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- PDB-8wfq: The Crystal Structure of RALDH1 from Biortus. -

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Basic information

Entry
Database: PDB / ID: 8wfq
TitleThe Crystal Structure of RALDH1 from Biortus.
ComponentsAldehyde dehydrogenase 1A1
KeywordsOXIDOREDUCTASE / Lipid metabolism / NAD / Nucleotide-binding
Function / homology
Function and homology information


fructosamine catabolic process / 3-deoxyglucosone dehydrogenase activity / benzaldehyde dehydrogenase (NAD+) / benzaldehyde dehydrogenase (NAD+) activity / maintenance of lens transparency / gamma-aminobutyric acid biosynthetic process / aminobutyraldehyde dehydrogenase activity / retinal dehydrogenase / aminobutyraldehyde dehydrogenase / Fructose catabolism ...fructosamine catabolic process / 3-deoxyglucosone dehydrogenase activity / benzaldehyde dehydrogenase (NAD+) / benzaldehyde dehydrogenase (NAD+) activity / maintenance of lens transparency / gamma-aminobutyric acid biosynthetic process / aminobutyraldehyde dehydrogenase activity / retinal dehydrogenase / aminobutyraldehyde dehydrogenase / Fructose catabolism / cellular aldehyde metabolic process / Ethanol oxidation / RA biosynthesis pathway / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / aldehyde dehydrogenase (NAD+) / cellular detoxification of aldehyde / androgen binding / aldehyde dehydrogenase (NAD+) activity / negative regulation of cold-induced thermogenesis / retinal dehydrogenase activity / retinol metabolic process / retinoid metabolic process / GTPase activator activity / NAD binding / axon / synapse / extracellular exosome / cytosol / cytoplasm
Similarity search - Function
Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Aldehyde dehydrogenase 1A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsWang, F. / Cheng, W. / Lv, Z. / Qi, J. / Shen, Z.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of RALDH1 from Biortus.
Authors: Wang, F. / Cheng, W. / Lv, Z. / Qi, J. / Shen, Z.
History
DepositionSep 20, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aldehyde dehydrogenase 1A1
B: Aldehyde dehydrogenase 1A1
C: Aldehyde dehydrogenase 1A1
D: Aldehyde dehydrogenase 1A1
E: Aldehyde dehydrogenase 1A1
F: Aldehyde dehydrogenase 1A1
G: Aldehyde dehydrogenase 1A1
H: Aldehyde dehydrogenase 1A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)445,02317
Polymers439,6378
Non-polymers5,3869
Water1,22568
1
A: Aldehyde dehydrogenase 1A1
B: Aldehyde dehydrogenase 1A1
C: Aldehyde dehydrogenase 1A1
D: Aldehyde dehydrogenase 1A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,5429
Polymers219,8194
Non-polymers2,7245
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25390 Å2
ΔGint-94 kcal/mol
Surface area58080 Å2
MethodPISA
2
E: Aldehyde dehydrogenase 1A1
F: Aldehyde dehydrogenase 1A1
G: Aldehyde dehydrogenase 1A1
H: Aldehyde dehydrogenase 1A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,4808
Polymers219,8194
Non-polymers2,6624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25430 Å2
ΔGint-96 kcal/mol
Surface area58280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.343, 149.560, 125.076
Angle α, β, γ (deg.)90.000, 95.428, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A
32A
42A
53A
63A
74A
84A
95A
105A
116A
126A
137A
147A
158A
168A
179A
189A
1910A
2010A
2111A
2211A
2312A
2412A
2513A
2613A
2714A
2814A
2915A
3015A
3116A
3216A
3317A
3417A
3518A
3618A
3719A
3819A
3920A
4020A
4121A
4221A
4322A
4422A
4523A
4623A
4724A
4824A
4925A
5025A
5126A
5226A
5327A
5427A
5528A
5628A

NCS domain segments:

Auth asym-ID: A / Label asym-ID: A

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth seq-IDLabel seq-ID
111ASPASPSERSER8 - 5019 - 502
211ASPASPSERSER8 - 5019 - 502
322ASPASPSERSER8 - 5019 - 502
422ASPASPSERSER8 - 5019 - 502
533ASPASPSERSER8 - 5019 - 502
633ASPASPSERSER8 - 5019 - 502
744ASPASPSERSER8 - 5019 - 502
844ASPASPSERSER8 - 5019 - 502
955LEULEUASNASN9 - 50010 - 501
1055LEULEUASNASN9 - 50010 - 501
1166ASPASPSERSER8 - 5019 - 502
1266ASPASPSERSER8 - 5019 - 502
1377LEULEUASNASN9 - 50010 - 501
1477LEULEUASNASN9 - 50010 - 501
1588ASPASPSERSER8 - 5019 - 502
1688ASPASPSERSER8 - 5019 - 502
1799ASPASPSERSER8 - 5019 - 502
1899ASPASPSERSER8 - 5019 - 502
191010ASPASPSERSER8 - 5019 - 502
201010ASPASPSERSER8 - 5019 - 502
211111LEULEUASNASN9 - 50010 - 501
221111LEULEUASNASN9 - 50010 - 501
231212ASPASPSERSER8 - 5019 - 502
241212ASPASPSERSER8 - 5019 - 502
251313LEULEUASNASN9 - 50010 - 501
261313LEULEUASNASN9 - 50010 - 501
271414ASPASPSERSER8 - 5019 - 502
281414ASPASPSERSER8 - 5019 - 502
291515ASPASPSERSER8 - 5019 - 502
301515ASPASPSERSER8 - 5019 - 502
311616LEULEUASNASN9 - 50010 - 501
321616LEULEUASNASN9 - 50010 - 501
331717ASPASPSERSER8 - 5019 - 502
341717ASPASPSERSER8 - 5019 - 502
351818LEULEUASNASN9 - 50010 - 501
361818LEULEUASNASN9 - 50010 - 501
371919ASPASPSERSER8 - 5019 - 502
381919ASPASPSERSER8 - 5019 - 502
392020LEULEUASNASN9 - 50010 - 501
402020LEULEUASNASN9 - 50010 - 501
412121ASPASPSERSER8 - 5019 - 502
422121ASPASPSERSER8 - 5019 - 502
432222LEULEUASNASN9 - 50010 - 501
442222LEULEUASNASN9 - 50010 - 501
452323LEULEUASNASN9 - 50010 - 501
462323LEULEUASNASN9 - 50010 - 501
472424ASPASPSERSER8 - 5019 - 502
482424ASPASPSERSER8 - 5019 - 502
492525LEULEUASNASN9 - 50010 - 501
502525LEULEUASNASN9 - 50010 - 501
512626LEULEUASNASN9 - 50010 - 501
522626LEULEUASNASN9 - 50010 - 501
532727LEULEUSERSER9 - 50110 - 502
542727LEULEUSERSER9 - 50110 - 502
552828LEULEUASNASN9 - 50010 - 501
562828LEULEUASNASN9 - 50010 - 501

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12
7Local NCS retraints between domains: 13 14
8Local NCS retraints between domains: 15 16
9Local NCS retraints between domains: 17 18
10Local NCS retraints between domains: 19 20
11Local NCS retraints between domains: 21 22
12Local NCS retraints between domains: 23 24
13Local NCS retraints between domains: 25 26
14Local NCS retraints between domains: 27 28
15Local NCS retraints between domains: 29 30
16Local NCS retraints between domains: 31 32
17Local NCS retraints between domains: 33 34
18Local NCS retraints between domains: 35 36
19Local NCS retraints between domains: 37 38
20Local NCS retraints between domains: 39 40
21Local NCS retraints between domains: 41 42
22Local NCS retraints between domains: 43 44
23Local NCS retraints between domains: 45 46
24Local NCS retraints between domains: 47 48
25Local NCS retraints between domains: 49 50
26Local NCS retraints between domains: 51 52
27Local NCS retraints between domains: 53 54
28Local NCS retraints between domains: 55 56

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Components

#1: Protein
Aldehyde dehydrogenase 1A1


Mass: 54954.648 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH1A1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00352
#2: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH / Nicotinamide adenine dinucleotide


Mass: 665.441 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M CaCl2, 0.1M MgCl2, 0.1M PIPES pH7, 22.5% PEG smear

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.95374 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 3.5→48.16 Å / Num. obs: 46102 / % possible obs: 98.5 % / Redundancy: 3 % / CC1/2: 0.95 / Net I/σ(I): 4.7
Reflection shellResolution: 3.5→3.62 Å / Num. unique obs: 4537 / CC1/2: 0.618

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→48.16 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.862 / SU B: 39.913 / SU ML: 0.566 / Cross valid method: FREE R-VALUE / ESU R Free: 0.764
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2543 2196 4.765 %
Rwork0.2302 43886 -
all0.231 --
obs-46082 98.283 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 64.069 Å2
Baniso -1Baniso -2Baniso -3
1-5.759 Å20 Å2-3.753 Å2
2---0.466 Å2-0 Å2
3----4.499 Å2
Refinement stepCycle: LAST / Resolution: 3.5→48.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30496 0 356 68 30920
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01231539
X-RAY DIFFRACTIONr_bond_other_d0.0010.01629117
X-RAY DIFFRACTIONr_angle_refined_deg0.6671.64542756
X-RAY DIFFRACTIONr_angle_other_deg0.2391.56367991
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0753942
X-RAY DIFFRACTIONr_dihedral_angle_2_deg2.65136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.684105374
X-RAY DIFFRACTIONr_dihedral_angle_6_deg10.535101318
X-RAY DIFFRACTIONr_chiral_restr0.0310.24750
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0235538
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026078
X-RAY DIFFRACTIONr_nbd_refined0.1740.26687
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1690.228737
X-RAY DIFFRACTIONr_nbtor_refined0.1680.215699
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.216223
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.2767
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.050.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2040.238
X-RAY DIFFRACTIONr_nbd_other0.2060.2130
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2360.26
X-RAY DIFFRACTIONr_mcbond_it1.5186.5315792
X-RAY DIFFRACTIONr_mcbond_other1.5186.5315792
X-RAY DIFFRACTIONr_mcangle_it2.6559.79119726
X-RAY DIFFRACTIONr_mcangle_other2.6559.79119727
X-RAY DIFFRACTIONr_scbond_it1.2636.70315747
X-RAY DIFFRACTIONr_scbond_other1.2636.70315748
X-RAY DIFFRACTIONr_scangle_it2.28710.01323030
X-RAY DIFFRACTIONr_scangle_other2.28710.01323031
X-RAY DIFFRACTIONr_lrange_it4.882.36535255
X-RAY DIFFRACTIONr_lrange_other4.882.36435256
X-RAY DIFFRACTIONr_ncsr_local_group_10.0490.0516061
X-RAY DIFFRACTIONr_ncsr_local_group_20.0440.0516103
X-RAY DIFFRACTIONr_ncsr_local_group_30.0450.0516072
X-RAY DIFFRACTIONr_ncsr_local_group_40.0480.0516108
X-RAY DIFFRACTIONr_ncsr_local_group_50.0550.0515988
X-RAY DIFFRACTIONr_ncsr_local_group_60.0470.0516047
X-RAY DIFFRACTIONr_ncsr_local_group_70.0510.0516085
X-RAY DIFFRACTIONr_ncsr_local_group_80.0410.0516161
X-RAY DIFFRACTIONr_ncsr_local_group_90.0440.0516118
X-RAY DIFFRACTIONr_ncsr_local_group_100.0450.0516149
X-RAY DIFFRACTIONr_ncsr_local_group_110.0510.0516059
X-RAY DIFFRACTIONr_ncsr_local_group_120.0480.0516119
X-RAY DIFFRACTIONr_ncsr_local_group_130.050.0516124
X-RAY DIFFRACTIONr_ncsr_local_group_140.0390.0516163
X-RAY DIFFRACTIONr_ncsr_local_group_150.0420.0516164
X-RAY DIFFRACTIONr_ncsr_local_group_160.0450.0516129
X-RAY DIFFRACTIONr_ncsr_local_group_170.0460.0516110
X-RAY DIFFRACTIONr_ncsr_local_group_180.0480.0516083
X-RAY DIFFRACTIONr_ncsr_local_group_190.0430.0516142
X-RAY DIFFRACTIONr_ncsr_local_group_200.0470.0516105
X-RAY DIFFRACTIONr_ncsr_local_group_210.0440.0516084
X-RAY DIFFRACTIONr_ncsr_local_group_220.050.0516058
X-RAY DIFFRACTIONr_ncsr_local_group_230.0490.0516069
X-RAY DIFFRACTIONr_ncsr_local_group_240.0470.0516102
X-RAY DIFFRACTIONr_ncsr_local_group_250.0480.0516083
X-RAY DIFFRACTIONr_ncsr_local_group_260.0510.0516041
X-RAY DIFFRACTIONr_ncsr_local_group_270.0490.0516121
X-RAY DIFFRACTIONr_ncsr_local_group_280.0430.0516125
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.049110.05011
12AX-RAY DIFFRACTIONLocal ncs0.049110.05011
23AX-RAY DIFFRACTIONLocal ncs0.043960.05011
24AX-RAY DIFFRACTIONLocal ncs0.043960.05011
35AX-RAY DIFFRACTIONLocal ncs0.045420.05011
36AX-RAY DIFFRACTIONLocal ncs0.045420.05011
47AX-RAY DIFFRACTIONLocal ncs0.048060.05011
48AX-RAY DIFFRACTIONLocal ncs0.048060.05011
59AX-RAY DIFFRACTIONLocal ncs0.054950.0501
510AX-RAY DIFFRACTIONLocal ncs0.054950.0501
611AX-RAY DIFFRACTIONLocal ncs0.047040.05011
612AX-RAY DIFFRACTIONLocal ncs0.047040.05011
713AX-RAY DIFFRACTIONLocal ncs0.050890.05011
714AX-RAY DIFFRACTIONLocal ncs0.050890.05011
815AX-RAY DIFFRACTIONLocal ncs0.040810.05011
816AX-RAY DIFFRACTIONLocal ncs0.040810.05011
917AX-RAY DIFFRACTIONLocal ncs0.043870.05011
918AX-RAY DIFFRACTIONLocal ncs0.043870.05011
1019AX-RAY DIFFRACTIONLocal ncs0.045470.05011
1020AX-RAY DIFFRACTIONLocal ncs0.045470.05011
1121AX-RAY DIFFRACTIONLocal ncs0.051080.05011
1122AX-RAY DIFFRACTIONLocal ncs0.051080.05011
1223AX-RAY DIFFRACTIONLocal ncs0.048230.05011
1224AX-RAY DIFFRACTIONLocal ncs0.048230.05011
1325AX-RAY DIFFRACTIONLocal ncs0.049860.05011
1326AX-RAY DIFFRACTIONLocal ncs0.049860.05011
1427AX-RAY DIFFRACTIONLocal ncs0.03930.05011
1428AX-RAY DIFFRACTIONLocal ncs0.03930.05011
1529AX-RAY DIFFRACTIONLocal ncs0.042040.05011
1530AX-RAY DIFFRACTIONLocal ncs0.042040.05011
1631AX-RAY DIFFRACTIONLocal ncs0.045150.05011
1632AX-RAY DIFFRACTIONLocal ncs0.045150.05011
1733AX-RAY DIFFRACTIONLocal ncs0.045920.05011
1734AX-RAY DIFFRACTIONLocal ncs0.045920.05011
1835AX-RAY DIFFRACTIONLocal ncs0.048090.05011
1836AX-RAY DIFFRACTIONLocal ncs0.048090.05011
1937AX-RAY DIFFRACTIONLocal ncs0.042880.05011
1938AX-RAY DIFFRACTIONLocal ncs0.042880.05011
2039AX-RAY DIFFRACTIONLocal ncs0.046880.05011
2040AX-RAY DIFFRACTIONLocal ncs0.046880.05011
2141AX-RAY DIFFRACTIONLocal ncs0.043780.05011
2142AX-RAY DIFFRACTIONLocal ncs0.043780.05011
2243AX-RAY DIFFRACTIONLocal ncs0.050250.05011
2244AX-RAY DIFFRACTIONLocal ncs0.050250.05011
2345AX-RAY DIFFRACTIONLocal ncs0.048830.05011
2346AX-RAY DIFFRACTIONLocal ncs0.048830.05011
2447AX-RAY DIFFRACTIONLocal ncs0.04740.05011
2448AX-RAY DIFFRACTIONLocal ncs0.04740.05011
2549AX-RAY DIFFRACTIONLocal ncs0.047810.05011
2550AX-RAY DIFFRACTIONLocal ncs0.047810.05011
2651AX-RAY DIFFRACTIONLocal ncs0.050770.05011
2652AX-RAY DIFFRACTIONLocal ncs0.050770.05011
2753AX-RAY DIFFRACTIONLocal ncs0.049320.05011
2754AX-RAY DIFFRACTIONLocal ncs0.049320.05011
2855AX-RAY DIFFRACTIONLocal ncs0.043330.05011
2856AX-RAY DIFFRACTIONLocal ncs0.043330.05011
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.5910.3641380.3223251X-RAY DIFFRACTION99.4133
3.591-3.6880.31420.33210X-RAY DIFFRACTION99.1423
3.688-3.7950.31250.2733066X-RAY DIFFRACTION98.8844
3.795-3.9110.2781510.2612978X-RAY DIFFRACTION98.4581
3.911-4.0380.2671530.2632880X-RAY DIFFRACTION98.3782
4.038-4.1790.2951340.2442789X-RAY DIFFRACTION98.6167
4.179-4.3350.281460.232677X-RAY DIFFRACTION98.8099
4.335-4.5110.2391110.2062631X-RAY DIFFRACTION98.9892
4.511-4.7090.2391050.1982489X-RAY DIFFRACTION98.8567
4.709-4.9370.2311240.2012392X-RAY DIFFRACTION98.1279
4.937-5.2010.1991100.2012182X-RAY DIFFRACTION95.5797
5.201-5.5120.2321150.2332110X-RAY DIFFRACTION96.5712
5.512-5.8880.2651170.222004X-RAY DIFFRACTION98.6053
5.888-6.3510.2881130.2371867X-RAY DIFFRACTION98.0198
6.351-6.9460.248950.221744X-RAY DIFFRACTION98.7118
6.946-7.7450.198900.1771553X-RAY DIFFRACTION97.9726
7.745-8.9050.183760.1551390X-RAY DIFFRACTION98.1258
8.905-10.8150.173660.1431184X-RAY DIFFRACTION97.8091
10.815-14.9240.228550.21920X-RAY DIFFRACTION96.8222
14.924-48.160.341300.326569X-RAY DIFFRACTION96.9256

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