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- PDB-7btc: Crystal structure of Rheb Y35N mutant bound to GDP -

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Basic information

Entry
Database: PDB / ID: 7btc
TitleCrystal structure of Rheb Y35N mutant bound to GDP
ComponentsGTP-binding protein Rheb
KeywordsSIGNALING PROTEIN / mTORC1 / small GTPase / Rheb
Function / homology
Function and homology information


regulation of type B pancreatic cell development / MTOR signalling / Amino acids regulate mTORC1 / Energy dependent regulation of mTOR by LKB1-AMPK / negative regulation of cold-induced thermogenesis / Macroautophagy / small GTPase-mediated signal transduction / positive regulation of oligodendrocyte differentiation / protein kinase activator activity / oligodendrocyte differentiation ...regulation of type B pancreatic cell development / MTOR signalling / Amino acids regulate mTORC1 / Energy dependent regulation of mTOR by LKB1-AMPK / negative regulation of cold-induced thermogenesis / Macroautophagy / small GTPase-mediated signal transduction / positive regulation of oligodendrocyte differentiation / protein kinase activator activity / oligodendrocyte differentiation / mTORC1-mediated signalling / cellular response to nutrient levels / positive regulation of TOR signaling / regulation of macroautophagy / endomembrane system / positive regulation of TORC1 signaling / protein serine/threonine kinase activator activity / Regulation of PTEN gene transcription / TP53 Regulates Metabolic Genes / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / spliceosomal complex / GDP binding / postsynaptic density / regulation of cell cycle / lysosomal membrane / Golgi membrane / GTPase activity / GTP binding / endoplasmic reticulum membrane / protein kinase binding / magnesium ion binding / signal transduction / extracellular exosome / membrane / plasma membrane / cytosol
Similarity search - Function
Small GTPase, Ras-type / small GTPase Ras family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase ...Small GTPase, Ras-type / small GTPase Ras family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GTP-binding protein Rheb
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.101 Å
AuthorsZhang, C. / Zhang, T. / Ding, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870722 China
CitationJournal: J Mol Cell Biol / Year: 2020
Title: Molecular basis for the functions of dominantly active Y35N and inactive D60K Rheb mutants in mTORC1 signaling.
Authors: Zhang, C. / Liu, Y. / Zhang, Y. / Wang, X. / Zhang, T. / Ding, J.
History
DepositionApr 1, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: GTP-binding protein Rheb
B: GTP-binding protein Rheb
C: GTP-binding protein Rheb
D: GTP-binding protein Rheb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,1728
Polymers80,4004
Non-polymers1,7734
Water4,486249
1
A: GTP-binding protein Rheb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5432
Polymers20,1001
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-7 kcal/mol
Surface area8350 Å2
MethodPISA
2
B: GTP-binding protein Rheb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5432
Polymers20,1001
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-7 kcal/mol
Surface area8530 Å2
MethodPISA
3
C: GTP-binding protein Rheb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5432
Polymers20,1001
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area690 Å2
ΔGint-7 kcal/mol
Surface area8600 Å2
MethodPISA
4
D: GTP-binding protein Rheb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5432
Polymers20,1001
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-8 kcal/mol
Surface area8210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.426, 78.656, 117.398
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
GTP-binding protein Rheb / Ras homolog enriched in brain


Mass: 20099.895 Da / Num. of mol.: 4 / Fragment: GTPase domain / Mutation: Y35N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RHEB, RHEB2 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q15382
#2: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.17 Å3/Da / Density % sol: 43.21 %
Crystal growTemperature: 290 K / Method: evaporation / pH: 5.5
Details: 0.10% n-Octyl-beta-D-glucoside: 0.1 M Sodium citrate tribasic, pH 5.5: 22% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 41416 / % possible obs: 99.9 % / Redundancy: 12.7 % / Biso Wilson estimate: 34.89 Å2 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.031 / Rrim(I) all: 0.113 / Χ2: 0.67 / Net I/σ(I): 4.1 / Num. measured all: 524442
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.149.70.57219980.9020.1820.6020.44997.7
2.14-2.1810.70.52820320.930.1630.5540.45499.5
2.18-2.2211.60.47920290.9580.1430.5010.463100
2.22-2.26120.44420400.9670.1320.4640.469100
2.26-2.3111.90.39720550.9760.1190.4140.478100
2.31-2.3713.20.35820450.980.1010.3720.479100
2.37-2.4213.70.33120440.9840.0920.3430.501100
2.42-2.4913.70.2820410.9860.0780.2910.504100
2.49-2.5613.50.23920420.9880.0670.2480.539100
2.56-2.6513.30.2220600.9830.0620.2290.536100
2.65-2.7412.80.20120490.9910.0580.2090.557100
2.74-2.8512.40.1720650.9930.050.1780.582100
2.85-2.9813.70.14720690.9930.0410.1530.646100
2.98-3.1413.60.12720920.9950.0350.1310.703100
3.14-3.3313.50.1120700.9960.0310.1140.803100
3.33-3.5912.70.09320820.9970.0270.0970.901100
3.59-3.9513.10.08420810.9970.0240.0881.03100
3.95-4.5213.50.07821120.9980.0220.0811.139100
4.52-5.712.30.07221410.9980.0210.0761.034100
5.7-5012.20.06622690.9990.020.0690.945100

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XTQ
Resolution: 2.101→39.328 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 24.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1991 4.82 %1
Rwork0.1866 39274 --
obs0.1888 41265 99.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.74 Å2 / Biso mean: 45.5736 Å2 / Biso min: 16.23 Å2
Refinement stepCycle: final / Resolution: 2.101→39.328 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5216 0 112 249 5577
Biso mean--36.28 43.14 -
Num. residues----662
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075411
X-RAY DIFFRACTIONf_angle_d0.9827325
X-RAY DIFFRACTIONf_chiral_restr0.056852
X-RAY DIFFRACTIONf_plane_restr0.005901
X-RAY DIFFRACTIONf_dihedral_angle_d9.9563242
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.101-2.15350.28151380.2306271998
2.1535-2.21170.26741350.2162775100
2.2117-2.27680.26671350.20912762100
2.2768-2.35030.30291460.19652761100
2.3503-2.43420.25351460.2042783100
2.4342-2.53170.25771560.19612785100
2.5317-2.64690.29231060.2032807100
2.6469-2.78640.27531180.21172824100
2.7864-2.96090.27261610.20912780100
2.9609-3.18950.26371770.2042779100
3.1895-3.51020.2481380.18262834100
3.5102-4.01770.19391570.16112821100
4.0177-5.06020.1661480.15472882100
5.0602-39.3280.23971300.1911296298
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)
15.1303-0.6789-0.99166.8035-0.85566.32120.2980.4087-0.1568-0.2391-0.22010.3886-0.3878-0.32-0.07830.20590.04-0.06830.3517-0.00110.2317-4.509-57.926-1.738
22.10084.1192.11986.22710.13822.4939-0.82370.39180.7846-1.371-0.16920.4387-1.2627-0.73911.01361.0490.1726-0.21690.93440.09960.5302-13.27-55.7276.864
32.8631-6.10747.16346.903-7.70352.48360.21860.0108-0.2232-0.7737-0.0905-0.08920.4015-0.4384-0.08380.36270.0982-0.00750.4887-0.04610.31432.771-62.587-1.488
47.4554-2.51-0.01283.8736-1.14435.45310.10650.1726-0.029-0.15160.02430.7856-0.8236-1.6112-0.11660.52250.25160.0310.76820.00960.3514-8.351-46.526-9.101
56.41391.43640.95915.95340.06467.2757-0.1706-0.14910.79260.08680.0091-0.0549-1.45630.03250.06030.60640.0506-0.01260.3615-0.02390.2746-14.062-56.823-11.444
62.17428.8744-7.95298.8058-7.33596.41870.9328-1.01320.38951.4156-0.8004-0.1019-1.51430.2932-0.18290.69090.1291-0.02570.5196-0.10790.3991-13.555-55.893-20.201
75.16630.2788-0.62529.5131-4.85786.631-0.1550.161-0.0969-0.0577-0.1108-0.5074-0.2560.54970.27560.2188-0.0177-0.05030.4124-0.05480.2215-6.213-63.488-10.265
85.509-3.05212.64846.6448-1.05973.5922-0.0696-0.1241-0.04010.31450.2173-0.5130.0346-0.1247-0.17850.2197-0.0475-0.02140.1828-0.06380.2005-36.579-52.06-28.241
95.03464.20663.45337.12862.87297.07030.1132-1.18110.67230.7127-0.32570.8604-0.8478-1.6590.21960.51230.14820.03160.7837-0.04790.4302-38.134-44.008-36.844
107.8786-1.09040.79037.50255.40527.7287-0.286-0.4927-0.31160.5258-0.12290.1587-0.3006-0.33940.27070.3247-0.017-0.09580.27370.05710.2711-31.905-58.554-30.855
116.6465-8.0294-5.57442.23712.06152.2433-0.1286-0.61930.07630.33970.1002-0.060.08020.2115-0.15270.3289-0.0481-0.01610.3046-0.05540.3706-31.945-61.807-26.661
127.5302-0.7674-2.65033.841.61356.64470.08530.22552.23880.1559-0.196-0.7876-1.2274-0.141-0.03160.8807-0.0075-0.18490.3853-0.00650.7343-52.452-48.113-23.996
137.4725-2.4532-2.82883.8062-0.18994.02490.093-0.79521.3756-0.061-0.0673-0.7346-0.6110.49650.02890.3765-0.03030.03580.21-0.01630.3704-42.588-51.267-22.12
142.17144.0542-6.51923.3082-2.4216.13690.06590.21411.7155-0.05050.2240.465-0.665-0.2578-0.31220.43120.0486-0.01660.19990.01440.325-48.056-46.06-16.528
157.58698.2262-4.8478.665-4.72493.7033-0.6657-0.2237-0.1167-0.8910.2507-0.37520.56350.12850.15630.3373-0.0096-0.02750.25570.05190.2519-40.294-54.01-15.648
164.4409-3.01473.07412.1537-2.36632.0673-0.0915-0.4297-0.459-0.00190.07220.46380.4049-1.03450.1250.359-0.03320.00360.44860.05770.3178-33.027-33.313-21.239
179.69578.3615-4.82617.5006-4.89822.1105-0.06990.5161-0.2634-0.341-0.0003-0.1007-0.0351-0.13070.11120.33540.0151-0.04720.27350.04210.2312-36.936-42.89-9.686
181.84133.007-1.74596.5825-6.08836.9632-0.31310.0901-0.1738-0.56940.2992-0.11750.7244-0.60820.11870.301-0.0396-0.05980.19240.04450.2725-31.458-44.413-19.829
196.55112.3242-5.04852.5343-4.33759.7906-0.29190.235-0.7986-0.9018-0.0698-0.5420.644-0.07260.33330.3546-0.01250.02530.1667-0.02610.326-29.461-54.597-20.002
204.0962.3721-0.72024.6487-0.60393.55280.1889-0.0916-0.33450.0557-0.1136-0.26910.42870.0834-0.08960.26630.0509-0.0350.1815-0.00360.184.3807-50.0536-30.8243
212.131.15880.30542.4842-0.15586.8282-0.2346-0.63570.13730.96480.0793-0.2538-0.13020.55670.17360.47130.0331-0.09250.2647-0.0360.37715.2074-41.2974-21.9911
222.95432.41211.73496.15982.22463.16750.4008-0.3367-0.83230.841-0.135-0.47990.9599-0.0901-0.21190.46260.05540.06480.3040.04430.37391.0209-58.1102-30.677
232.92512.412-0.78615.00381.15755.0888-0.0917-0.1831-0.55570.01490.0776-1.32850.41191.09380.0130.28410.09040.04830.4015-0.00540.412113.7465-44.8097-35.8024
245.5008-7.1466-1.37362.08993.89779.75750.3354-0.0880.3047-0.71020.215-0.7718-0.17931.0688-0.41740.2421-0.04020.10730.32360.00180.351815.1937-40.6655-41.818
258.6074-7.2674-3.26099.43971.66774.0283-0.10650.4526-0.5160.2794-0.0075-0.50951.07740.9268-0.0190.47930.1536-0.01520.4711-0.12320.422810.3593-51.7761-43.2653
263.12790.2273-2.40952.3890.00946.36550.06650.22520.0056-0.1122-0.06020.1957-0.0419-0.25480.00560.1480.0187-0.05430.18860.01750.1843-0.0891-42.8603-40.9255
272.08556.72922.41455.71351.37574.4153-0.1945-0.37151.0108-0.6862-0.8761.89750.1499-1.84191.1310.4646-0.0658-0.04810.8678-0.28330.8698-33.7831-58.2743-55.3412
289.96660.50483.32238.44197.66479.9037-0.48370.85210.0402-1.58760.4299-0.2296-0.75210.60940.08010.3912-0.12520.00430.4128-0.04320.2066-19.3201-56.3731-59.066
296.3253-7.61233.84412.1067-1.21486.7096-0.51921.59030.642-0.5209-0.63750.8399-2.07910.81430.98090.9327-0.2052-0.16870.7221-0.09580.7399-18.3097-57.8684-65.5646
307.80350.12362.881910.04862.42878.49050.0761-0.3499-0.3559-0.319-0.45561.15250.6181-1.86480.29090.6583-0.1962-0.08820.9153-0.22490.4627-32.3737-64.2391-58.9323
319.73833.0748-0.83957.45581.79252.2059-0.9228-0.35951.36950.15090.13250.6179-1.9853-1.2440.67350.95210.1216-0.25160.79780.02050.5444-27.2013-44.4518-53.5007
328.9588-4.1247-3.26954.01970.90568.3917-0.27520.21760.6061-0.1871-0.046-0.0162-1.0567-0.72440.34070.51510.0137-0.1110.2982-0.08170.2659-21.5296-48.5319-47.5113
332.2039-2.6097-5.11653.66492.70749.0246-0.62030.9997-0.68310.3393-0.15940.5730.43-1.53520.88580.4416-0.10060.03440.5994-0.12390.3216-23.1935-56.1461-47.2749
347.498-0.1875-0.99092.11191.0222.0488-0.74670.7169-0.6588-0.53820.0571-0.38140.13071.35970.42940.4308-0.09270.02960.4751-0.05590.3392-5.2469-56.8129-48.578
357.1711-1.9302-0.38574.26020.99269.5818-0.301-0.4125-0.14390.34370.08290.00280.2193-0.44320.23210.3354-0.0429-0.00020.1966-0.02650.2192-17.7868-58.7144-43.6938
362.1933-2.8312-8.343.3711.48142.2952-0.57850.38-1.24830.4987-0.2410.22411.3599-1.32530.73530.5862-0.201-0.01550.732-0.19970.4471-27.7237-65.5029-49.4645
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 28 )A3 - 28
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 40 )A29 - 40
3X-RAY DIFFRACTION3chain 'A' and (resid 41 through 60 )A41 - 60
4X-RAY DIFFRACTION4chain 'A' and (resid 61 through 107 )A61 - 107
5X-RAY DIFFRACTION5chain 'A' and (resid 108 through 130 )A108 - 130
6X-RAY DIFFRACTION6chain 'A' and (resid 131 through 141 )A131 - 141
7X-RAY DIFFRACTION7chain 'A' and (resid 142 through 170 )A142 - 170
8X-RAY DIFFRACTION8chain 'B' and (resid 3 through 28 )B3 - 28
9X-RAY DIFFRACTION9chain 'B' and (resid 29 through 40 )B29 - 40
10X-RAY DIFFRACTION10chain 'B' and (resid 41 through 49 )B41 - 49
11X-RAY DIFFRACTION11chain 'B' and (resid 50 through 60 )B50 - 60
12X-RAY DIFFRACTION12chain 'B' and (resid 61 through 72 )B61 - 72
13X-RAY DIFFRACTION13chain 'B' and (resid 73 through 89 )B73 - 89
14X-RAY DIFFRACTION14chain 'B' and (resid 90 through 107 )B90 - 107
15X-RAY DIFFRACTION15chain 'B' and (resid 108 through 119 )B108 - 119
16X-RAY DIFFRACTION16chain 'B' and (resid 120 through 130 )B120 - 130
17X-RAY DIFFRACTION17chain 'B' and (resid 131 through 141 )B131 - 141
18X-RAY DIFFRACTION18chain 'B' and (resid 142 through 152 )B142 - 152
19X-RAY DIFFRACTION19chain 'B' and (resid 153 through 170 )B153 - 170
20X-RAY DIFFRACTION20chain 'C' and (resid 2 through 28 )C2 - 28
21X-RAY DIFFRACTION21chain 'C' and (resid 29 through 40 )C29 - 40
22X-RAY DIFFRACTION22chain 'C' and (resid 41 through 60 )C41 - 60
23X-RAY DIFFRACTION23chain 'C' and (resid 61 through 89 )C61 - 89
24X-RAY DIFFRACTION24chain 'C' and (resid 90 through 105 )C90 - 105
25X-RAY DIFFRACTION25chain 'C' and (resid 106 through 119 )C106 - 119
26X-RAY DIFFRACTION26chain 'C' and (resid 120 through 170 )C120 - 170
27X-RAY DIFFRACTION27chain 'D' and (resid 4 through 13 )D4 - 13
28X-RAY DIFFRACTION28chain 'D' and (resid 14 through 27 )D14 - 27
29X-RAY DIFFRACTION29chain 'D' and (resid 28 through 40 )D28 - 40
30X-RAY DIFFRACTION30chain 'D' and (resid 41 through 60 )D41 - 60
31X-RAY DIFFRACTION31chain 'D' and (resid 61 through 79 )D61 - 79
32X-RAY DIFFRACTION32chain 'D' and (resid 80 through 107 )D80 - 107
33X-RAY DIFFRACTION33chain 'D' and (resid 108 through 123 )D108 - 123
34X-RAY DIFFRACTION34chain 'D' and (resid 124 through 130 )D124 - 130
35X-RAY DIFFRACTION35chain 'D' and (resid 131 through 152 )D131 - 152
36X-RAY DIFFRACTION36chain 'D' and (resid 153 through 171 )D153 - 171

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