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- PDB-5jhc: Crystal structure of the self-assembled propeptides from Ape1 -

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Basic information

Entry
Database: PDB / ID: 5jhc
TitleCrystal structure of the self-assembled propeptides from Ape1
ComponentsVacuolar aminopeptidase 1
KeywordsHYDROLASE / Trimeric coiled-coil
Function / homology
Function and homology information


aminopeptidase I / Cvt complex / cytoplasm to vacuole targeting by the Cvt pathway / fungal-type vacuole / metalloaminopeptidase activity / proteolysis / zinc ion binding / identical protein binding / cytoplasm
Similarity search - Function
Peptidase M18 / Peptidase M18, domain 2 / Aminopeptidase I zinc metalloprotease (M18)
Similarity search - Domain/homology
Vacuolar aminopeptidase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3.4 Å
AuthorsYamasaki, A. / Noda, N.N.
CitationJournal: Cell Rep / Year: 2016
Title: Structural Basis for Receptor-Mediated Selective Autophagy of Aminopeptidase I Aggregates
Authors: Yamasaki, A. / Watanabe, Y. / Adachi, W. / Suzuki, K. / Matoba, K. / Kirisako, H. / Kumeta, H. / Nakatogawa, H. / Ohsumi, Y. / Inagaki, F. / Noda, N.N.
History
DepositionApr 20, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2016Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vacuolar aminopeptidase 1
C: Vacuolar aminopeptidase 1
E: Vacuolar aminopeptidase 1
G: Vacuolar aminopeptidase 1
I: Vacuolar aminopeptidase 1
K: Vacuolar aminopeptidase 1
M: Vacuolar aminopeptidase 1
O: Vacuolar aminopeptidase 1
Q: Vacuolar aminopeptidase 1
S: Vacuolar aminopeptidase 1
U: Vacuolar aminopeptidase 1
W: Vacuolar aminopeptidase 1
Y: Vacuolar aminopeptidase 1
B: Vacuolar aminopeptidase 1
a: Vacuolar aminopeptidase 1
b: Vacuolar aminopeptidase 1
D: Vacuolar aminopeptidase 1
F: Vacuolar aminopeptidase 1
c: Vacuolar aminopeptidase 1
H: Vacuolar aminopeptidase 1
d: Vacuolar aminopeptidase 1
J: Vacuolar aminopeptidase 1
e: Vacuolar aminopeptidase 1
L: Vacuolar aminopeptidase 1
f: Vacuolar aminopeptidase 1
N: Vacuolar aminopeptidase 1
g: Vacuolar aminopeptidase 1
P: Vacuolar aminopeptidase 1
h: Vacuolar aminopeptidase 1
R: Vacuolar aminopeptidase 1
i: Vacuolar aminopeptidase 1
T: Vacuolar aminopeptidase 1
j: Vacuolar aminopeptidase 1
V: Vacuolar aminopeptidase 1
k: Vacuolar aminopeptidase 1
X: Vacuolar aminopeptidase 1
l: Vacuolar aminopeptidase 1
Z: Vacuolar aminopeptidase 1
m: Vacuolar aminopeptidase 1


Theoretical massNumber of molelcules
Total (without water)111,55439
Polymers111,55439
Non-polymers00
Water00
1
A: Vacuolar aminopeptidase 1
B: Vacuolar aminopeptidase 1
a: Vacuolar aminopeptidase 1


Theoretical massNumber of molelcules
Total (without water)8,5813
Polymers8,5813
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Vacuolar aminopeptidase 1
b: Vacuolar aminopeptidase 1
D: Vacuolar aminopeptidase 1


Theoretical massNumber of molelcules
Total (without water)8,5813
Polymers8,5813
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Vacuolar aminopeptidase 1
F: Vacuolar aminopeptidase 1
c: Vacuolar aminopeptidase 1


Theoretical massNumber of molelcules
Total (without water)8,5813
Polymers8,5813
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Vacuolar aminopeptidase 1
H: Vacuolar aminopeptidase 1
d: Vacuolar aminopeptidase 1


Theoretical massNumber of molelcules
Total (without water)8,5813
Polymers8,5813
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: Vacuolar aminopeptidase 1
J: Vacuolar aminopeptidase 1
e: Vacuolar aminopeptidase 1


Theoretical massNumber of molelcules
Total (without water)8,5813
Polymers8,5813
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K: Vacuolar aminopeptidase 1
L: Vacuolar aminopeptidase 1
f: Vacuolar aminopeptidase 1


Theoretical massNumber of molelcules
Total (without water)8,5813
Polymers8,5813
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
M: Vacuolar aminopeptidase 1
N: Vacuolar aminopeptidase 1
g: Vacuolar aminopeptidase 1


Theoretical massNumber of molelcules
Total (without water)8,5813
Polymers8,5813
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
O: Vacuolar aminopeptidase 1
P: Vacuolar aminopeptidase 1
h: Vacuolar aminopeptidase 1


Theoretical massNumber of molelcules
Total (without water)8,5813
Polymers8,5813
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
Q: Vacuolar aminopeptidase 1
R: Vacuolar aminopeptidase 1
i: Vacuolar aminopeptidase 1


Theoretical massNumber of molelcules
Total (without water)8,5813
Polymers8,5813
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
S: Vacuolar aminopeptidase 1
T: Vacuolar aminopeptidase 1
j: Vacuolar aminopeptidase 1


Theoretical massNumber of molelcules
Total (without water)8,5813
Polymers8,5813
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
U: Vacuolar aminopeptidase 1
V: Vacuolar aminopeptidase 1
k: Vacuolar aminopeptidase 1


Theoretical massNumber of molelcules
Total (without water)8,5813
Polymers8,5813
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
W: Vacuolar aminopeptidase 1
X: Vacuolar aminopeptidase 1
l: Vacuolar aminopeptidase 1


Theoretical massNumber of molelcules
Total (without water)8,5813
Polymers8,5813
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
13
Y: Vacuolar aminopeptidase 1
Z: Vacuolar aminopeptidase 1
m: Vacuolar aminopeptidase 1


Theoretical massNumber of molelcules
Total (without water)8,5813
Polymers8,5813
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)248.758, 248.758, 164.403
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein/peptide ...
Vacuolar aminopeptidase 1 / Aminopeptidase yscI / Leucine aminopeptidase IV / LAPIV / Lysosomal aminopeptidase III / ...Aminopeptidase yscI / Leucine aminopeptidase IV / LAPIV / Lysosomal aminopeptidase III / Polypeptidase / Vacuolar aminopeptidase I


Mass: 2860.367 Da / Num. of mol.: 39 / Fragment: UNP residues 1-22 / Mutation: P22L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: APE1, API, LAP4, YSC1, YKL103C, YKL455 / Production host: Escherichia coli (E. coli) / References: UniProt: P14904, aminopeptidase I

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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: 4.39 Å3/Da / Density % sol: 71.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 500 mM magnesium sulfate, 100 mM sodium acetate

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→500 Å / Num. obs: 26941 / % possible obs: 99.9 % / Redundancy: 11.3 % / Net I/σ(I): 22.4
Reflection shellResolution: 3.4→3.46 Å / Redundancy: 11.4 % / Mean I/σ(I) obs: 4.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SIRAS / Resolution: 3.4→39.519 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3109 1326 4.93 %
Rwork0.2764 --
obs0.2781 26875 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.4→39.519 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6607 0 0 0 6607
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016605
X-RAY DIFFRACTIONf_angle_d1.2928941
X-RAY DIFFRACTIONf_dihedral_angle_d16.2092469
X-RAY DIFFRACTIONf_chiral_restr0.0561195
X-RAY DIFFRACTIONf_plane_restr0.0061143
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.53140.43411570.37292766X-RAY DIFFRACTION99
3.5314-3.6920.41711540.38212824X-RAY DIFFRACTION100
3.692-3.88650.34081220.35052835X-RAY DIFFRACTION100
3.8865-4.12970.3191440.2952840X-RAY DIFFRACTION100
4.1297-4.44820.31571640.29352811X-RAY DIFFRACTION99
4.4482-4.89510.28031870.2512779X-RAY DIFFRACTION99
4.8951-5.60170.33341110.28612874X-RAY DIFFRACTION100
5.6017-7.05110.44311430.38022886X-RAY DIFFRACTION100
7.0511-39.52150.22441440.19472934X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.66620.04070.06450.47550.20150.4862-0.33510.2130.1924-0.3729-0.3545-0.07040.72250.062-0.53831.0339-0.25270.03290.6244-0.06891.148943.8132-6.884632.0661
20.1555-0.05320.05430.1168-0.0810.04840.3147-0.4492-0.10760.5878-0.12540.2977-0.20860.03430.0011.6647-0.1272-0.03090.7549-0.01541.963264.1953-12.196839.3382
30.8654-0.7635-0.59821.00970.25110.6383-0.30790.5381-0.8522-0.8523-0.38890.30770.6577-0.2259-0.18360.9358-0.2009-0.10260.6519-0.18520.908954.8263-10.081122.2367
40.0258-0.0367-0.04580.04060.008-0.00690.04710.49460.23120.02070.0847-0.24350.38870.6044-0.14830.5882-0.19750.12910.6646-0.24061.185149.593811.328627.3722
50.17850.09710.34710.13160.19110.6765-0.3178-0.25490.25540.6138-0.111.25370.0831-0.3139-0.36560.4820.2210.99040.80270.237-0.104619.095654.079939.0738
60.2522-0.0688-0.13180.1238-0.12670.2566-0.49770.5558-0.11380.47240.3377-0.16720.2803-0.0174-0.02170.14340.0525-0.02231.18770.41471.439235.03238.659631.9764
70.0266-0.0102-0.02780.04520.0088-0.0401-0.5723-0.47710.08930.1841-0.14250.80430.0627-0.19430.00090.6720.06890.11491.30020.26181.378414.622341.871831.3315
80.48150.3208-0.01070.3179-0.08030.0893-0.08410.95530.6423-0.0783-0.010.60220.35770.34380.03520.57960.16780.08880.8920.2761.33419.063461.935320.7437
90.10770.13310.03250.27990.0470.1207-0.08740.0605-0.18260.7226-0.2674-0.66270.00570.1734-0.02310.88070.01480.11071.0678-0.07841.174775.07047.221916.0543
10-0.01520.0727-0.0128-0.06170.04050.03750.64840.2714-0.54170.12270.8010.2004-0.3722-0.1212-0.00270.7022-0.04-0.01270.8890.13590.849446.458764.712215.3414
110.174-0.33590.25770.8568-0.29110.8631-0.35570.32420.0923-0.5286-0.6325-0.4307-0.06350.3388-0.38590.28650.2560.29070.5487-1.0404-1.505275.51632.45631.3129
120.09990.1259-0.07080.80260.47460.7429-0.27970.40180.4115-0.74110.17030.7584-0.2592-0.0043-0.0730.39870.1816-0.42770.93020.3296-1.606544.34237.80994.3331
13-0.00250.0289-0.02050.07-0.09670.1025-0.0516-0.110.10860.34450.4921-0.2726-0.2154-0.49710.04941.04810.4904-0.20840.04390.2021.823159.643442.382722.2473
140.3097-0.15180.67510.0813-0.32962.12510.05260.13540.2476-0.02730.0016-0.1713-0.6689-0.2083-0.1310.9576-0.07660.11930.4388-0.02421.721341.44463.458338.8182
150.0427-0.0110.06390.0222-0.10830.332-0.1724-0.388-0.9343-0.2837-0.07650.00650.69370.04460.23831.4064-0.31410.13940.92010.06190.747944.3161-14.500143.1401
160.09860.0031-0.04580.0403-0.02630.1032-0.04530.4956-0.4403-0.1314-0.3582-0.03090.42390.3672-0.10341.3814-0.4261-0.1932-0.12460.90830.024354.3001-12.349546.2541
170.63990.2704-0.17331.9065-0.61961.3045-0.6233-0.3046-0.63891.0134-0.2966-0.4815-0.13660.2441-0.42310.2218-0.29140.12270.00770.46850.834257.9488-3.942441.636
180.1868-0.0421-0.20230.3826-0.10220.1931-0.1515-0.1164-0.32190.4218-0.26320.0428-0.06490.0902-0.45870.6712-0.12640.2220.4157-0.15980.662967.0308-8.770122.3861
190.0313-0.0023-0.06840.03810.01030.0648-0.27340.0131-0.1645-0.2678-0.17650.0012-0.0222-0.21450.07590.7119-0.09370.11840.8315-0.28661.016655.6388-0.316911.4974
200.5557-0.71910.37781.0954-0.79671.0679-0.51330.15160.38190.4113-0.2754-0.9459-0.0425-0.0845-0.36440.6892-0.25890.25450.6502-0.33850.42160.34986.152428.9319
210.03970.0052-0.0330.02310.02220.12740.10810.2395-0.02440.09840.2401-0.4782-0.209-0.1539-0.00181.1569-0.1997-0.04121.0308-0.29711.914555.51537.236418.655
220.02740.00560.01080.10570.04540.0066-0.0062-0.13870.5127-0.1147-0.00930.253-0.2324-0.2303-0.1150.8150.11980.27990.8279-0.21691.038126.169864.262636.0407
230.1429-0.04270.08910.0620.07370.1161-0.1026-0.308-0.24360.10160.0334-0.0338-0.13640.0093-0.18610.2919-0.21010.64621.04570.82340.821530.265750.699148.1699
240.02340.0133-0.05030.0614-0.01720.02940.4146-0.06120.39610.0812-0.18090.1964-0.02990.02830.10830.5316-0.02690.15890.86090.05360.483835.390950.462429.3215
250.4980.1517-0.09970.08670.15170.47940.385-0.39960.3520.42260.5531-0.19880.1728-0.75860.3830.5731-0.03030.17281.56920.22950.273335.298546.640440.1057
260.11060.0256-0.02310.48140.21450.1047-0.0287-0.2639-0.08550.18180.2736-0.44190.1067-0.52710.17210.5137-0.02670.0221.0703-0.07610.826221.516734.224923.2906
270.06450.06550.09530.0588-0.00310.0940.0663-0.06260.1022-0.5166-0.0330.0969-0.1218-0.77240.00010.76040.0954-0.07131.34470.00951.42836.552145.412420.6431
280.2056-0.02290.19070.0040.01170.1271-0.16440.41560.04150.3008-0.1474-0.02320.1080.2176-0.05260.34910.2984-0.1470.93470.77990.166823.756251.555518.1945
290.07840.02470.06740.07460.00870.0379-0.34270.0360.060.31180.73050.3262-0.4774-0.00520.08810.81730.448-0.12551.15170.18980.511211.977353.214318.2484
300.28130.13940.08160.0326-0.05460.01370.16480.12250.04290.16240.57190.7251-0.2215-1.11190.03260.4811-0.1673-0.14211.02030.01720.81966.556918.55410.3298
310.04860.0055-0.12640.11050.08480.15250.0691-0.03240.0219-0.4679-0.0496-0.08090.20580.2705-0.00081.01270.0030.09531.2555-0.4271.790377.919412.33167.0027
320.57990.22050.66630.82310.17590.77340.10310.8936-0.2131-0.92830.0466-1.1979-0.00310.96720.12260.4524-0.0799-0.01760.89770.57180.15654.188752.71259.7878
330.0298-0.04430.04850.1242-0.01570.1325-0.41-0.25330.60630.1841-0.2141.159-0.5615-0.06210.00060.93030.0623-0.15081.24560.6540.056841.119458.80328.7387
340.01670.01340.0120.0529-0.02360.10190.02110.43850.0779-0.4111-0.0785-0.01870.0648-0.41790.00050.83240.10460.15381.6553-0.40910.814267.428725.5791-0.9315
350.06870.08710.0101-0.023-0.07710.09420.1909-0.02410.15510.1196-0.4303-0.48640.13920.09-0.18150.5596-0.03860.1140.8903-0.09540.611481.07830.2069.6404
360.03790.033-0.0170.0915-0.0130.12530.22660.2651-0.3595-0.2230.808-0.63260.0862-0.0502-0.00280.72920.0678-0.09991.1670.1290.637150.548645.083-0.2211
370.0207-0.00190.03260.0412-0.01010.1842-0.0089-0.2708-0.49140.3167-0.25350.2911-0.386-0.02940.00060.7305-0.0365-0.09691.10920.12640.719839.101940.938612.6532
380.02280.01990.0148-0.01460.0113-0.00690.0414-0.0022-0.1194-0.01360.23110.4071-0.2246-0.12290.00040.6493-0.406-1.46172.08520.30110.433552.749132.736115.296
390.03860.0198-0.0372-0.02350.01870.0102-0.16580.08210.03990.27710.2642-0.2807-0.14910.83540.00022.3021.6016-0.4974-0.0598-0.38322.264965.24431.143222.2335
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 22 )
2X-RAY DIFFRACTION2chain 'C' and (resid -1 through 22 )
3X-RAY DIFFRACTION3chain 'E' and (resid -1 through 22 )
4X-RAY DIFFRACTION4chain 'G' and (resid -1 through 22 )
5X-RAY DIFFRACTION5chain 'I' and (resid -1 through 22 )
6X-RAY DIFFRACTION6chain 'K' and (resid -1 through 22 )
7X-RAY DIFFRACTION7chain 'M' and (resid -1 through 22 )
8X-RAY DIFFRACTION8chain 'O' and (resid -1 through 22 )
9X-RAY DIFFRACTION9chain 'Q' and (resid -1 through 22 )
10X-RAY DIFFRACTION10chain 'S' and (resid -1 through 22 )
11X-RAY DIFFRACTION11chain 'U' and (resid -1 through 22 )
12X-RAY DIFFRACTION12chain 'W' and (resid -1 through 22 )
13X-RAY DIFFRACTION13chain 'Y' and (resid -1 through 18 )
14X-RAY DIFFRACTION14chain 'B' and (resid -1 through 22 )
15X-RAY DIFFRACTION15chain 'a' and (resid 0 through 22 )
16X-RAY DIFFRACTION16chain 'b' and (resid 1 through 22 )
17X-RAY DIFFRACTION17chain 'D' and (resid 1 through 22 )
18X-RAY DIFFRACTION18chain 'F' and (resid -1 through 22 )
19X-RAY DIFFRACTION19chain 'c' and (resid -1 through 22 )
20X-RAY DIFFRACTION20chain 'H' and (resid 0 through 22 )
21X-RAY DIFFRACTION21chain 'd' and (resid -1 through 22 )
22X-RAY DIFFRACTION22chain 'J' and (resid -1 through 22 )
23X-RAY DIFFRACTION23chain 'e' and (resid -1 through 22 )
24X-RAY DIFFRACTION24chain 'L' and (resid -1 through 22 )
25X-RAY DIFFRACTION25chain 'f' and (resid -1 through 22 )
26X-RAY DIFFRACTION26chain 'N' and (resid -1 through 22 )
27X-RAY DIFFRACTION27chain 'g' and (resid -1 through 22 )
28X-RAY DIFFRACTION28chain 'P' and (resid 0 through 22 )
29X-RAY DIFFRACTION29chain 'h' and (resid -1 through 22 )
30X-RAY DIFFRACTION30chain 'R' and (resid 0 through 22 )
31X-RAY DIFFRACTION31chain 'i' and (resid -1 through 22 )
32X-RAY DIFFRACTION32chain 'T' and (resid -1 through 22 )
33X-RAY DIFFRACTION33chain 'j' and (resid -1 through 22 )
34X-RAY DIFFRACTION34chain 'V' and (resid -1 through 22 )
35X-RAY DIFFRACTION35chain 'k' and (resid -1 through 22 )
36X-RAY DIFFRACTION36chain 'X' and (resid 0 through 22 )
37X-RAY DIFFRACTION37chain 'l' and (resid -1 through 22 )
38X-RAY DIFFRACTION38chain 'Z' and (resid -1 through 12 )
39X-RAY DIFFRACTION39chain 'm' and (resid 1 through 22 )

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