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- PDB-9sku: Cryo-EM structure of H. neapolitanus CsoSCA in reducing condition... -

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Basic information

Entry
Database: PDB / ID: 9sku
TitleCryo-EM structure of H. neapolitanus CsoSCA in reducing conditions, hexamer
ComponentsMaltose/maltodextrin-binding periplasmic protein,Carboxysome shell carbonic anhydrase
KeywordsLYASE / Carbonic anhydrase / carboxysome / CO2 concentration mechanism
Function / homology
Function and homology information


carboxysome / carbon fixation / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing ...carboxysome / carbon fixation / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / carbonic anhydrase / carbonate dehydratase activity / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane / metal ion binding
Similarity search - Function
Carboxysome shell carbonic anhydrase / Carboxysome shell carbonic anhydrase, N-terminal / Carboxysome shell carbonic anhydrase, C-terminal / : / : / : / Carboxysome Shell Carbonic Anhydrase, C-terminal / Carboxysome Shell Carbonic Anhydrase, catalytic domain / Carboxysome Shell Carbonic Anhydrase, N-terminal / Maltose/Cyclodextrin ABC transporter, substrate-binding protein ...Carboxysome shell carbonic anhydrase / Carboxysome shell carbonic anhydrase, N-terminal / Carboxysome shell carbonic anhydrase, C-terminal / : / : / : / Carboxysome Shell Carbonic Anhydrase, C-terminal / Carboxysome Shell Carbonic Anhydrase, catalytic domain / Carboxysome Shell Carbonic Anhydrase, N-terminal / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
Carboxysome shell carbonic anhydrase / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Halothiobacillus neapolitanus c2 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.06 Å
AuthorsGaullier, G. / Vogiatzi, N. / Blikstad, C.
Funding support Sweden, 3items
OrganizationGrant numberCountry
Swedish Research Council2019-03700_VR Sweden
Formas, a Swedish research council for sustainable development2019-01171_Formas Sweden
Swedish Research Council2023-05296_VR Sweden
CitationJournal: Biorxiv / Year: 2026
Title: Molecular mechanism of redox regulation of the alpha-carboxysomal carbonic anhydrase CsoSCA
Authors: Vogiatzi, N. / Gaullier, G. / Leufstadius, J. / Andersson, T. / Scherbauer, T. / Blikstad, C.
History
DepositionSep 2, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Mask / Part number: 2 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Mask / Part number: 3 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 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: Maltose/maltodextrin-binding periplasmic protein,Carboxysome shell carbonic anhydrase
B: Maltose/maltodextrin-binding periplasmic protein,Carboxysome shell carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,2204
Polymers204,0902
Non-polymers1312
Water7,170398
1
A: Maltose/maltodextrin-binding periplasmic protein,Carboxysome shell carbonic anhydrase
B: Maltose/maltodextrin-binding periplasmic protein,Carboxysome shell carbonic anhydrase
hetero molecules

A: Maltose/maltodextrin-binding periplasmic protein,Carboxysome shell carbonic anhydrase
B: Maltose/maltodextrin-binding periplasmic protein,Carboxysome shell carbonic anhydrase
hetero molecules

A: Maltose/maltodextrin-binding periplasmic protein,Carboxysome shell carbonic anhydrase
B: Maltose/maltodextrin-binding periplasmic protein,Carboxysome shell carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)612,66112
Polymers612,2696
Non-polymers3926
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation2
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
2generate(-0.5, -0.866025404), (0.866025404, -0.5), (1)369.099963, 98.900037
3generate(-0.5, 0.866025404), (-0.866025404, -0.5), (1)98.900037, 369.099963

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Components

#1: Protein Maltose/maltodextrin-binding periplasmic protein,Carboxysome shell carbonic anhydrase / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / CsoSCA / Carbonic anhydrase / ...MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / CsoSCA / Carbonic anhydrase / CA / Carboxysome shell protein CsoS3


Mass: 102044.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: This is a fusion protein with an N-terminal Strep-MBP tag and a TEV protease site between the MBP tag and CsoSCA. The MBP tag and the disordered N-terminus of CsoSCA are not visible in the ...Details: This is a fusion protein with an N-terminal Strep-MBP tag and a TEV protease site between the MBP tag and CsoSCA. The MBP tag and the disordered N-terminus of CsoSCA are not visible in the map.,This is a fusion protein with an N-terminal Strep-MBP tag and a TEV protease site between the MBP tag and CsoSCA. The MBP tag and the disordered N-terminus of CsoSCA are not visible in the map.
Source: (gene. exp.) Escherichia coli K-12 (bacteria), (gene. exp.) Halothiobacillus neapolitanus c2 (bacteria)
Gene: malE, b4034, JW3994, csoS3, ORF1, Hneap_0919 / Plasmid: pET14 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: P0AEX9, UniProt: O85042, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / Source method: isolated from a natural source / Formula: H2O
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: HnCsoSCA / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.61154982 MDa / Experimental value: NO
Source (natural)Organism: Halothiobacillus neapolitanus c2 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21 (bacteria)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTris1
2150 mMsodium chlorideNaCl1
31 mMTCEP1
SpecimenConc.: 0.795 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Performed with a Pelco easiGlow with a current of 20 mA.
Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K
Details: 4C, 100% relative humidity, delay time 0s, blot time 3s, blot force 0

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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: 1800 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.6 sec. / Electron dose: 64.757 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9745
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1Topaz0.2.5particle selection
2EPU3.6.0image acquisition
4cryoSPARC4.7CTF correction
7UCSF ChimeraX1.9model fittingInitial rigid-body fitting and trimming of segments not supported by density
8ISOLDE1.9model fittingFlexible fitting by iMDFF
10cryoSPARC4.7initial Euler assignment
11cryoSPARC4.7final Euler assignment
12cryoSPARC4.7classification
13cryoSPARC4.73D reconstruction
14Servalcat0.4.99model refinementFinal refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 818243
Details: Particles were picked with topaz, trained with a set of about 1000 particles picked manually from micrographs denoised by CryoSPARC. Topaz was trained and applied on raw micrographs.
SymmetryPoint symmetry: D3 (2x3 fold dihedral)
3D reconstructionResolution: 2.06 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 545287 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: RECIPROCAL
Atomic model buildingAccession code: AF-O85042-F1 / Source name: AlphaFold / Type: in silico model
RefinementResolution: 2.06→312 Å / Num. reflection obs: 7276599 / Average fsc work: 0.7795
Displacement parametersBiso mean: 90.72 Å2
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
ELECTRON MICROSCOPYs_bond_nonh_d0.009774920.0118
ELECTRON MICROSCOPYs_angle_nonh_deg1.8675101681.8135
ELECTRON MICROSCOPYs_dihedral_angle_1_deg6.95689325
ELECTRON MICROSCOPYs_dihedral_angle_2_deg3.42062765
ELECTRON MICROSCOPYs_dihedral_angle_3_deg12.2739183410
ELECTRON MICROSCOPYs_dihedral_angle_6_deg13.548943810
ELECTRON MICROSCOPYs_chiral_restr0.080111260.1311
ELECTRON MICROSCOPYs_planes0.0085108680.02
ELECTRON MICROSCOPYs_nbd0.2222113710.2
ELECTRON MICROSCOPYs_nbtor0.2326127640.2
ELECTRON MICROSCOPYs_hbond_nbd0.23445470.2
ELECTRON MICROSCOPYs_metal_ion0.121540.2
ELECTRON MICROSCOPYs_symmetry_nbd0.1348320.2
ELECTRON MICROSCOPYs_symmetry_hbond_nbd0.062710.2
LS refinement shell
Resolution (Å)Refine-IDNum. reflection obsFsc work
2.06-2.073ELECTRON MICROSCOPY1358050.3752
2.073-2.087ELECTRON MICROSCOPY1414170.3971
2.087-2.101ELECTRON MICROSCOPY1400950.4145
2.101-2.115ELECTRON MICROSCOPY1377930.4394
2.115-2.13ELECTRON MICROSCOPY1357810.4698
2.13-2.144ELECTRON MICROSCOPY1343610.4975
2.144-2.159ELECTRON MICROSCOPY1324870.5174
2.159-2.174ELECTRON MICROSCOPY1301770.5273
2.174-2.189ELECTRON MICROSCOPY1272090.5435
2.189-2.205ELECTRON MICROSCOPY1273510.5642
2.205-2.221ELECTRON MICROSCOPY1249530.5894
2.221-2.237ELECTRON MICROSCOPY1234090.6128
2.237-2.253ELECTRON MICROSCOPY1207090.6318
2.253-2.269ELECTRON MICROSCOPY1191990.6424
2.269-2.286ELECTRON MICROSCOPY1189090.6558
2.286-2.303ELECTRON MICROSCOPY1164810.6717
2.303-2.32ELECTRON MICROSCOPY1136470.6927
2.32-2.337ELECTRON MICROSCOPY1131570.7121
2.337-2.355ELECTRON MICROSCOPY1107610.7296
2.355-2.373ELECTRON MICROSCOPY1104970.7449
2.373-2.391ELECTRON MICROSCOPY1069590.7611
2.391-2.409ELECTRON MICROSCOPY1062130.7757
2.409-2.428ELECTRON MICROSCOPY1053330.7809
2.428-2.447ELECTRON MICROSCOPY1027510.7829
2.447-2.466ELECTRON MICROSCOPY1010250.7942
2.466-2.486ELECTRON MICROSCOPY990370.8133
2.486-2.506ELECTRON MICROSCOPY991270.829
2.506-2.526ELECTRON MICROSCOPY962850.8409
2.526-2.547ELECTRON MICROSCOPY951250.8449
2.547-2.568ELECTRON MICROSCOPY936210.8492
2.568-2.589ELECTRON MICROSCOPY922150.8549
2.589-2.611ELECTRON MICROSCOPY909010.8651
2.611-2.633ELECTRON MICROSCOPY883890.8746
2.633-2.655ELECTRON MICROSCOPY869470.8816
2.655-2.678ELECTRON MICROSCOPY864930.8871
2.678-2.701ELECTRON MICROSCOPY849250.8917
2.701-2.725ELECTRON MICROSCOPY824970.8932
2.725-2.749ELECTRON MICROSCOPY820510.8935
2.749-2.773ELECTRON MICROSCOPY803290.8965
2.774-2.798ELECTRON MICROSCOPY789330.9014
2.798-2.823ELECTRON MICROSCOPY766990.9062
2.824-2.849ELECTRON MICROSCOPY759570.9079
2.849-2.875ELECTRON MICROSCOPY753250.9095
2.876-2.902ELECTRON MICROSCOPY731550.9121
2.902-2.929ELECTRON MICROSCOPY717970.9159
2.93-2.957ELECTRON MICROSCOPY702970.9187
2.957-2.986ELECTRON MICROSCOPY702690.9213
2.986-3.014ELECTRON MICROSCOPY669430.9256
3.015-3.044ELECTRON MICROSCOPY668610.9308
3.044-3.074ELECTRON MICROSCOPY654970.934
3.074-3.104ELECTRON MICROSCOPY640950.9356
3.105-3.136ELECTRON MICROSCOPY629050.9372
3.136-3.167ELECTRON MICROSCOPY610450.9363
3.168-3.2ELECTRON MICROSCOPY611490.9367
3.2-3.233ELECTRON MICROSCOPY593830.939
3.233-3.267ELECTRON MICROSCOPY579450.9385
3.267-3.301ELECTRON MICROSCOPY561610.9351
3.302-3.337ELECTRON MICROSCOPY553630.9337
3.337-3.373ELECTRON MICROSCOPY542730.9365
3.373-3.41ELECTRON MICROSCOPY531730.9372
3.41-3.447ELECTRON MICROSCOPY518850.9378
3.448-3.486ELECTRON MICROSCOPY512950.9389
3.486-3.525ELECTRON MICROSCOPY498450.9403
3.525-3.566ELECTRON MICROSCOPY486370.9418
3.566-3.607ELECTRON MICROSCOPY472390.9443
3.607-3.649ELECTRON MICROSCOPY465690.9456
3.649-3.692ELECTRON MICROSCOPY457690.9459
3.692-3.736ELECTRON MICROSCOPY440670.9469
3.737-3.781ELECTRON MICROSCOPY432730.949
3.782-3.828ELECTRON MICROSCOPY423330.9513
3.828-3.876ELECTRON MICROSCOPY415930.953
3.876-3.924ELECTRON MICROSCOPY400150.9514
3.925-3.974ELECTRON MICROSCOPY391890.9479
3.975-4.025ELECTRON MICROSCOPY378610.9438
4.026-4.078ELECTRON MICROSCOPY374550.943
4.079-4.132ELECTRON MICROSCOPY363730.944
4.133-4.187ELECTRON MICROSCOPY350130.9428
4.188-4.245ELECTRON MICROSCOPY348490.9385
4.245-4.303ELECTRON MICROSCOPY333430.9379
4.304-4.363ELECTRON MICROSCOPY328650.9391
4.364-4.425ELECTRON MICROSCOPY312850.9389
4.426-4.488ELECTRON MICROSCOPY306030.9384
4.489-4.554ELECTRON MICROSCOPY303130.9389
4.555-4.622ELECTRON MICROSCOPY287410.9392
4.622-4.691ELECTRON MICROSCOPY284550.9389
4.692-4.763ELECTRON MICROSCOPY271570.9385
4.763-4.837ELECTRON MICROSCOPY270450.938
4.837-4.913ELECTRON MICROSCOPY257770.9376
4.915-4.992ELECTRON MICROSCOPY244350.9341
4.992-5.072ELECTRON MICROSCOPY242770.9297
5.073-5.156ELECTRON MICROSCOPY233170.9213
5.157-5.243ELECTRON MICROSCOPY228510.9114
5.244-5.332ELECTRON MICROSCOPY217450.9094
5.334-5.425ELECTRON MICROSCOPY210330.9169
5.426-5.521ELECTRON MICROSCOPY207130.9153
5.522-5.621ELECTRON MICROSCOPY196470.899
5.622-5.724ELECTRON MICROSCOPY188410.8914
5.725-5.83ELECTRON MICROSCOPY182170.8894
5.832-5.942ELECTRON MICROSCOPY177270.8826
5.943-6.057ELECTRON MICROSCOPY171250.8816
6.06-6.176ELECTRON MICROSCOPY161250.8906
6.179-6.302ELECTRON MICROSCOPY158710.8916
6.303-6.432ELECTRON MICROSCOPY152250.8873
6.433-6.567ELECTRON MICROSCOPY145330.889
6.569-6.709ELECTRON MICROSCOPY137530.8892
6.71-6.854ELECTRON MICROSCOPY130590.8829
6.858-7.01ELECTRON MICROSCOPY129730.8702
7.013-7.171ELECTRON MICROSCOPY120210.8625
7.173-7.338ELECTRON MICROSCOPY117310.8633
7.342-7.516ELECTRON MICROSCOPY109810.8583
7.519-7.702ELECTRON MICROSCOPY107250.8568
7.704-7.897ELECTRON MICROSCOPY101170.8645
7.899-8.102ELECTRON MICROSCOPY93750.8652
8.105-8.315ELECTRON MICROSCOPY91330.8691
8.321-8.546ELECTRON MICROSCOPY85770.8702
8.549-8.786ELECTRON MICROSCOPY82270.8747
8.79-9.037ELECTRON MICROSCOPY75970.8806
9.044-9.31ELECTRON MICROSCOPY73770.8757
9.314-9.597ELECTRON MICROSCOPY69010.8867
9.601-9.901ELECTRON MICROSCOPY63030.9057
9.906-10.225ELECTRON MICROSCOPY60730.9172
10.231-10.566ELECTRON MICROSCOPY56130.9243
10.578-10.942ELECTRON MICROSCOPY52750.9362
10.949-11.34ELECTRON MICROSCOPY49810.9403
11.347-11.759ELECTRON MICROSCOPY45330.9364
11.776-12.228ELECTRON MICROSCOPY43030.9298
12.238-12.727ELECTRON MICROSCOPY40170.9353
12.737-13.268ELECTRON MICROSCOPY35650.9418
13.28-13.856ELECTRON MICROSCOPY33010.9444
13.87-14.484ELECTRON MICROSCOPY29910.9363
14.516-15.206ELECTRON MICROSCOPY28570.9287
15.224-15.984ELECTRON MICROSCOPY25170.9451
16.026-16.822ELECTRON MICROSCOPY21790.9525
16.871-17.807ELECTRON MICROSCOPY20850.9338
17.836-18.883ELECTRON MICROSCOPY18610.9048
18.918-20.098ELECTRON MICROSCOPY16690.9223
20.224-21.479ELECTRON MICROSCOPY13110.9488
21.53-23.001ELECTRON MICROSCOPY12490.9583
23.127-24.9ELECTRON MICROSCOPY10890.9613
25.06-27.054ELECTRON MICROSCOPY9070.9712
27.156-29.35ELECTRON MICROSCOPY7290.965
29.748-32.706ELECTRON MICROSCOPY6250.9614
32.888-36.517ELECTRON MICROSCOPY5710.9672
36.77-41.325ELECTRON MICROSCOPY3810.9611
41.693-47.58ELECTRON MICROSCOPY3010.9844
48.143-55.154ELECTRON MICROSCOPY2250.9962
56.963-68.084ELECTRON MICROSCOPY1750.9973
69.765-86.533ELECTRON MICROSCOPY1050.995
90.067-110.309ELECTRON MICROSCOPY490.9962
127.373-312ELECTRON MICROSCOPY400.9378

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