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- PDB-9y3p: Eukaryotic translation initiation factor 2-B in its apo form (act... -

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Basic information

Entry
Database: PDB / ID: 9y3p
TitleEukaryotic translation initiation factor 2-B in its apo form (active-state)
Components
  • (Translation initiation factor eIF2B subunit ...) x 5
  • Translation initiation factor eIF-2B subunit alpha
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
IMIDAZOLE / 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: 2.9 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: Pharmacological activation and viral suppression of the integrated stress response reveal a disordering switch in eIF2B
Authors: Dalwadi, U. / Subramanian, 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

Downloads & links

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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 eIF2B subunit delta
F: Translation initiation factor eIF2B subunit delta
G: Translation initiation factor eIF-2B subunit alpha
H: Translation initiation factor eIF-2B subunit alpha
I: Translation initiation factor eIF2B subunit gamma
J: Translation initiation factor eIF2B subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)425,44425
Polymers424,78510
Non-polymers65915
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 ... , 5 types, 8 molecules ABCDEFIJ

#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: 38395.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2B2, EIF2BB / Production host: Escherichia coli (E. coli) / References: UniProt: P49770
#3: Protein Translation initiation factor eIF2B subunit delta / eIF2B GDP-GTP exchange factor subunit delta


Mass: 39617.582 Da / Num. of mol.: 1
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
#4: Protein Translation initiation factor eIF2B subunit delta / eIF2B GDP-GTP exchange factor subunit delta


Mass: 39489.453 Da / Num. of mol.: 1
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
#6: Protein Translation initiation factor eIF2B subunit gamma / eIF2B GDP-GTP exchange factor subunit gamma


Mass: 49304.109 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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Protein , 1 types, 2 molecules GH

#5: Protein Translation initiation factor eIF-2B subunit alpha / eIF-2B 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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Non-polymers , 3 types, 15 molecules

#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#9: 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-#6 / 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: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 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: 2 / Num. of real images: 18826
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 10 eV
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.2.1particle selection
2EPUimage acquisition
4cryoSPARC4.2.1CTF correction
7ISOLDEmodel fitting
9Servalcatmodel refinement
10cryoSPARC4.2.1initial Euler assignment
11cryoSPARC4.2.1final Euler assignment
12cryoSPARC4.2.1classification
13cryoSPARC4.2.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 890578
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 60012 / 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: 2.9→457.523 Å / Num. reflection obs: 8225149 / Average fsc work: 0.789
Displacement parametersBiso mean: 64.4 Å2
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
ELECTRON MICROSCOPYs_bond_nonh_d0.008294590.0119
ELECTRON MICROSCOPYs_angle_nonh_deg1.7153399101.8236
ELECTRON MICROSCOPYs_dihedral_angle_1_deg7.391236935
ELECTRON MICROSCOPYs_dihedral_angle_2_deg3.98498995
ELECTRON MICROSCOPYs_dihedral_angle_3_deg11.1609793210
ELECTRON MICROSCOPYs_dihedral_angle_6_deg15.0625146310
ELECTRON MICROSCOPYs_chiral_restr0.067546570.131
ELECTRON MICROSCOPYs_planes0.0053408960.02
ELECTRON MICROSCOPYs_nbd0.2104412670.2
ELECTRON MICROSCOPYs_nbtor0.2263529060.2
ELECTRON MICROSCOPYs_hbond_nbd0.11587030.2
ELECTRON MICROSCOPYs_metal_ion0.225830.2
LS refinement shell
Resolution (Å)Refine-IDNum. reflection obsFsc work
2.9-2.923ELECTRON MICROSCOPY1969330.4135
2.923-2.942ELECTRON MICROSCOPY1529290.4494
2.942-2.961ELECTRON MICROSCOPY1499790.4766
2.961-2.981ELECTRON MICROSCOPY1497490.4957
2.981-3ELECTRON MICROSCOPY1472370.5092
3-3.02ELECTRON MICROSCOPY1449430.5238
3.02-3.04ELECTRON MICROSCOPY1425850.54
3.04-3.06ELECTRON MICROSCOPY1414170.5592
3.06-3.081ELECTRON MICROSCOPY1400950.576
3.081-3.102ELECTRON MICROSCOPY1377930.5935
3.102-3.123ELECTRON MICROSCOPY1357810.6118
3.123-3.144ELECTRON MICROSCOPY1343610.6285
3.145-3.166ELECTRON MICROSCOPY1324870.6452
3.166-3.188ELECTRON MICROSCOPY1301770.6634
3.188-3.211ELECTRON MICROSCOPY1272090.6809
3.211-3.233ELECTRON MICROSCOPY1273510.6975
3.233-3.256ELECTRON MICROSCOPY1249530.7125
3.256-3.28ELECTRON MICROSCOPY1234090.7275
3.28-3.303ELECTRON MICROSCOPY1207090.741
3.303-3.327ELECTRON MICROSCOPY1191990.7523
3.327-3.352ELECTRON MICROSCOPY1189090.7656
3.352-3.376ELECTRON MICROSCOPY1164810.779
3.377-3.402ELECTRON MICROSCOPY1136470.7921
3.402-3.427ELECTRON MICROSCOPY1131570.8048
3.427-3.453ELECTRON MICROSCOPY1107610.8149
3.453-3.479ELECTRON MICROSCOPY1104970.8244
3.479-3.506ELECTRON MICROSCOPY1069590.834
3.506-3.533ELECTRON MICROSCOPY1062130.8434
3.533-3.56ELECTRON MICROSCOPY1053330.8529
3.561-3.588ELECTRON MICROSCOPY1027510.8596
3.588-3.617ELECTRON MICROSCOPY1010250.8654
3.617-3.645ELECTRON MICROSCOPY990370.8696
3.646-3.675ELECTRON MICROSCOPY991270.8749
3.675-3.705ELECTRON MICROSCOPY962850.8802
3.705-3.735ELECTRON MICROSCOPY951250.8875
3.735-3.766ELECTRON MICROSCOPY936210.8936
3.766-3.797ELECTRON MICROSCOPY922150.8987
3.797-3.829ELECTRON MICROSCOPY909010.902
3.829-3.861ELECTRON MICROSCOPY883890.9049
3.861-3.893ELECTRON MICROSCOPY869470.9062
3.894-3.927ELECTRON MICROSCOPY864930.9082
3.927-3.961ELECTRON MICROSCOPY849250.9139
3.961-3.996ELECTRON MICROSCOPY824970.9205
3.996-4.031ELECTRON MICROSCOPY820510.9257
4.031-4.067ELECTRON MICROSCOPY803290.9274
4.067-4.103ELECTRON MICROSCOPY789330.9272
4.103-4.14ELECTRON MICROSCOPY766990.928
4.141-4.178ELECTRON MICROSCOPY759570.9306
4.178-4.217ELECTRON MICROSCOPY753250.9346
4.217-4.256ELECTRON MICROSCOPY731550.9369
4.256-4.296ELECTRON MICROSCOPY717970.9385
4.296-4.337ELECTRON MICROSCOPY702970.9392
4.337-4.378ELECTRON MICROSCOPY702690.9397
4.378-4.42ELECTRON MICROSCOPY669430.9417
4.421-4.463ELECTRON MICROSCOPY668610.9436
4.464-4.507ELECTRON MICROSCOPY654970.9442
4.508-4.552ELECTRON MICROSCOPY640950.9432
4.553-4.598ELECTRON MICROSCOPY629050.9421
4.598-4.644ELECTRON MICROSCOPY610450.9416
4.645-4.692ELECTRON MICROSCOPY611490.9428
4.693-4.741ELECTRON MICROSCOPY593830.9452
4.741-4.791ELECTRON MICROSCOPY579450.9464
4.791-4.841ELECTRON MICROSCOPY561610.9466
4.842-4.893ELECTRON MICROSCOPY553630.9441
4.893-4.946ELECTRON MICROSCOPY542730.9419
4.946-5ELECTRON MICROSCOPY531730.9404
5-5.055ELECTRON MICROSCOPY518850.9381
5.056-5.112ELECTRON MICROSCOPY512950.935
5.112-5.17ELECTRON MICROSCOPY498450.9307
5.17-5.229ELECTRON MICROSCOPY486370.9265
5.229-5.289ELECTRON MICROSCOPY472390.9227
5.289-5.351ELECTRON MICROSCOPY465690.9199
5.351-5.414ELECTRON MICROSCOPY457690.9174
5.415-5.479ELECTRON MICROSCOPY440670.9145
5.48-5.545ELECTRON MICROSCOPY432730.9107
5.546-5.613ELECTRON MICROSCOPY423330.906
5.614-5.683ELECTRON MICROSCOPY415930.901
5.684-5.755ELECTRON MICROSCOPY400150.8943
5.755-5.828ELECTRON MICROSCOPY391890.8888
5.828-5.903ELECTRON MICROSCOPY378610.8863
5.904-5.98ELECTRON MICROSCOPY374550.8859
5.981-6.06ELECTRON MICROSCOPY363730.8825
6.06-6.14ELECTRON MICROSCOPY350130.8762
6.141-6.224ELECTRON MICROSCOPY348490.8705
6.225-6.31ELECTRON MICROSCOPY333430.8665
6.311-6.398ELECTRON MICROSCOPY328650.8651
6.399-6.489ELECTRON MICROSCOPY312850.8636
6.49-6.582ELECTRON MICROSCOPY306030.8643
6.583-6.679ELECTRON MICROSCOPY303130.8677
6.679-6.778ELECTRON MICROSCOPY287410.8668
6.778-6.879ELECTRON MICROSCOPY284550.8587
6.88-6.984ELECTRON MICROSCOPY271570.8504
6.985-7.093ELECTRON MICROSCOPY270450.8456
7.094-7.204ELECTRON MICROSCOPY257770.8451
7.207-7.32ELECTRON MICROSCOPY244350.8508
7.321-7.438ELECTRON MICROSCOPY242770.8593
7.44-7.562ELECTRON MICROSCOPY233170.8661
7.563-7.689ELECTRON MICROSCOPY228510.8685
7.69-7.819ELECTRON MICROSCOPY217450.8692
7.821-7.956ELECTRON MICROSCOPY210330.8682
7.957-8.097ELECTRON MICROSCOPY207130.8669
8.098-8.243ELECTRON MICROSCOPY196470.8655
8.244-8.394ELECTRON MICROSCOPY188410.87
8.395-8.549ELECTRON MICROSCOPY182170.8772
8.552-8.714ELECTRON MICROSCOPY177270.8851
8.715-8.883ELECTRON MICROSCOPY171250.8854
8.886-9.057ELECTRON MICROSCOPY161250.8874
9.06-9.241ELECTRON MICROSCOPY158710.8931
9.243-9.432ELECTRON MICROSCOPY152250.8994
9.434-9.63ELECTRON MICROSCOPY145330.9025
9.633-9.838ELECTRON MICROSCOPY137530.9039
9.84-10.051ELECTRON MICROSCOPY130590.9083
10.056-10.279ELECTRON MICROSCOPY129730.9178
10.285-10.516ELECTRON MICROSCOPY120210.9276
10.518-10.76ELECTRON MICROSCOPY117310.9325
10.766-11.022ELECTRON MICROSCOPY109810.9346
11.025-11.294ELECTRON MICROSCOPY107250.9341
11.298-11.58ELECTRON MICROSCOPY101170.9327
11.584-11.881ELECTRON MICROSCOPY93750.9309
11.885-12.193ELECTRON MICROSCOPY91330.9304
12.202-12.531ELECTRON MICROSCOPY85770.9307
12.536-12.884ELECTRON MICROSCOPY82270.9308
12.889-13.252ELECTRON MICROSCOPY75970.933
13.263-13.653ELECTRON MICROSCOPY73770.9277
13.659-14.073ELECTRON MICROSCOPY69010.9223
14.079-14.519ELECTRON MICROSCOPY63030.9235
14.526-14.995ELECTRON MICROSCOPY60730.9285
15.003-15.494ELECTRON MICROSCOPY56130.9329
15.511-16.046ELECTRON MICROSCOPY52750.9341
16.056-16.629ELECTRON MICROSCOPY49810.9304
16.64-17.244ELECTRON MICROSCOPY45330.9294
17.268-17.932ELECTRON MICROSCOPY43030.9246
17.946-18.663ELECTRON MICROSCOPY40170.9258
18.678-19.456ELECTRON MICROSCOPY35650.9247
19.473-20.319ELECTRON MICROSCOPY33010.9185
20.339-21.24ELECTRON MICROSCOPY29910.9184
21.286-22.298ELECTRON MICROSCOPY28570.9303
22.325-23.44ELECTRON MICROSCOPY25170.9411
23.501-24.668ELECTRON MICROSCOPY21790.9499
24.74-26.112ELECTRON MICROSCOPY20850.954
26.155-27.691ELECTRON MICROSCOPY18610.9573
27.741-29.472ELECTRON MICROSCOPY16690.9594
29.657-31.497ELECTRON MICROSCOPY13110.9614
31.572-33.729ELECTRON MICROSCOPY12490.9674
33.914-36.514ELECTRON MICROSCOPY10890.9808
36.749-39.672ELECTRON MICROSCOPY9070.9865
39.822-43.04ELECTRON MICROSCOPY7290.9876
43.623-47.961ELECTRON MICROSCOPY6250.9886
48.227-53.549ELECTRON MICROSCOPY5710.9902
53.92-60.6ELECTRON MICROSCOPY3810.9914
61.139-69.772ELECTRON MICROSCOPY3010.991
70.597-80.879ELECTRON MICROSCOPY2250.9939
83.532-99.84ELECTRON MICROSCOPY1750.9967
102.305-126.894ELECTRON MICROSCOPY1050.9977
132.076-161.759ELECTRON MICROSCOPY490.9978
186.783-457.523ELECTRON MICROSCOPY400.8785

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