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- PDB-9tdm: Cryo-EM structure of AccA3/AccD4/AccD5/AccE5 in complex with Prop... -

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Basic information

Entry
Database: PDB / ID: 9tdm
TitleCryo-EM structure of AccA3/AccD4/AccD5/AccE5 in complex with Propionyl-CoA
Components
  • (Propionyl-CoA carboxylase beta ...) x 2
  • Acetyl-/propionyl-coenzyme A carboxylase AccE5
  • Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit
KeywordsTRANSFERASE / Bio-dependent acyl-CoA carboxylase / long chain/short chain acyl-CoA carboxylase
Function / homology
Function and homology information


propionyl-CoA carboxylase / biotin carboxylase / propionyl-CoA carboxylase activity / acetyl-CoA carboxylase complex / biotin carboxylase activity / acetyl-CoA carboxylase activity / carbon fixation / fatty acid biosynthetic process / ATP binding / metal ion binding
Similarity search - Function
Biotin-dependent acetyl-/propionyl-coenzyme A carboxylase epsilon subunit / Acyl-CoA carboxylase epsilon subunit / : / : / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain ...Biotin-dependent acetyl-/propionyl-coenzyme A carboxylase epsilon subunit / Acyl-CoA carboxylase epsilon subunit / : / : / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain / Biotin-binding site / Biotin-requiring enzymes attachment site. / Biotin carboxylase-like, N-terminal domain / Biotin carboxylase, C-terminal / Biotin carboxylation domain / Biotin carboxylase, N-terminal domain / Biotin carboxylase C-terminal domain / Biotin carboxylation domain profile. / Biotin carboxylase C-terminal domain / Carbamoyl-phosphate synthase subdomain signature 1. / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / Biotin-requiring enzyme / Rudiment single hybrid motif / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / ClpP/crotonase-like domain superfamily / Carbamoyl-phosphate synthase subdomain signature 2.
Similarity search - Domain/homology
propionyl Coenzyme A / ADENOSINE-5'-TRIPHOSPHATE / Chem-BTI / Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit / Acetyl-/propionyl-coenzyme A carboxylase AccE5 / Propionyl-CoA carboxylase beta chain / Propionyl-CoA carboxylase beta chain
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsMullapudi, E. / Thai, H.M. / de Carvalho, L.P.S. / Wilmanns, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of AccA3/AccD4/AccD5/AccE5 in complex with Propionyl-CoA
Authors: Mullapudi, E. / Thai, H.M. / de Carvalho, L.P.S. / Wilmanns, M.
History
DepositionNov 24, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 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
A3a: Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit
A3b: Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit
A3c: Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit
A3d: Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit
A3e: Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit
A3f: Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit
A3g: Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit
A3h: Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit
D4a: Propionyl-CoA carboxylase beta chain
D4b: Propionyl-CoA carboxylase beta chain
D5a: Propionyl-CoA carboxylase beta chain
D5b: Propionyl-CoA carboxylase beta chain
D5c: Propionyl-CoA carboxylase beta chain
D5d: Propionyl-CoA carboxylase beta chain
E5a: Acetyl-/propionyl-coenzyme A carboxylase AccE5
E5b: Acetyl-/propionyl-coenzyme A carboxylase AccE5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)878,30827
Polymers872,85716
Non-polymers5,45011
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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Protein , 2 types, 10 molecules A3aA3bA3cA3dA3eA3fA3gA3hE5aE5b

#1: Protein
Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit


Mass: 63215.176 Da / Num. of mol.: 8 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QTE1, biotin carboxylase
#4: Protein Acetyl-/propionyl-coenzyme A carboxylase AccE5


Mass: 10357.693 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QTE6

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Propionyl-CoA carboxylase beta ... , 2 types, 6 molecules D4aD4bD5aD5bD5cD5d

#2: Protein Propionyl-CoA carboxylase beta chain


Mass: 56234.070 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R616, propionyl-CoA carboxylase
#3: Protein
Propionyl-CoA carboxylase beta chain


Mass: 58488.074 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QTE7, propionyl-CoA carboxylase

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Non-polymers , 3 types, 11 molecules

#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#6: Chemical
ChemComp-BTI / 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL


Mass: 228.311 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H16N2O2S / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-1VU / propionyl Coenzyme A


Mass: 823.597 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H40N7O17P3S / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
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: Cryo-EM structure of AccA3/AccD4/AccD5/AccE5 in complex with Propionyl-CoA
Type: COMPLEX / Entity ID: #1-#4 / Source: NATURAL
Molecular weightValue: 0.8 MDa / Experimental value: NO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTrisTris-HCl1
2150 mMSodium chlorideNaCl1
32 mMDTTDTT1
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277.15 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: 2250 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 44.4 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.4.1particle selection
2EPUimage acquisition
4cryoSPARC4.4.1CTF correction
7UCSF ChimeraX1.10.1model fitting
9Servalcatmodel refinement
10cryoSPARC4.4.1initial Euler assignment
11cryoSPARC4.4.1final Euler assignment
12cryoSPARC4.4.1classification
13cryoSPARC4.4.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 6398521
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 52469 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementResolution: 2.4→380.8 Å / Num. reflection obs: 8365654 / Average fsc work: 0.7075
Displacement parametersBiso mean: 131.43 Å2
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
ELECTRON MICROSCOPYs_bond_nonh_d0.0102590920.0119
ELECTRON MICROSCOPYs_angle_nonh_deg1.9935802421.819
ELECTRON MICROSCOPYs_dihedral_angle_1_deg7.425575865
ELECTRON MICROSCOPYs_dihedral_angle_2_deg6.016817885
ELECTRON MICROSCOPYs_dihedral_angle_3_deg10.7091482910
ELECTRON MICROSCOPYs_dihedral_angle_6_deg15.5369334510
ELECTRON MICROSCOPYs_chiral_restr0.079490950.1295
ELECTRON MICROSCOPYs_planes0.0069834220.02
ELECTRON MICROSCOPYs_nbd0.2051664570.2
ELECTRON MICROSCOPYs_nbtor0.2149982130.2
ELECTRON MICROSCOPYs_hbond_nbd0.09188640.2
LS refinement shell
Resolution (Å)Refine-IDNum. reflection obsFsc work
2.4-2.418ELECTRON MICROSCOPY1820410.3414
2.418-2.433ELECTRON MICROSCOPY1553970.3669
2.433-2.449ELECTRON MICROSCOPY1529290.3888
2.449-2.465ELECTRON MICROSCOPY1499790.4025
2.465-2.481ELECTRON MICROSCOPY1497490.4082
2.481-2.497ELECTRON MICROSCOPY1472370.4197
2.497-2.513ELECTRON MICROSCOPY1449430.4332
2.514-2.53ELECTRON MICROSCOPY1425850.4466
2.53-2.547ELECTRON MICROSCOPY1414170.4542
2.547-2.564ELECTRON MICROSCOPY1400950.4621
2.564-2.582ELECTRON MICROSCOPY1377930.474
2.582-2.599ELECTRON MICROSCOPY1357810.494
2.599-2.617ELECTRON MICROSCOPY1343610.5074
2.617-2.635ELECTRON MICROSCOPY1324870.5171
2.635-2.654ELECTRON MICROSCOPY1301770.5254
2.654-2.672ELECTRON MICROSCOPY1272090.5318
2.672-2.691ELECTRON MICROSCOPY1273510.5371
2.691-2.71ELECTRON MICROSCOPY1249530.5459
2.71-2.73ELECTRON MICROSCOPY1234090.55
2.73-2.749ELECTRON MICROSCOPY1207090.5564
2.749-2.769ELECTRON MICROSCOPY1191990.5628
2.769-2.79ELECTRON MICROSCOPY1189090.5762
2.79-2.81ELECTRON MICROSCOPY1164810.5918
2.81-2.831ELECTRON MICROSCOPY1136470.6088
2.831-2.852ELECTRON MICROSCOPY1131570.6226
2.852-2.874ELECTRON MICROSCOPY1107610.6384
2.874-2.896ELECTRON MICROSCOPY1104970.6542
2.896-2.918ELECTRON MICROSCOPY1069590.6699
2.918-2.94ELECTRON MICROSCOPY1062130.6801
2.941-2.963ELECTRON MICROSCOPY1053330.6921
2.963-2.987ELECTRON MICROSCOPY1027510.7071
2.987-3.01ELECTRON MICROSCOPY1010250.7207
3.01-3.034ELECTRON MICROSCOPY990370.7348
3.034-3.059ELECTRON MICROSCOPY991270.7509
3.059-3.083ELECTRON MICROSCOPY962850.7616
3.083-3.108ELECTRON MICROSCOPY951250.7649
3.109-3.134ELECTRON MICROSCOPY936210.7751
3.134-3.16ELECTRON MICROSCOPY922150.787
3.16-3.187ELECTRON MICROSCOPY909010.7995
3.187-3.213ELECTRON MICROSCOPY883890.8056
3.214-3.241ELECTRON MICROSCOPY869470.8104
3.241-3.269ELECTRON MICROSCOPY864930.8199
3.269-3.297ELECTRON MICROSCOPY849250.8336
3.297-3.326ELECTRON MICROSCOPY824970.8447
3.326-3.355ELECTRON MICROSCOPY820510.8517
3.355-3.385ELECTRON MICROSCOPY803290.861
3.385-3.415ELECTRON MICROSCOPY789330.8724
3.415-3.446ELECTRON MICROSCOPY766990.8814
3.446-3.477ELECTRON MICROSCOPY759570.8895
3.478-3.51ELECTRON MICROSCOPY753250.8967
3.51-3.542ELECTRON MICROSCOPY731550.9027
3.542-3.575ELECTRON MICROSCOPY717970.9065
3.576-3.609ELECTRON MICROSCOPY702970.91
3.61-3.644ELECTRON MICROSCOPY702690.912
3.644-3.679ELECTRON MICROSCOPY669430.916
3.679-3.715ELECTRON MICROSCOPY668610.9217
3.715-3.751ELECTRON MICROSCOPY654970.9264
3.752-3.789ELECTRON MICROSCOPY640950.9305
3.789-3.827ELECTRON MICROSCOPY629050.9344
3.827-3.866ELECTRON MICROSCOPY610450.9362
3.866-3.905ELECTRON MICROSCOPY611490.9382
3.906-3.946ELECTRON MICROSCOPY593830.9399
3.946-3.987ELECTRON MICROSCOPY579450.9425
3.987-4.029ELECTRON MICROSCOPY561610.9454
4.03-4.072ELECTRON MICROSCOPY553630.9491
4.073-4.117ELECTRON MICROSCOPY542730.9505
4.117-4.162ELECTRON MICROSCOPY531730.9501
4.162-4.207ELECTRON MICROSCOPY518850.9495
4.208-4.255ELECTRON MICROSCOPY512950.9507
4.255-4.303ELECTRON MICROSCOPY498450.9528
4.303-4.352ELECTRON MICROSCOPY486370.9543
4.352-4.402ELECTRON MICROSCOPY472390.955
4.402-4.453ELECTRON MICROSCOPY465690.9568
4.454-4.506ELECTRON MICROSCOPY457690.9593
4.507-4.56ELECTRON MICROSCOPY440670.9611
4.561-4.615ELECTRON MICROSCOPY432730.9624
4.616-4.672ELECTRON MICROSCOPY423330.9636
4.672-4.73ELECTRON MICROSCOPY415930.9646
4.731-4.79ELECTRON MICROSCOPY400150.9643
4.79-4.851ELECTRON MICROSCOPY391890.9619
4.851-4.913ELECTRON MICROSCOPY378610.958
4.914-4.977ELECTRON MICROSCOPY374550.9553
4.978-5.043ELECTRON MICROSCOPY363730.9563
5.044-5.111ELECTRON MICROSCOPY350130.956
5.112-5.181ELECTRON MICROSCOPY348490.9529
5.181-5.252ELECTRON MICROSCOPY333430.9471
5.253-5.325ELECTRON MICROSCOPY328650.9443
5.326-5.401ELECTRON MICROSCOPY312850.944
5.402-5.478ELECTRON MICROSCOPY306030.9422
5.479-5.559ELECTRON MICROSCOPY303130.9385
5.559-5.641ELECTRON MICROSCOPY287410.9349
5.642-5.725ELECTRON MICROSCOPY284550.9319
5.726-5.813ELECTRON MICROSCOPY271570.9283
5.814-5.903ELECTRON MICROSCOPY270450.9211
5.904-5.996ELECTRON MICROSCOPY257770.9149
5.999-6.092ELECTRON MICROSCOPY244350.9119
6.093-6.19ELECTRON MICROSCOPY242770.9112
6.192-6.294ELECTRON MICROSCOPY233170.9131
6.294-6.399ELECTRON MICROSCOPY228510.9143
6.4-6.508ELECTRON MICROSCOPY217450.911
6.51-6.622ELECTRON MICROSCOPY210330.9097
6.623-6.739ELECTRON MICROSCOPY207130.9107
6.74-6.86ELECTRON MICROSCOPY196470.9104
6.862-6.986ELECTRON MICROSCOPY188410.9044
6.987-7.116ELECTRON MICROSCOPY182170.9018
7.118-7.252ELECTRON MICROSCOPY177270.9027
7.254-7.393ELECTRON MICROSCOPY171250.9037
7.396-7.538ELECTRON MICROSCOPY161250.9058
7.541-7.692ELECTRON MICROSCOPY158710.9078
7.693-7.85ELECTRON MICROSCOPY152250.9097
7.852-8.016ELECTRON MICROSCOPY145330.9046
8.017-8.188ELECTRON MICROSCOPY137530.904
8.19-8.366ELECTRON MICROSCOPY130590.9049
8.37-8.556ELECTRON MICROSCOPY129730.8984
8.56-8.752ELECTRON MICROSCOPY120210.8971
8.755-8.956ELECTRON MICROSCOPY117310.9051
8.961-9.174ELECTRON MICROSCOPY109810.9105
9.177-9.4ELECTRON MICROSCOPY107250.914
9.403-9.638ELECTRON MICROSCOPY101170.9139
9.641-9.888ELECTRON MICROSCOPY93750.9109
9.892-10.148ELECTRON MICROSCOPY91330.9136
10.156-10.43ELECTRON MICROSCOPY85770.922
10.434-10.724ELECTRON MICROSCOPY82270.9228
10.728-11.03ELECTRON MICROSCOPY75970.9165
11.039-11.363ELECTRON MICROSCOPY73770.9165
11.368-11.713ELECTRON MICROSCOPY69010.9213
11.718-12.084ELECTRON MICROSCOPY63030.9229
12.09-12.48ELECTRON MICROSCOPY60730.9237
12.487-12.896ELECTRON MICROSCOPY56130.9338
12.91-13.355ELECTRON MICROSCOPY52750.9377
13.363-13.84ELECTRON MICROSCOPY49810.9347
13.85-14.352ELECTRON MICROSCOPY45330.9341
14.372-14.925ELECTRON MICROSCOPY43030.9353
14.936-15.533ELECTRON MICROSCOPY40170.9292
15.546-16.193ELECTRON MICROSCOPY35650.9277
16.208-16.912ELECTRON MICROSCOPY33010.9373
16.929-17.678ELECTRON MICROSCOPY29910.9457
17.716-18.559ELECTRON MICROSCOPY28570.9481
18.581-19.509ELECTRON MICROSCOPY25170.9531
19.56-20.531ELECTRON MICROSCOPY21790.9571
20.591-21.733ELECTRON MICROSCOPY20850.9586
21.769-23.047ELECTRON MICROSCOPY18610.9494
23.089-24.529ELECTRON MICROSCOPY16690.9376
24.684-26.215ELECTRON MICROSCOPY13110.9482
26.278-28.073ELECTRON MICROSCOPY12490.9541
28.227-30.391ELECTRON MICROSCOPY10890.9551
30.587-33.02ELECTRON MICROSCOPY9070.9611
33.144-35.823ELECTRON MICROSCOPY7290.9615
36.308-39.919ELECTRON MICROSCOPY6250.9498
40.14-44.569ELECTRON MICROSCOPY5710.9263
44.878-50.438ELECTRON MICROSCOPY3810.9386
50.887-58.071ELECTRON MICROSCOPY3010.9575
58.759-67.317ELECTRON MICROSCOPY2250.9636
69.524-83.097ELECTRON MICROSCOPY1750.9703
85.149-105.615ELECTRON MICROSCOPY1050.9236
109.927-134.633ELECTRON MICROSCOPY490.6822
155.461-380.8ELECTRON MICROSCOPY400.8248

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