[English] 日本語
Yorodumi
- PDB-8ar7: Bovine glutamate dehydrogenase in ternary complex with the allost... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ar7
TitleBovine glutamate dehydrogenase in ternary complex with the allosteric activators ADP and leucine
ComponentsGlutamate dehydrogenase (NAD(P)(+))
KeywordsCYTOSOLIC PROTEIN / Glutamate dehydrogenase / allosteric regulator / ADP / Leucine
Function / homology
Function and homology information


Glutamate and glutamine metabolism / Transcriptional activation of mitochondrial biogenesis / tricarboxylic acid metabolic process / glutamate dehydrogenase [NAD(P)+] / glutamate dehydrogenase (NAD+) activity / glutamate catabolic process / glutamine metabolic process / Mitochondrial protein degradation / positive regulation of insulin secretion / mitochondrial matrix ...Glutamate and glutamine metabolism / Transcriptional activation of mitochondrial biogenesis / tricarboxylic acid metabolic process / glutamate dehydrogenase [NAD(P)+] / glutamate dehydrogenase (NAD+) activity / glutamate catabolic process / glutamine metabolic process / Mitochondrial protein degradation / positive regulation of insulin secretion / mitochondrial matrix / nucleotide binding / mitochondrion
Similarity search - Function
NAD(P) binding domain of glutamate dehydrogenase / Leu/Phe/Val dehydrogenases active site / Glu / Leu / Phe / Val dehydrogenases active site. / Glutamate/phenylalanine/leucine/valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, dimerisation domain / Glu/Leu/Phe/Val dehydrogenase, dimerisation domain / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, C-terminal / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / : / LEUCINE / Glutamate dehydrogenase 1, mitochondrial
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.448 Å
AuthorsAleshin, V.A. / Bellinzoni, M.
Funding support France, 1items
OrganizationGrant numberCountry
Pasteur Institute France
Citation
Journal: Int J Mol Sci / Year: 2022
Title: Structural Basis for the Binding of Allosteric Activators Leucine and ADP to Mammalian Glutamate Dehydrogenase.
Authors: Aleshin, V.A. / Bunik, V.I. / Bruch, E.M. / Bellinzoni, M.
#1: Journal: Preprints / Year: 2022
Title: Structural Basis for the Binding of Allosteric Activators Leucine and ADP to Mammalian Glutamate Dehydrogenase
Authors: Aleshin, V.A. / Bunik, V.I. / Bruch, E.M. / Bellinzoni, M.
History
DepositionAug 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutamate dehydrogenase (NAD(P)(+))
B: Glutamate dehydrogenase (NAD(P)(+))
C: Glutamate dehydrogenase (NAD(P)(+))
D: Glutamate dehydrogenase (NAD(P)(+))
E: Glutamate dehydrogenase (NAD(P)(+))
F: Glutamate dehydrogenase (NAD(P)(+))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)373,87624
Polymers370,2916
Non-polymers3,58518
Water7,909439
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41910 Å2
ΔGint-175 kcal/mol
Surface area98580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.877, 178.705, 123.884
Angle α, β, γ (deg.)90, 104, 90
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Glutamate dehydrogenase (NAD(P)(+))


Mass: 61715.160 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle)
References: UniProt: A0A140T871, glutamate dehydrogenase [NAD(P)+]
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-LEU / LEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H13NO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 439 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% EtOH, 30% 2-methyl-2,4-pentanediol (MPD)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.448→120.203 Å / Num. obs: 82997 / % possible obs: 92 % / Redundancy: 5.37 %
Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways throughout the data processing steps (rejection of overloaded or too partial reflections, outlier/misfit rejections during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary!
CC1/2: 0.989 / CC1/2 anomalous: -0.026 / Rmerge(I) obs: 0.198 / Rpim(I) all: 0.0945 / Rrim(I) all: 0.2201 / AbsDiff over sigma anomalous: 0.773 / Baniso tensor eigenvalue 1: 14.7539 Å2 / Baniso tensor eigenvalue 2: 35.9606 Å2 / Baniso tensor eigenvalue 3: 0 Å2 / Baniso tensor eigenvector 1 ortho1: 0.9732 / Baniso tensor eigenvector 1 ortho2: 0 / Baniso tensor eigenvector 1 ortho3: 0.2301 / Baniso tensor eigenvector 2 ortho1: 0 / Baniso tensor eigenvector 2 ortho2: 1 / Baniso tensor eigenvector 2 ortho3: 0 / Baniso tensor eigenvector 3 ortho1: -0.2301 / Baniso tensor eigenvector 3 ortho2: 0 / Baniso tensor eigenvector 3 ortho3: 0.9732 / Aniso diffraction limit 1: 3.035 Å / Aniso diffraction limit 2: 3.121 Å / Aniso diffraction limit 3: 2.448 Å / Aniso diffraction limit axis 1 ortho1: 0.94808 / Aniso diffraction limit axis 1 ortho2: 0 / Aniso diffraction limit axis 1 ortho3: 0.31799 / Aniso diffraction limit axis 2 ortho1: 0 / Aniso diffraction limit axis 2 ortho2: 1 / Aniso diffraction limit axis 2 ortho3: 0 / Aniso diffraction limit axis 3 ortho1: -0.31799 / Aniso diffraction limit axis 3 ortho2: 0 / Aniso diffraction limit axis 3 ortho3: 0.94808 / Net I/σ(I): 6.82 / Num. measured all: 445692 / Observed signal threshold: 1.2 / Orthogonalization convention: pdb / % possible anomalous: 91.4 / % possible ellipsoidal: 92 / % possible ellipsoidal anomalous: 91.4 / % possible spherical: 59 / % possible spherical anomalous: 58.3 / Redundancy anomalous: 2.74 / Signal type: local
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2CC1/2 anomalousRpim(I) allRrim(I) allAbsDiff over sigma anomalous% possible anomalous% possible ellipsoidal% possible ellipsoidal anomalous% possible spherical% possible spherical anomalousRedundancy anomalous% possible all
7.931-120.2034.910.077316.12039720397415041500.9920.0530.03830.08680.7279797.99797.9972.5897.9
6.296-7.9315.130.100213.152127121271415041500.987-0.0380.04830.11170.78898.599.398.599.398.52.6499.3
5.488-6.2965.130.121710.992129721297414941490.983-0.1310.05910.13590.77596.197.696.197.696.12.6497.6
4.985-5.4885.440.127911.082256922569415041500.983-0.1510.06040.14190.78998.499.498.499.498.42.7999.4
4.628-4.9855.430.116211.732252922529415041500.986-0.0420.05480.12890.77498.899.398.899.398.82.7799.3
4.354-4.6285.30.128910.972200322003414941490.983-0.1240.06190.14350.77898.899.398.899.398.82.799.3
4.134-4.3545.340.15589.492216122161415141510.977-0.0630.07440.17320.7797.298.297.298.297.22.7398.2
3.954-4.1345.330.18388.422211522115415041500.971-0.0740.0880.20440.78498.899.198.899.198.82.7199.1
3.801-3.9545.510.22677.522288622886415041500.965-0.0950.10660.25130.76598.69998.69998.62.899
3.67-3.8015.560.27366.522307623076414941490.96-0.0330.12810.30290.77298.899.198.899.198.82.8299.1
3.555-3.675.60.35855.462322723227415041500.933-0.0490.16720.39660.78498.89998.89998.82.8499
3.453-3.5555.360.45314.462225022250415041500.8950.0090.21670.5040.77798.69998.69998.62.7299
3.362-3.4535.40.55453.782239822398414941490.848-0.0230.26410.61610.77898.298.998.298.998.22.7498.9
3.279-3.3625.510.69983.212285022850414941490.773-0.0270.32870.77540.75898.198.898.198.898.12.898.8
3.203-3.2795.270.82652.642189421894415241520.69500.39850.92070.78996.497.596.497.596.42.6997.5
3.13-3.2035.30.88652.352201322013415041500.676-0.0190.42660.9870.76991.792.291.792.291.72.6992.2
3.047-3.135.290.8622.422192421924414741470.6070.0040.41630.96030.7679.480.279.473.472.62.6980.2
2.947-3.0475.321.02242.132209222092415141510.52-0.070.48981.13710.76279.980.879.954.253.22.7280.8
2.793-2.9475.540.95792.282298322983415041500.544-0.0540.44691.05960.77469.869.969.829.4292.8269.9
2.448-2.7935.721.21131.782375723757415141510.407-0.0810.55111.33310.7926160.9619.18.92.9160.9

-
Processing

Software
NameVersionClassification
BUSTER2.10.4 (8-JUN-2022)refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JCZ

3jcz


Resolution: 2.448→120.2 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.927 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.322
RfactorNum. reflection% reflectionSelection details
Rfree0.2145 4196 -RANDOM
Rwork0.1919 ---
obs0.193 82997 59 %-
Displacement parametersBiso mean: 68.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.782 Å20 Å20.7712 Å2
2--1.2819 Å20 Å2
3----2.064 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 2.448→120.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22994 0 222 439 23655
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00623708HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.7532098HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d10896SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes4077HARMONIC5
X-RAY DIFFRACTIONt_it23708HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion3114SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact19680SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.44
X-RAY DIFFRACTIONt_other_torsion2.69
LS refinement shellResolution: 2.45→2.65 Å
RfactorNum. reflection% reflection
Rfree0.3145 81 -
Rwork0.2964 --
obs0.2972 1660 5.63 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.2232-0.6522-0.86173.56180.41312.4736-0.1882-0.04470.3433-0.04470.1277-0.37180.3433-0.37180.06040.0182-0.08320.0023-0.0121-0.0253-0.1046-4.422716.974224.6825
23.50120.5480.34557.9152-1.02223.7498-0.1968-1.55880.8553-1.55880.5203-0.60730.8553-0.6073-0.32350.058-0.2302-0.32890.16170.0273-0.0162-6.955711.2823-1.0094
33.3719-3.3113-0.95183.26483.27288.10460.3464-0.6294-0.4783-0.6294-0.27860.6577-0.47830.6577-0.06780.10280.0450.05180.06340.0647-0.166725.956127.5937-7.2632
42.93581.2382-0.23486.65151.36482.3018-0.1944-0.47081.2848-0.47080.0656-0.17561.2848-0.17560.1289-0.01780.00640.0828-0.1501-0.1682-0.03487.19243.869814.3063
52.75090.5092-0.54351.7584-0.03442.1906-0.03310.33740.52270.33740.01650.53810.52270.53810.0166-0.03950.2356-0.03120.0589-0.0466-0.136131.340716.423438.4353
67.8658-0.08180.09983.55260.62382.81910.1280.06990.82220.06990.16370.62650.82220.6265-0.29170.07430.2904-0.02780.022-0.06060.06245.96463.42420.3173
73.55061.3611-2.67891.0923-3.72041.3805-0.1483-0.60021.1269-0.6002-0.0752-0.23491.1269-0.23490.22340.34480.18470.0590.0576-0.0598-0.125122.893415.5897-6.1452
87.3561-1.0398-1.38661.45810.04681.6105-0.1614-0.10910.0395-0.10910.59321.22760.03951.2276-0.4319-0.18780.12230.02580.15910.0563-0.165242.704625.060223.8068
93.0612-0.85770.36382.0050.05373.79740.0322-0.0975-0.3422-0.09750.03740.044-0.34220.044-0.0695-0.0733-0.02570.0672-0.09190.0104-0.063616.011149.423426.3402
104.736-0.5415-0.05314.6867-1.82763.9837-0.0166-0.0329-0.8054-0.0329-0.26480.4922-0.80540.49220.28140.0563-0.09450.1135-0.09270.09020.315229.140456.00984.4146
112.12170.9827-0.0042.80941.760810.90720.0376-0.36840.6945-0.3684-0.05831.30860.69451.30860.02070.00360.27390.11250.12420.1199-0.066234.041819.5169-2.5595
12-0.7073-1.29522.11965.7244-2.96034.66070.3777-0.5847-0.432-0.5847-0.0683-0.3955-0.432-0.3955-0.3093-0.01180.0176-0.0249-0.1064-0.0468-0.15899.732445.72917.3297
132.15850.0491-0.69383.1701-0.40563.1265-0.22860.13610.25630.13610.18380.5710.25630.5710.0448-0.09950.2252-0.05790.1063-0.0546-0.170125.126923.831559.7373
141.9321-0.63920.3344.7858-0.4714.2038-0.20540.777-0.03560.7770.10461.0003-0.03561.00030.1008-0.12010.2747-0.21770.4421-0.1370.032228.192328.038885.4276
153.62441.51-3.09662.2175-0.89237.88760.16490.7113-1.06420.7113-0.02390.0414-1.06420.0414-0.1410.25980.2195-0.0277-0.0157-0.0708-0.1791-5.479745.033285.517
161.7214-1.66710.86182.8925-0.8263.0185-0.29160.52180.64030.52180.29950.23970.64030.2397-0.00790.00250.21730.08570.04920.1006-0.08313.812215.637175.0367
172.8587-1.12630.03122.25750.16862.1307-0.0178-0.10630.5609-0.1063-0.002-0.25460.5609-0.25460.01980.0251-0.0530.0419-0.05630.0134-0.0698-10.922717.506247.3478
184.19521.03-0.08042.862-0.3152.2760.00190.31780.43760.31780.0966-0.30240.4376-0.3024-0.09860.10350.00820.0853-0.10010.047-0.0228-25.263112.418469.1475
193.598-2.4897-5.42527.284.798911.1184-0.25980.75530.05090.75530.22460.92020.05090.92020.03520.07430.1541-0.05010.11860.0502-0.1781-2.22333.626289.0057
206.4318-0.1509-0.61361.86820.12910.6164-0.15690.162-0.01940.1620.288-0.7945-0.0194-0.7945-0.1311-0.11690.04710.0506-0.11110.01260.0282-22.178731.138257.6174
212.21440.63630.22931.76610.30853.2141-0.0178-0.0367-0.4374-0.03670.14620.1101-0.43740.1101-0.12840.00310.05910.0295-0.0759-0.03260.02224.162553.50846.3105
222.3796-0.1564-0.3776.62850.26351.86590.07360.3445-0.43310.34450.1884-0.1695-0.4331-0.1695-0.2620.06420.14580.0747-0.11580.0056-0.0178-8.970866.834665.201
23-0.2301-0.6031-0.09552.0970.490712.62410.05070.4234-0.07210.42340.057-0.7921-0.0721-0.7921-0.10770.05850.14410.07930.0723-0.0261-0.0413-13.548235.715684.2805
242.29722.09410.58465.48781.25842.17660.19340.3496-0.35680.34960.00570.3117-0.35680.3117-0.19920.06160.029-0.104-0.1023-0.0313-0.077410.664156.635165.4057
25-1.4016-2.08382.63012.4532-0.86151.44350.1208-0.21010.0406-0.2101-0.37620.46110.04060.46110.25540.30440.07740.0620.09970.0237-0.24912.40678.715718.5833
263.0193-5.81540.70610-1.57810.1644-0.2194-1.2994-0.3004-1.29940.19770.3752-0.30040.37520.02170.2390.1634-0.05890.1393-0.1294-0.038335.315928.747723.604
273.3127-3.6269-6.19812.1481-5.3918-3.29750.2696-0.13410.0897-0.13410.1930.58110.08970.5811-0.46260.18030.08160.27380.26430.1185-0.00758.800438.628411.5031
28-3.3862-7.60216.447201.9763.44510.02830.58110.0180.5811-0.215-0.14470.018-0.14470.18670.39420.2271-0.17280.0279-0.0843-0.15098.46218.251468.6038
293.27190.3094-3.78584.2061-4.92621.0417-0.07611.2114-0.62321.2114-0.08710.2592-0.62320.25920.1632-0.00290.0004-0.03120.19570.1859-0.0993-14.798134.72556.453
30-1.4156-2.52932.66160.1163-1.98951.41560.11910.21470.04340.21470.02980.07620.04340.0762-0.14890.00840.16940.01240.0186-0.10930.112311.731748.579163.945
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|65 - A|270 A|701 }A65 - 270
2X-RAY DIFFRACTION1{ A|65 - A|270 A|701 }A701
3X-RAY DIFFRACTION2{ A|271 - A|451 }A271 - 451
4X-RAY DIFFRACTION3{ A|452 - A|505 }A452 - 505
5X-RAY DIFFRACTION4{ A|506 - A|560 A|661 }A506 - 560
6X-RAY DIFFRACTION4{ A|506 - A|560 A|661 }A661
7X-RAY DIFFRACTION5{ B|64 - B|270 B|701 }B64 - 270
8X-RAY DIFFRACTION5{ B|64 - B|270 B|701 }B701
9X-RAY DIFFRACTION6{ B|271 - B|451 }B271 - 451
10X-RAY DIFFRACTION7{ B|452 - B|505 }B452 - 505
11X-RAY DIFFRACTION8{ B|506 - B|560 B|661 }B506 - 560
12X-RAY DIFFRACTION8{ B|506 - B|560 B|661 }B661
13X-RAY DIFFRACTION9{ C|67 - C|270 C|701 }C67 - 270
14X-RAY DIFFRACTION9{ C|67 - C|270 C|701 }C701
15X-RAY DIFFRACTION10{ C|271 - C|451 }C271 - 451
16X-RAY DIFFRACTION11{ C|452 - C|505 }C452 - 505
17X-RAY DIFFRACTION12{ C|506 - C|560 C|661 }C506 - 560
18X-RAY DIFFRACTION12{ C|506 - C|560 C|661 }C661
19X-RAY DIFFRACTION13{ D|64 - D|270 D|701 }D64 - 270
20X-RAY DIFFRACTION13{ D|64 - D|270 D|701 }D701
21X-RAY DIFFRACTION14{ D|271 - D|451 }D271 - 451
22X-RAY DIFFRACTION15{ D|452 - D|505 }D452 - 505
23X-RAY DIFFRACTION16{ D|506 - D|560 D|661 }D506 - 560
24X-RAY DIFFRACTION16{ D|506 - D|560 D|661 }D661
25X-RAY DIFFRACTION17{ E|62 - E|270 E|701 }E62 - 270
26X-RAY DIFFRACTION17{ E|62 - E|270 E|701 }E701
27X-RAY DIFFRACTION18{ E|271 - E|451 }E271 - 451
28X-RAY DIFFRACTION19{ E|452 - E|505 }E452 - 505
29X-RAY DIFFRACTION20{ E|506 - E|560 E|661 }E506 - 560
30X-RAY DIFFRACTION20{ E|506 - E|560 E|661 }E661
31X-RAY DIFFRACTION21{ F|62 - F|270 F|701 }F62 - 270
32X-RAY DIFFRACTION21{ F|62 - F|270 F|701 }F701
33X-RAY DIFFRACTION22{ F|271 - F|451 }F271 - 451
34X-RAY DIFFRACTION23{ F|452 - F|505 }F452 - 505
35X-RAY DIFFRACTION24{ F|506 - F|560 F|661 }F506 - 560
36X-RAY DIFFRACTION24{ F|506 - F|560 F|661 }F661
37X-RAY DIFFRACTION25{ A|601 }A601
38X-RAY DIFFRACTION26{ B|601 }B601
39X-RAY DIFFRACTION27{ C|601 }C601
40X-RAY DIFFRACTION28{ D|602 }D602
41X-RAY DIFFRACTION29{ E|602 }E602
42X-RAY DIFFRACTION30{ F|601 }F601

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • 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

-
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

Read more