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- PDB-9t97: cryo-EM structure of AccA3/AccD4/AccD5/AccE5 complex from Mycobac... -

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Basic information

Entry
Database: PDB / ID: 9t97
Titlecryo-EM structure of AccA3/AccD4/AccD5/AccE5 complex from Mycobacterium smegmatis
Components
  • (Propionyl-CoA carboxylase beta chain) 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
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: 2.35 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)4/AccE5 complex from Mycobacterium smegmatis
Authors: Mullapudi, E. / Thai, H.M. / de Carvalho, L.P.S. / Wilmanns, M.
History
DepositionNov 14, 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
A3f: Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit
A3g: Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit
A3i: 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)810,78420
Polymers809,64215
Non-polymers1,1425
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A3a
21A3b
32A3a
42A3c
53A3a
63A3d
74A3a
84A3f
95A3a
105A3g
116A3a
126A3i
137A3b
147A3c
158A3b
168A3d
179A3b
189A3f
1910A3b
2010A3g
2111A3b
2211A3i
2312A3c
2412A3d
2513A3c
2613A3f
2714A3c
2814A3g
2915A3c
3015A3i
3116A3d
3216A3f
3317A3d
3417A3g
3518A3d
3618A3i
3719A3f
3819A3g
3920A3f
4020A3i
4121A3g
4221A3i
4322D4a
4422D4b
4523D5a
4623D5b
4724D5a
4824D5c
4925D5a
5025D5d
5126D5b
5226D5c
5327D5b
5427D5d
5528D5c
5628D5d
5729E5a
5829E5b

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LYSLYSLYSLYSA3aA8 - 5988 - 598
211LYSLYSLYSLYSA3bB8 - 5988 - 598
322ILEILEVALVALA3aA9 - 4909 - 490
422ILEILEVALVALA3cC9 - 4909 - 490
533LYSLYSLYSLYSA3aA8 - 5988 - 598
633LYSLYSLYSLYSA3dD8 - 5988 - 598
744ILEILELYSLYSA3aA9 - 5989 - 598
844LYSLYSLYSLYSA3fE525 - 598525 - 598
955LYSLYSLYSLYSA3aA8 - 5988 - 598
1055LYSLYSLYSLYSA3gF525 - 598525 - 598
1166LYSLYSLYSLYSA3aA8 - 5988 - 598
1266GLYGLYGLYGLYA3iG508 - 520508 - 520
1377ILEILEVALVALA3bB9 - 4909 - 490
1477ILEILEVALVALA3cC9 - 4909 - 490
1588SERSERLYSLYSA3bB7 - 5987 - 598
1688SERSERLYSLYSA3dD7 - 5987 - 598
1799ILEILELYSLYSA3bB9 - 5989 - 598
1899LYSLYSLYSLYSA3fE525 - 598525 - 598
191010SERSERLYSLYSA3bB7 - 5987 - 598
201010LYSLYSLYSLYSA3gF525 - 598525 - 598
211111SERSERLYSLYSA3bB7 - 5987 - 598
221111GLYGLYGLYGLYA3iG508 - 520508 - 520
231212ILEILEVALVALA3cC9 - 4909 - 490
241212ILEILEVALVALA3dD9 - 4909 - 490
251313ILEILEVALVALA3cC9 - 4909 - 490
261313LYSLYSLYSLYSA3fE525 - 598525 - 598
271414ILEILEVALVALA3cC9 - 4909 - 490
281414LYSLYSLYSLYSA3gF525 - 598525 - 598
291515ILEILEVALVALA3cC9 - 4909 - 490
301515GLYGLYGLYGLYA3iG508 - 520508 - 520
311616ILEILELYSLYSA3dD9 - 5989 - 598
321616LYSLYSLYSLYSA3fE525 - 598525 - 598
331717SERSERLYSLYSA3dD7 - 5987 - 598
341717LYSLYSLYSLYSA3gF525 - 598525 - 598
351818SERSERLYSLYSA3dD7 - 5987 - 598
361818GLYGLYGLYGLYA3iG508 - 520508 - 520
371919LYSLYSLYSLYSA3fE525 - 598525 - 598
381919LYSLYSLYSLYSA3gF525 - 598525 - 598
392020LYSLYSLYSLYSA3fE525 - 598525 - 598
402020GLYGLYGLYGLYA3iG508 - 520508 - 520
412121LYSLYSLYSLYSA3gF525 - 598525 - 598
422121GLYGLYGLYGLYA3iG508 - 520508 - 520
432222ASNASNLEULEUD4aH3 - 5173 - 517
442222ASNASNLEULEUD4bI3 - 5173 - 517
452323ASPASPLEULEUD5aJ14 - 54214 - 542
462323ASPASPLEULEUD5bK14 - 54214 - 542
472424ASPASPLEULEUD5aJ14 - 54214 - 542
482424ASPASPLEULEUD5cL14 - 54214 - 542
492525ASPASPLEULEUD5aJ14 - 54214 - 542
502525ASPASPLEULEUD5dM14 - 54214 - 542
512626ASPASPLEULEUD5bK14 - 54214 - 542
522626ASPASPLEULEUD5cL14 - 54214 - 542
532727ASPASPLEULEUD5bK14 - 54214 - 542
542727ASPASPLEULEUD5dM14 - 54214 - 542
552828ASPASPLEULEUD5cL14 - 54214 - 542
562828ASPASPLEULEUD5dM14 - 54214 - 542
572929ALAALAARGARGE5aN28 - 9428 - 94
582929GLUGLUARGARGE5bO63 - 9463 - 94

NCS ensembles :
IDDetails (eV)
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 1 3
3Local NCS retraints between domains: 1 4
4Local NCS retraints between domains: 1 5
5Local NCS retraints between domains: 1 6
6Local NCS retraints between domains: 1 7
7Local NCS retraints between domains: 1 8
8Local NCS retraints between domains: 2 3
9Local NCS retraints between domains: 2 4
10Local NCS retraints between domains: 2 5
11Local NCS retraints between domains: 2 6
12Local NCS retraints between domains: 2 7
13Local NCS retraints between domains: 2 8
14Local NCS retraints between domains: 3 4
15Local NCS retraints between domains: 3 5
16Local NCS retraints between domains: 3 6
17Local NCS retraints between domains: 3 7
18Local NCS retraints between domains: 3 8
19Local NCS retraints between domains: 4 5
20Local NCS retraints between domains: 4 6
21Local NCS retraints between domains: 4 7
22Local NCS retraints between domains: 4 8
23Local NCS retraints between domains: 5 6
24Local NCS retraints between domains: 5 7
25Local NCS retraints between domains: 5 8
26Local NCS retraints between domains: 6 7
27Local NCS retraints between domains: 6 8
28Local NCS retraints between domains: 7 8
29Local NCS retraints between domains: 9 10
30Local NCS retraints between domains: 11 12
31Local NCS retraints between domains: 11 13
32Local NCS retraints between domains: 11 14
33Local NCS retraints between domains: 12 13
34Local NCS retraints between domains: 12 14
35Local NCS retraints between domains: 13 14
36Local NCS retraints between domains: 15 16

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Components

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


Mass: 63215.176 Da / Num. of mol.: 7 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QTE1, biotin carboxylase
#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
#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
#5: 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
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: AccA3/AccD4/AccD5/AccE5 complex from Mycobacterium smegmatis
Type: COMPLEX / Entity ID: #1-#4 / Source: NATURAL
Molecular weightValue: 0.275 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: 1279569
3D reconstructionResolution: 2.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 251974 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementResolution: 2.35→184.96 Å / Cor.coef. Fo:Fc: 0.895 / WRfactor Rwork: 0.344 / SU B: 6.933 / SU ML: 0.142 / Average fsc free: 0 / Average fsc overall: 0.7489 / Average fsc work: 0.7489 / ESU R: 0.193
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rwork0.3438 910016 -
all0.344 --
Rfree--0 %
obs--100 %
Solvent computationSolvent model: NONE
Displacement parametersBiso mean: 156.578 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0090.01243006
ELECTRON MICROSCOPYr_bond_other_d00.01641301
ELECTRON MICROSCOPYr_angle_refined_deg1.9071.82558368
ELECTRON MICROSCOPYr_angle_other_deg0.6311.75495091
ELECTRON MICROSCOPYr_dihedral_angle_1_deg6.88655542
ELECTRON MICROSCOPYr_dihedral_angle_2_deg6.2645323
ELECTRON MICROSCOPYr_dihedral_angle_3_deg11.946107026
ELECTRON MICROSCOPYr_dihedral_angle_6_deg15.931101883
ELECTRON MICROSCOPYr_chiral_restr0.0880.26621
ELECTRON MICROSCOPYr_gen_planes_refined0.0070.0251299
ELECTRON MICROSCOPYr_gen_planes_other0.0010.029401
ELECTRON MICROSCOPYr_nbd_refined0.1790.25861
ELECTRON MICROSCOPYr_symmetry_nbd_other0.1770.229800
ELECTRON MICROSCOPYr_nbtor_refined0.1490.219573
ELECTRON MICROSCOPYr_symmetry_nbtor_other0.0710.220364
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.080.2357
ELECTRON MICROSCOPYr_mcbond_it5.6915.47722231
ELECTRON MICROSCOPYr_mcbond_other5.6915.47722231
ELECTRON MICROSCOPYr_mcangle_it8.52527.97827752
ELECTRON MICROSCOPYr_mcangle_other8.52527.97827753
ELECTRON MICROSCOPYr_scbond_it7.34816.11620775
ELECTRON MICROSCOPYr_scbond_other7.34816.11620776
ELECTRON MICROSCOPYr_scangle_it11.74829.40830616
ELECTRON MICROSCOPYr_scangle_other11.74829.40830617
ELECTRON MICROSCOPYr_lrange_it17.018186.321151044
ELECTRON MICROSCOPYr_lrange_other17.018186.321151045
ELECTRON MICROSCOPYr_ncsr_local_group_10.2230.0512535
ELECTRON MICROSCOPYr_ncsr_local_group_20.2250.0511120
ELECTRON MICROSCOPYr_ncsr_local_group_30.2270.0512359
ELECTRON MICROSCOPYr_ncsr_local_group_40.2320.0511057
ELECTRON MICROSCOPYr_ncsr_local_group_50.2350.0512199
ELECTRON MICROSCOPYr_ncsr_local_group_60.220.0511205
ELECTRON MICROSCOPYr_ncsr_local_group_70.2920.051276
ELECTRON MICROSCOPYr_ncsr_local_group_80.1280.0513118
ELECTRON MICROSCOPYr_ncsr_local_group_90.1070.0513636
ELECTRON MICROSCOPYr_ncsr_local_group_100.1120.0513679
ELECTRON MICROSCOPYr_ncsr_local_group_110.1010.0513704
ELECTRON MICROSCOPYr_ncsr_local_group_120.0940.0513822
ELECTRON MICROSCOPYr_ncsr_local_group_130.1050.0513693
ELECTRON MICROSCOPYr_ncsr_local_group_140.110.0513694
ELECTRON MICROSCOPYr_ncsr_local_group_150.1560.05800
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11A3aELECTRON MICROSCOPYLocal ncs0.222650.05004
12A3aELECTRON MICROSCOPYLocal ncs0.222650.05004
23A3aELECTRON MICROSCOPYLocal ncs0.224610.05004
24A3aELECTRON MICROSCOPYLocal ncs0.224610.05004
35A3aELECTRON MICROSCOPYLocal ncs0.226590.05004
36A3aELECTRON MICROSCOPYLocal ncs0.226590.05004
47A3aELECTRON MICROSCOPYLocal ncs0.231920.05004
48A3aELECTRON MICROSCOPYLocal ncs0.231920.05004
59A3aELECTRON MICROSCOPYLocal ncs0.234980.05004
510A3aELECTRON MICROSCOPYLocal ncs0.234980.05004
611A3aELECTRON MICROSCOPYLocal ncs0.219710.05004
612A3aELECTRON MICROSCOPYLocal ncs0.219710.05004
713A3aELECTRON MICROSCOPYLocal ncs0.291730.05003
714A3aELECTRON MICROSCOPYLocal ncs0.291730.05003
815A3aELECTRON MICROSCOPYLocal ncs0.12850.05007
816A3aELECTRON MICROSCOPYLocal ncs0.12850.05007
917A3aELECTRON MICROSCOPYLocal ncs0.106520.05008
918A3aELECTRON MICROSCOPYLocal ncs0.106520.05008
1019A3aELECTRON MICROSCOPYLocal ncs0.111910.05008
1020A3aELECTRON MICROSCOPYLocal ncs0.111910.05008
1121A3aELECTRON MICROSCOPYLocal ncs0.101350.05008
1122A3aELECTRON MICROSCOPYLocal ncs0.101350.05008
1223A3aELECTRON MICROSCOPYLocal ncs0.093670.05008
1224A3aELECTRON MICROSCOPYLocal ncs0.093670.05008
1325A3aELECTRON MICROSCOPYLocal ncs0.104770.05008
1326A3aELECTRON MICROSCOPYLocal ncs0.104770.05008
1427A3aELECTRON MICROSCOPYLocal ncs0.109820.05008
1428A3aELECTRON MICROSCOPYLocal ncs0.109820.05008
1529A3aELECTRON MICROSCOPYLocal ncs0.156340.05008
1530A3aELECTRON MICROSCOPYLocal ncs0.156340.05008
LS refinement shell

Refine-ID: ELECTRON MICROSCOPY / Num. reflection Rfree: _ / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc workWRfactor Rwork
2.35-2.4110.713674180.713674180.3740.713
2.411-2.4770.591655820.591655820.460.591
2.477-2.5490.562638500.562638500.5280.562
2.549-2.6270.539620320.539620320.5880.539
2.627-2.7130.508601020.508601020.6450.508
2.713-2.8090.464580720.464580720.70.464
2.809-2.9150.417560490.417560490.7630.417
2.915-3.0340.364539770.364539770.8150.364
3.034-3.1690.308516440.308516440.8650.308
3.169-3.3230.283495920.283495920.90.283
3.323-3.5030.27469600.27469600.9290.27
3.503-3.7150.265445680.265445680.9420.265
3.715-3.9720.261416900.261416900.9510.261
3.972-4.290.246389180.246389180.9550.246
4.29-4.6990.229357370.229357370.9610.229
4.699-5.2530.214323340.214323340.9530.214
5.253-6.0650.252286090.252286090.9220.252
6.065-7.4260.372240250.372240250.8820.372
7.426-10.4930.395186290.395186290.8490.395
10.493-184.960.678102290.678102290.9330.678

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  • 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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