELECTRON MICROSCOPYs_hbond_nbd0.11558510.2
LS refinement shell
Resolution (Å)Refine-IDNum. reflection obsFsc work
2.35-2.358ELECTRON MICROSCOPY867430.3392
2.358-2.373ELECTRON MICROSCOPY1553970.3584
2.373-2.389ELECTRON MICROSCOPY1529290.3779
2.389-2.404ELECTRON MICROSCOPY1499790.3916
2.404-2.42ELECTRON MICROSCOPY1497490.4078
2.42-2.436ELECTRON MICROSCOPY1472370.4221
2.436-2.452ELECTRON MICROSCOPY1449430.4336
2.452-2.468ELECTRON MICROSCOPY1425850.4453
2.468-2.484ELECTRON MICROSCOPY1414170.4574
2.485-2.501ELECTRON MICROSCOPY1400950.4664
2.501-2.518ELECTRON MICROSCOPY1377930.4791
2.518-2.535ELECTRON MICROSCOPY1357810.4933
2.535-2.553ELECTRON MICROSCOPY1343610.5051
2.553-2.57ELECTRON MICROSCOPY1324870.5109
2.571-2.588ELECTRON MICROSCOPY1301770.5142
2.589-2.607ELECTRON MICROSCOPY1272090.5233
2.607-2.625ELECTRON MICROSCOPY1273510.5347
2.625-2.644ELECTRON MICROSCOPY1249530.5473
2.644-2.663ELECTRON MICROSCOPY1234090.5604
2.663-2.682ELECTRON MICROSCOPY1207090.5776
2.682-2.701ELECTRON MICROSCOPY1191990.5928
2.701-2.721ELECTRON MICROSCOPY1189090.6066
2.721-2.741ELECTRON MICROSCOPY1164810.6193
2.741-2.762ELECTRON MICROSCOPY1136470.6337
2.762-2.782ELECTRON MICROSCOPY1131570.6541
2.782-2.803ELECTRON MICROSCOPY1107610.6721
2.803-2.825ELECTRON MICROSCOPY1104970.6855
2.825-2.846ELECTRON MICROSCOPY1069590.6964
2.846-2.868ELECTRON MICROSCOPY1062130.7063
2.868-2.891ELECTRON MICROSCOPY1053330.7156
2.891-2.913ELECTRON MICROSCOPY1027510.7246
2.913-2.936ELECTRON MICROSCOPY1010250.7356
2.936-2.96ELECTRON MICROSCOPY990370.7501
2.96-2.983ELECTRON MICROSCOPY991270.7614
2.983-3.008ELECTRON MICROSCOPY962850.7721
3.008-3.032ELECTRON MICROSCOPY951250.778
3.032-3.057ELECTRON MICROSCOPY936210.7817
3.057-3.082ELECTRON MICROSCOPY922150.7902
3.083-3.108ELECTRON MICROSCOPY909010.801
3.108-3.134ELECTRON MICROSCOPY883890.8126
3.135-3.161ELECTRON MICROSCOPY869470.8212
3.161-3.188ELECTRON MICROSCOPY864930.8307
3.188-3.216ELECTRON MICROSCOPY849250.8382
3.216-3.244ELECTRON MICROSCOPY824970.8422
3.244-3.273ELECTRON MICROSCOPY820510.8456
3.273-3.302ELECTRON MICROSCOPY803290.8521
3.302-3.331ELECTRON MICROSCOPY789330.8556
3.331-3.361ELECTRON MICROSCOPY766990.858
3.361-3.392ELECTRON MICROSCOPY759570.8619
3.392-3.423ELECTRON MICROSCOPY753250.8686
3.424-3.455ELECTRON MICROSCOPY731550.8748
3.455-3.487ELECTRON MICROSCOPY717970.8805
3.488-3.521ELECTRON MICROSCOPY702970.883
3.521-3.554ELECTRON MICROSCOPY702690.8845
3.554-3.589ELECTRON MICROSCOPY669430.8856
3.589-3.624ELECTRON MICROSCOPY668610.8884
3.624-3.659ELECTRON MICROSCOPY654970.8912
3.66-3.696ELECTRON MICROSCOPY640950.8953
3.696-3.733ELECTRON MICROSCOPY629050.8991
3.733-3.771ELECTRON MICROSCOPY610450.9021
3.771-3.809ELECTRON MICROSCOPY611490.9048
3.81-3.849ELECTRON MICROSCOPY593830.9055
3.849-3.889ELECTRON MICROSCOPY579450.9058
3.889-3.93ELECTRON MICROSCOPY561610.9057
3.931-3.972ELECTRON MICROSCOPY553630.9069
3.973-4.015ELECTRON MICROSCOPY542730.9101
4.016-4.059ELECTRON MICROSCOPY531730.9141
4.06-4.104ELECTRON MICROSCOPY518850.9153
4.104-4.15ELECTRON MICROSCOPY512950.9151
4.15-4.197ELECTRON MICROSCOPY498450.9173
4.197-4.245ELECTRON MICROSCOPY486370.9205
4.245-4.294ELECTRON MICROSCOPY472390.9237
4.294-4.344ELECTRON MICROSCOPY465690.9248
4.344-4.396ELECTRON MICROSCOPY457690.9232
4.396-4.448ELECTRON MICROSCOPY440670.922
4.449-4.502ELECTRON MICROSCOPY432730.9222
4.502-4.557ELECTRON MICROSCOPY423330.9243
4.558-4.614ELECTRON MICROSCOPY415930.928
4.614-4.672ELECTRON MICROSCOPY400150.93
4.672-4.731ELECTRON MICROSCOPY391890.9302
4.732-4.792ELECTRON MICROSCOPY378610.93
4.793-4.855ELECTRON MICROSCOPY374550.9285
4.856-4.919ELECTRON MICROSCOPY363730.924
4.92-4.985ELECTRON MICROSCOPY350130.9196
4.986-5.053ELECTRON MICROSCOPY348490.9159
5.054-5.123ELECTRON MICROSCOPY333430.911
5.123-5.195ELECTRON MICROSCOPY328650.9048
5.195-5.268ELECTRON MICROSCOPY312850.8973
5.269-5.343ELECTRON MICROSCOPY306030.8904
5.345-5.422ELECTRON MICROSCOPY303130.8874
5.423-5.502ELECTRON MICROSCOPY287410.885
5.503-5.584ELECTRON MICROSCOPY284550.8788
5.586-5.67ELECTRON MICROSCOPY271570.8706
5.671-5.758ELECTRON MICROSCOPY270450.8622
5.759-5.849ELECTRON MICROSCOPY257770.8581
5.851-5.942ELECTRON MICROSCOPY244350.8563
5.943-6.038ELECTRON MICROSCOPY242770.8535
6.04-6.139ELECTRON MICROSCOPY233170.8507
6.14-6.242ELECTRON MICROSCOPY228510.8474
6.243-6.348ELECTRON MICROSCOPY217450.8401
6.35-6.459ELECTRON MICROSCOPY210330.8301
6.46-6.573ELECTRON MICROSCOPY207130.8235
6.574-6.692ELECTRON MICROSCOPY196470.8226
6.693-6.815ELECTRON MICROSCOPY188410.8264
6.816-6.941ELECTRON MICROSCOPY182170.8239
6.943-7.074ELECTRON MICROSCOPY177270.8186
7.075-7.211ELECTRON MICROSCOPY171250.8179
7.214-7.353ELECTRON MICROSCOPY161250.8223
7.356-7.503ELECTRON MICROSCOPY158710.8313
7.504-7.657ELECTRON MICROSCOPY152250.8361
7.659-7.818ELECTRON MICROSCOPY145330.8338
7.82-7.987ELECTRON MICROSCOPY137530.8261
7.988-8.16ELECTRON MICROSCOPY130590.8243
8.164-8.345ELECTRON MICROSCOPY129730.8338
8.35-8.537ELECTRON MICROSCOPY120210.8412
8.539-8.736ELECTRON MICROSCOPY117310.845
8.74-8.948ELECTRON MICROSCOPY109810.8558
8.951-9.169ELECTRON MICROSCOPY107250.8635
9.172-9.401ELECTRON MICROSCOPY101170.8618
9.404-9.645ELECTRON MICROSCOPY93750.8676
9.649-9.899ELECTRON MICROSCOPY91330.88
9.906-10.174ELECTRON MICROSCOPY85770.8918
10.177-10.46ELECTRON MICROSCOPY82270.9013
10.464-10.758ELECTRON MICROSCOPY75970.9108
10.768-11.084ELECTRON MICROSCOPY73770.911
11.089-11.425ELECTRON MICROSCOPY69010.9078
11.43-11.787ELECTRON MICROSCOPY63030.9079
11.793-12.173ELECTRON MICROSCOPY60730.9051
12.18-12.579ELECTRON MICROSCOPY56130.9068
12.593-13.027ELECTRON MICROSCOPY52750.9119
13.035-13.5ELECTRON MICROSCOPY49810.9092
13.509-13.999ELECTRON MICROSCOPY45330.9046
14.019-14.558ELECTRON MICROSCOPY43030.9108
14.569-15.151ELECTRON MICROSCOPY40170.9149
15.164-15.795ELECTRON MICROSCOPY35650.9188
15.81-16.496ELECTRON MICROSCOPY33010.9142
16.513-17.244ELECTRON MICROSCOPY29910.9111
17.281-18.103ELECTRON MICROSCOPY28570.9104
18.124-19.029ELECTRON MICROSCOPY25170.9158
19.08-20.027ELECTRON MICROSCOPY21790.9222
20.085-21.199ELECTRON MICROSCOPY20850.9182
21.234-22.481ELECTRON MICROSCOPY18610.9208
22.522-23.927ELECTRON MICROSCOPY16690.9369
24.077-25.571ELECTRON MICROSCOPY13110.9443
25.632-27.383ELECTRON MICROSCOPY12490.9515
27.533-29.644ELECTRON MICROSCOPY10890.9662
29.835-32.208ELECTRON MICROSCOPY9070.9783
32.33-34.942ELECTRON MICROSCOPY7290.9852
35.415-38.937ELECTRON MICROSCOPY6250.9893
39.153-43.474ELECTRON MICROSCOPY5710.9873
43.775-49.198ELECTRON MICROSCOPY3810.9817
49.636-56.644ELECTRON MICROSCOPY3010.9838
57.314-65.662ELECTRON MICROSCOPY2250.9859
67.815-81.055ELECTRON MICROSCOPY1750.9819
83.057-103.019ELECTRON MICROSCOPY1050.9702
107.225-131.324ELECTRON MICROSCOPY490.9754
151.64-371.44ELECTRON MICROSCOPY400.8834

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