[English] 日本語
Yorodumi
- PDB-8owm: Crystal structure of glutamate dehydrogenase 2 from Arabidopsis t... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8owm
TitleCrystal structure of glutamate dehydrogenase 2 from Arabidopsis thaliana binding Ca, NAD and 2,2-dihydroxyglutarate
ComponentsGlutamate dehydrogenase 2
KeywordsOXIDOREDUCTASE / glutamic acid / calcium / NAD cofactor / nitrogen metabolism / 2 / 2-dihydroxyglutarate
Function / homology
Function and homology information


glutamate dehydrogenase [NAD(P)+] activity / glutamate dehydrogenase [NAD(P)+] / glutamate dehydrogenase (NADP+) activity / glutamate dehydrogenase (NAD+) activity / plant-type vacuole / amino acid metabolic process / cobalt ion binding / copper ion binding / mitochondrion / zinc ion binding ...glutamate dehydrogenase [NAD(P)+] activity / glutamate dehydrogenase [NAD(P)+] / glutamate dehydrogenase (NADP+) activity / glutamate dehydrogenase (NAD+) activity / plant-type vacuole / amino acid metabolic process / cobalt ion binding / copper ion binding / mitochondrion / zinc ion binding / ATP binding / plasma membrane
Similarity search - Function
Glutamate dehydrogenase / 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 ...Glutamate dehydrogenase / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / 2,2-bis(oxidanyl)pentanedioic acid / Glutamate dehydrogenase 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsGrzechowiak, M. / Ruszkowski, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre2018/31/D/NZ1/03630 Poland
CitationJournal: Plant Physiol Biochem / Year: 2023
Title: Structural and functional studies of Arabidopsis thaliana glutamate dehydrogenase isoform 2 demonstrate enzyme dynamics and identify its calcium binding site.
Authors: Marta Grzechowiak / Joanna Sliwiak / Mariusz Jaskolski / Milosz Ruszkowski /
Abstract: Glutamate dehydrogenase (GDH) is an enzyme at the crossroad of plant nitrogen and carbon metabolism. GDH catalyzes the conversion of 2-oxoglutarate into glutamate (2OG → Glu), utilizing ammonia as ...Glutamate dehydrogenase (GDH) is an enzyme at the crossroad of plant nitrogen and carbon metabolism. GDH catalyzes the conversion of 2-oxoglutarate into glutamate (2OG → Glu), utilizing ammonia as cosubstrate and NADH as coenzyme. The GDH reaction is reversible, meaning that the NAD-dependent reaction (Glu → 2OG) releases ammonia. In Arabidopsis thaliana, three GDH isoforms exist, AtGDH1, AtGDH2, and AtGDH3. The subject of this work is AtGDH2. Previous reports have suggested that enzymes homologous to AtGDH2 contain a calcium-binding EF-hand motif located in the coenzyme binding domain. Here, we show that while AtGDH2 indeed does bind calcium, the binding occurs elsewhere and the region predicted to be the EF-hand motif has a completely different structure. As the true calcium binding site is > 20 Å away from the active site, it seems to play a structural, rather than catalytic role. We also performed comparative kinetic characterization of AtGDH1 and AtGDH2 using spectroscopic methods and isothermal titration calorimetry, to note that the isoenzymes generally exhibit similar behavior, with calcium having only a minor effect. However, the spatial and temporal changes in the gene expression profiles of the three AtGDH genes point to AtGDH2 as the most prevalent isoform.
History
DepositionApr 28, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutamate dehydrogenase 2
B: Glutamate dehydrogenase 2
C: Glutamate dehydrogenase 2
D: Glutamate dehydrogenase 2
E: Glutamate dehydrogenase 2
F: Glutamate dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)279,32072
Polymers270,1636
Non-polymers9,15766
Water37,6512090
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40100 Å2
ΔGint-165 kcal/mol
Surface area74940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.544, 95.629, 95.841
Angle α, β, γ (deg.)90.416, 93.590, 117.775
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

-
Components

-
Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Glutamate dehydrogenase 2 / / GDH 2


Mass: 45027.188 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: GDH2, At5g07440, T2I1_150 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Gold
References: UniProt: Q38946, glutamate dehydrogenase [NAD(P)+]

-
Non-polymers , 8 types, 2156 molecules

#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: C2H6O2
#5: Chemical
ChemComp-U5C / 2,2-bis(oxidanyl)pentanedioic acid / 2,2-dihydroxyglutarate / 2,2-dihydroxypentanedioic acid


Mass: 164.113 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H8O6 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: Ca
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#8: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2090 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.16 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.12MMonosaccharides (0.02M D-Glucose; 0.02M D-Mannose; 0.02M D-Galactose; 0.02M L-Fucose; 0.02M D-Xylose; 0.02M N-Acetyl-D-Glucosamine ),0.1M Imidazole/MES buffer pH 6.5, 20% v/v Glycerol and 10% w/v PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.7→65.7 Å / Num. obs: 318817 / % possible obs: 96.9 % / Redundancy: 3.55 % / Biso Wilson estimate: 23.46 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.075 / Net I/σ(I): 10.76
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 2.92 % / Rmerge(I) obs: 0.758 / Mean I/σ(I) obs: 1.32 / Num. unique obs: 50659 / CC1/2: 0.624 / Rrim(I) all: 0.927 / % possible all: 95.2

-
Processing

Software
NameVersionClassification
PHENIX1.18.1_3865refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6yei
Resolution: 1.7→65.7 Å / SU ML: 0.1703 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 18.7346
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1721 3188 1 %
Rwork0.1438 315548 -
obs0.1441 318736 96.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.58 Å2
Refinement stepCycle: LAST / Resolution: 1.7→65.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18890 0 592 2090 21572
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009420188
X-RAY DIFFRACTIONf_angle_d0.994727343
X-RAY DIFFRACTIONf_chiral_restr0.0583017
X-RAY DIFFRACTIONf_plane_restr0.00723551
X-RAY DIFFRACTIONf_dihedral_angle_d16.50967550
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.730.28561350.280113268X-RAY DIFFRACTION94.06
1.73-1.750.32721360.267913495X-RAY DIFFRACTION95.6
1.75-1.780.25111370.256713570X-RAY DIFFRACTION95.78
1.78-1.810.31491370.24213563X-RAY DIFFRACTION95.9
1.81-1.850.27041380.223913644X-RAY DIFFRACTION96.16
1.85-1.880.23681370.209413624X-RAY DIFFRACTION96.22
1.88-1.920.18821380.189513593X-RAY DIFFRACTION96.44
1.92-1.960.18821380.17213663X-RAY DIFFRACTION96.62
1.96-2.010.19151380.165213688X-RAY DIFFRACTION96.72
2.01-2.060.22821380.151613686X-RAY DIFFRACTION96.89
2.06-2.110.18441400.143313791X-RAY DIFFRACTION96.99
2.11-2.180.16351390.134513782X-RAY DIFFRACTION97.07
2.18-2.250.18571380.133113668X-RAY DIFFRACTION97.27
2.25-2.330.15851390.128513747X-RAY DIFFRACTION96.96
2.33-2.420.16451390.131913725X-RAY DIFFRACTION97.23
2.42-2.530.1481390.132113804X-RAY DIFFRACTION97.31
2.53-2.660.17411400.128113831X-RAY DIFFRACTION97.68
2.66-2.830.16031400.127913882X-RAY DIFFRACTION98.11
2.83-3.050.17211400.132613847X-RAY DIFFRACTION98.23
3.05-3.350.18121400.13613874X-RAY DIFFRACTION98.19
3.35-3.840.14321410.122313960X-RAY DIFFRACTION98.37
3.84-4.840.12791400.110913894X-RAY DIFFRACTION98.19
4.84-65.70.16821410.1613949X-RAY DIFFRACTION98.66
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)
10.918407999068-0.543067566609-0.2366907703141.138868526390.3849030065590.5767139302950.0396707796760.0202040962834-0.0911445507128-0.03594878585-0.05043330415250.08859031640550.0408641545889-0.1156119240880.01368998319870.19889503708-0.00396249581458-0.01104781080310.204978474990.001155165827650.1624282586845.80431.36565.433
20.670110492942-0.111759484681-0.0914423459410.6735341510740.08491693616061.12371214299-0.0458088516369-0.128292354553-0.0853198160810.1217233341310.03717998414890.06272621199310.157287427573-0.08850891660590.01031852176680.2024345529280.003787846911060.003269872540260.2034002598090.005518196961220.164024474045.6333.83984.885
31.899979799210.1849632969320.06519120933520.5946856392570.09283248595560.7990757624980.02974560579020.1277109116330.0543818897822-0.02665728014580.0268525731059-0.0357833790585-0.2151216107140.0352344373553-0.05313032947430.2568940351810.002388662288150.01555741504380.157890880896-0.01035716652140.15772869170521.50366.01350.606
40.801093616941-0.367389459981-0.09228114481270.80302334770.2564104087091.059459061090.0267169826171-0.1038598217390.1992036925140.03197073658190.0311325177446-0.0554636284498-0.3969751199030.0326795137336-0.0419872144950.341631545861-0.02566541632910.002675758155940.16082688259-0.01933419729040.17830823376623.79876.97366.557
50.370048514438-0.0171358764553-0.02717532802260.984645901133-0.5477038758330.995646473706-0.02913843927210.0682569062207-0.0187177562998-0.04066781587480.0624825538091-0.04742901076820.0791963615550.118053132358-0.02367698926840.1728438486890.00349818264883-0.01894826611660.246209630685-0.02984346660270.18911291937445.76933.42456.686
60.9858648280750.3204010143710.05049479722630.6637429281480.001210139710810.4500543113920.0178277378146-0.034201092946-0.01834465370640.1323273370990.027424717301-0.164108335335-0.005978596307410.14488111702-0.04144168218450.2205141665150.0345051591872-0.03080582962160.25007388841-0.04171341889350.20828846696954.35937.39473.659
71.314853001080.618131212538-1.205471024481.4025757104-1.041123130532.276863656490.01087198226260.129307343883-0.215975902066-0.0803814550841-0.115962709315-0.3215224689380.1635806686310.3812152166210.1328834064050.2172966215830.0460317124269-0.0189620835660.42487954797-0.01917372231390.29793602445248.79625.42836.326
80.9188420311340.395824958147-0.6667264591880.910539010134-0.7790723544311.631727091080.05358719042450.0155758336284-0.1981909742990.0810122434808-0.0877632688742-0.07006603968750.1025976636020.2530382142630.05733530091820.2348251790090.0292524023979-0.03605024768930.225617298658-0.02475778812020.23902156156335.91317.7644.323
91.532212905360.347806326995-1.071955090990.732699062261-1.061982995672.190928903650.0415127672221-0.00560314748657-0.1976336774750.0675549336803-0.217599176324-0.2649559883590.1293320016740.3930854895270.1131226733410.288247262660.0511351593923-0.05594202388150.269799906127-0.05691791369640.26143678310338.31418.46636.02
100.8045232110850.00483477762449-0.09889162924450.990241651566-0.1436190974511.247702022210.05357674518490.231317753065-0.170952850942-0.150396923373-0.0198812897686-0.04570921005360.228472857140.142866495553-0.0250875415380.2363199024620.0455509573454-0.02641632568850.25069523271-0.05141765882190.22913120384128.51214.09232.624
111.53854821530.02323372348520.5937241785541.78952537438-0.01813524910332.942275332780.1008849482720.291895634343-0.492859518874-0.0996962583910.0409723548364-0.02878641891770.6833041311510.27314156454-0.02107667620750.6076493789190.186940244239-0.05109632764480.51426419565-0.1769548546480.53184194917436.514-6.33823.487
122.93609804175-0.957062607161-1.356008148872.7173992120.3110204353931.675406300970.111307453091-0.0207641777454-0.5299010941210.269466292537-0.0259822737230.12709908050.6272185824390.145347035583-0.006844730072150.7511957982990.106315138111-0.0694432800990.472439266749-0.1252709704880.63555643485831.353-9.21930.141
131.43646411976-0.109779620538-0.1219350582462.02875119931-0.007171706261491.22813600982-0.02032623402020.109144701373-0.26975705852-0.233026647671-0.0982763861513-0.4175000185290.4302003644790.331434872179-0.002928514395250.47921691390.1820924191860.05733589653580.538030316778-0.07540348513450.48606144716548.435.76624.474
143.93278416415-1.6750986488-0.7827092374483.18150041104-0.3464038933721.843869129170.05162496494730.22827774724-0.270081218808-0.0409237780613-0.05259823100490.03356994411040.0915707020238-0.147492515968-0.04225503910390.2217206334630.0261018104568-0.01504887989310.271087765673-0.02823472760620.2206675779622.12523.57126.038
158.078094275561.69822376855-1.820879867622.0046922154-0.5027100551381.60135809579-0.01583061104130.7214607746340.00757297834479-0.3733121930330.0167342053977-0.07726720699770.006694966164280.00386714906043-0.0299863541020.4196272603410.0671976117222-0.003312850703950.542430518589-0.06003983937190.25563867339935.4821.02714.712
160.713028488795-0.363286657958-0.07724638320383.037618092170.6435115672061.168920795110.0316491522520.267558229087-0.158570324191-0.241195407232-0.00143782762194-0.3339344153350.1302318245330.259642919084-0.02240440796410.2310632558190.0329955025880.01861223714970.467937653297-0.02182507725030.27994224839846.07331.38824.453
171.44501754703-0.2388985532140.2843780697230.335302247091-0.1692566704770.8674448376220.0253223474306-0.02269778106160.0993139513935-0.00944578069819-0.0192097677206-0.02038657041-0.190038089774-0.0126066255555-0.00491937389590.2495207706370.00252595895420.006899362775490.222966286664-0.006607732839280.17060247694725.80358.54629.808
180.6843740979730.05366685926460.09304626468550.438018949893-0.1209181281821.186413929030.008526686117370.1670139973980.0620211103429-0.0481286706607-0.00519619617495-0.04157038241-0.1647411795530.136214968492-0.003478208009750.2250625676180.0104438399461-0.00181953675860.251340107389-0.00151651848410.15947473019324.40157.09110.353
190.561878234389-0.6525081587320.08162207906543.067057438920.187331495170.689135642239-0.030678115832-0.0373217640998-0.1170519161260.1845202527230.09400333416630.3269059753120.105823462543-0.214726738464-0.06460068841570.198655515114-0.007922617983570.002457570192940.2837268366540.01272143921510.204161162911-3.47727.02447.33
200.409019153941-0.102036082657-0.2183911032583.551923618480.4865395262960.712025018275-0.0606038093505-0.0554547426169-0.1083796802960.1744504535650.08608154058510.2657059890230.0844206338527-0.174323357229-0.02801679568830.1949282945310.00915383618442-0.02670367279590.343711387313-0.01201710454350.198221621896-4.14329.53740.85
210.8477515518060.0227583063025-0.005177874914951.409434793130.1046152246350.991155939164-0.008359708395410.157081117548-0.0799476878685-0.1906996222970.06306597635040.1163596799180.0757300040683-0.228519636071-0.09262795825360.204960954330.00146265165312-0.007153314387060.2927034910520.006428610686870.174785544152-3.65836.12531.765
221.92983010985-0.2189528670020.2902836495481.79100848923-0.520789784221.63987283103-0.05967028917250.2374905251950.00496408371975-0.1875951077640.2755750007580.483875818434-0.0687789177922-0.628129626786-0.191561258940.322455176375-0.0385613441146-0.07677868122420.6659295381040.08111057114930.460467033245-24.63130.85227.534
232.927407043550.784246920554-0.2092275513181.54461016764-0.2932141629631.10468782044-0.01749635746460.13036030365-0.297934206279-0.1220594270810.1197041195970.17425749580.183994501336-0.338531972223-0.09776564218040.251889694373-0.0183521090925-0.03238678857880.3500019513670.001192913160350.261829177425-5.37424.23330.806
242.179970774391.7946517704-0.6544259321127.80722001701-3.047974115612.33069236172-0.1419010487740.333533823241-0.320611756167-0.675223133690.237351311432-0.07134252256290.468172153597-0.0938063447103-0.02341365125420.392945772311-0.0389385175726-0.01835751791710.421699819649-0.1014199787720.280518547574-0.40517.89123.064
253.576109416410.06944108677231.801749987070.712501368067-0.02890265974132.294621036590.06187938298920.073188694463-0.356833256694-0.1095943289960.09212775490370.1186218346880.240192419818-0.155554597131-0.1311134248870.338544159961-0.0427176769346-0.01017545744730.266863656921-0.01830900084990.282907573933.62812.52639.412
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 0:161 )A0 - 161
2X-RAY DIFFRACTION2( CHAIN A AND RESID 162:411 )A162 - 411
3X-RAY DIFFRACTION3( CHAIN B AND RESID 0:161 )B0 - 161
4X-RAY DIFFRACTION4( CHAIN B AND RESID 162:411 )B162 - 411
5X-RAY DIFFRACTION5( CHAIN C AND RESID -1:161 )C-1 - 161
6X-RAY DIFFRACTION6( CHAIN C AND RESID 162:411 )C162 - 411
7X-RAY DIFFRACTION7( CHAIN D AND RESID 0:42 )D0 - 42
8X-RAY DIFFRACTION8( CHAIN D AND RESID 43:76 )D43 - 76
9X-RAY DIFFRACTION9( CHAIN D AND RESID 77:113 )D77 - 113
10X-RAY DIFFRACTION10( CHAIN D AND RESID 114:227 )D114 - 227
11X-RAY DIFFRACTION11( CHAIN D AND RESID 228:249 )D228 - 249
12X-RAY DIFFRACTION12( CHAIN D AND RESID 250:273 )D250 - 273
13X-RAY DIFFRACTION13( CHAIN D AND RESID 274:338 )D274 - 338
14X-RAY DIFFRACTION14( CHAIN D AND RESID 339:358 )D339 - 358
15X-RAY DIFFRACTION15( CHAIN D AND RESID 359:384 )D359 - 384
16X-RAY DIFFRACTION16( CHAIN D AND RESID 385:411 )D385 - 411
17X-RAY DIFFRACTION17( CHAIN E AND RESID 0:161 )E0 - 161
18X-RAY DIFFRACTION18( CHAIN E AND RESID 162:411 )E162 - 411
19X-RAY DIFFRACTION19( CHAIN F AND RESID 0:76 )F0 - 76
20X-RAY DIFFRACTION20( CHAIN F AND RESID 77:113 )F77 - 113
21X-RAY DIFFRACTION21( CHAIN F AND RESID 114:227 )F114 - 227
22X-RAY DIFFRACTION22( CHAIN F AND RESID 228:308 )F228 - 308
23X-RAY DIFFRACTION23( CHAIN F AND RESID 309:358 )F309 - 358
24X-RAY DIFFRACTION24( CHAIN F AND RESID 359:384 )F359 - 384
25X-RAY DIFFRACTION25( CHAIN F AND RESID 385:411 )F385 - 411

+
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://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