[English] 日本語
Yorodumi
- PDB-8e8v: Structure of the short LOR domain of human AASS bound to N-ethyls... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8e8v
TitleStructure of the short LOR domain of human AASS bound to N-ethylsuccinimide
ComponentsAlpha-aminoadipic semialdehyde synthase, mitochondrial
KeywordsOXIDOREDUCTASE / lysine metabolism / ketoglutarate / mitochondrial / reductase
Function / homology
Function and homology information


saccharopine dehydrogenase (NADP+, L-lysine-forming) / saccharopine dehydrogenase (NAD+, L-glutamate-forming) / saccharopine dehydrogenase (NADP+, L-lysine-forming) activity / saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity / saccharopine dehydrogenase activity / saccharopine dehydrogenase (NAD+, L-lysine-forming) activity / lysine catabolic process / L-lysine catabolic process to acetyl-CoA via saccharopine / Lysine catabolism / lysine biosynthetic process via aminoadipic acid ...saccharopine dehydrogenase (NADP+, L-lysine-forming) / saccharopine dehydrogenase (NAD+, L-glutamate-forming) / saccharopine dehydrogenase (NADP+, L-lysine-forming) activity / saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity / saccharopine dehydrogenase activity / saccharopine dehydrogenase (NAD+, L-lysine-forming) activity / lysine catabolic process / L-lysine catabolic process to acetyl-CoA via saccharopine / Lysine catabolism / lysine biosynthetic process via aminoadipic acid / transcription corepressor activity / histone binding / mitochondrial matrix / intracellular membrane-bounded organelle / negative regulation of transcription by RNA polymerase II / mitochondrion / nucleus / cytoplasm / cytosol
Similarity search - Function
: / Saccharopine dehydrogenase, NADP binding domain / Saccharopine dehydrogenase-like, C-terminal / Saccharopine dehydrogenase NADP binding domain / Saccharopine dehydrogenase C-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, N-terminal / Alanine dehydrogenase/PNT, N-terminal domain / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/PNT, N-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, NAD(H)-binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
1-ETHYL-PYRROLIDINE-2,5-DIONE / Alpha-aminoadipic semialdehyde synthase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsKhamrui, S. / Lazarus, M.B.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM124838 United States
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)R21HD102745 United States
CitationJournal: Open Biology / Year: 2022
Title: Characterization and structure of the human lysine-2-oxoglutarate reductase domain, a novel therapeutic target for treatment of glutaric aciduria type 1.
Authors: Leandro, J. / Khamrui, S. / Suebsuwong, C. / Chen, P.J. / Secor, C. / Dodatko, T. / Yu, C. / Sanchez, R. / DeVita, R.J. / Houten, S.M. / Lazarus, M.B.
History
DepositionAug 25, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alpha-aminoadipic semialdehyde synthase, mitochondrial
B: Alpha-aminoadipic semialdehyde synthase, mitochondrial
C: Alpha-aminoadipic semialdehyde synthase, mitochondrial
D: Alpha-aminoadipic semialdehyde synthase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,8978
Polymers193,3894
Non-polymers5094
Water00
1
A: Alpha-aminoadipic semialdehyde synthase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4742
Polymers48,3471
Non-polymers1271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-aminoadipic semialdehyde synthase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4742
Polymers48,3471
Non-polymers1271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Alpha-aminoadipic semialdehyde synthase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4742
Polymers48,3471
Non-polymers1271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Alpha-aminoadipic semialdehyde synthase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4742
Polymers48,3471
Non-polymers1271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.099, 155.963, 78.352
Angle α, β, γ (deg.)90.000, 100.200, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Alpha-aminoadipic semialdehyde synthase, mitochondrial / LKR/SDH


Mass: 48347.137 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AASS / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9UDR5, saccharopine dehydrogenase (NADP+, L-lysine-forming), saccharopine dehydrogenase (NAD+, L-glutamate-forming)
#2: Chemical
ChemComp-NEN / 1-ETHYL-PYRROLIDINE-2,5-DIONE


Mass: 127.141 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H9NO2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.69 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.2 M NaCl, 0.1M HEPES, 25% PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 16, 2022
RadiationMonochromator: si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.45→47.49 Å / Num. obs: 66842 / % possible obs: 99.9 % / Redundancy: 5.2 % / CC1/2: 0.994 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.071 / Rrim(I) all: 0.164 / Net I/σ(I): 6.5 / Num. measured all: 350595 / Scaling rejects: 164
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.45-2.515.22.3782325244520.4281.1442.6440.899.2
11.49-47.495.10.06934126700.9920.0330.07719.198.7

-
Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8E8T

8e8t


Resolution: 2.45→47.49 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2578 3247 4.87 %
Rwork0.234 63424 -
obs0.2351 66671 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 233.49 Å2 / Biso mean: 84.5537 Å2 / Biso min: 37.13 Å2
Refinement stepCycle: final / Resolution: 2.45→47.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12703 0 36 0 12739
Biso mean--72.59 --
Num. residues----1616
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.45-2.48660.39941120.39532789
2.4866-2.52540.3661300.39222753
2.5254-2.56680.40811770.35932720
2.5668-2.61110.41091210.36032767
2.6111-2.65860.33321370.33432751
2.6586-2.70970.33451310.33132749
2.7097-2.7650.361750.32562735
2.765-2.82510.34191230.31372730
2.8251-2.89080.331440.2962757
2.8908-2.96310.33991560.29382730
2.9631-3.04320.28521380.27842733
3.0432-3.13270.27361570.26732767
3.1327-3.23380.30191540.26872731
3.2338-3.34940.28361470.27492748
3.3494-3.48350.29041540.2522747
3.4835-3.64190.25921580.23532719
3.6419-3.83390.21991300.21392788
3.8339-4.0740.23151560.19782755
4.074-4.38830.23621160.20132789
4.3883-4.82950.19791110.18382792
4.8295-5.52750.22611350.20142787
5.5275-6.96050.22541500.21382774
6.9605-47.490.20031350.18032813
Refinement TLS params.

Method: refined / 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)
12.3613-1.15351.51795.3451.19623.014-0.38090.9897-0.7419-1.04410.36670.3485-0.26330.11190.12120.7438-0.12070.05250.9759-0.39411.0528-9.358-12.261-33.406
22.84760.7950.15663.8871-1.17691.1018-0.1090.3308-0.46840.08930.0734-0.43240.43440.25670.07120.60620.04680.01060.7847-0.25720.7499-7.725-15.576-24.522
34.47280.1982-0.08966.5057-0.06266.68771.1612.0509-1.1166-2.16330.2961-0.68081.71440.8559-1.57981.32490.1558-0.15931.3516-0.39611.1923-11.308-15.914-41.468
45.0926-1.5635-1.1048.27061.89014.8160.96010.5733-0.3787-1.6616-0.8712-0.28930.9068-0.40060.0071.01250.0416-0.00841.0086-0.28170.9759-13.541-23.133-36.736
50.041-0.2354-0.2943.48953.79734.1759-0.34860.5947-0.5439-0.7804-0.17930.11031.81340.45930.25821.7549-0.04660.15611.6024-0.61651.4534-17.944-24.548-46.981
61.7186-0.2184-2.45080.07850.25483.56550.72710.9217-0.7531-0.88640.39080.46360.1215-0.4677-0.48011.8502-0.36820.0371.8901-0.1121.3928-14.323-31.028-43.831
72.5594-0.8304-0.20686.64712.59044.2360.0507-0.0191-0.5036-0.17950.05330.84110.23860.0482-0.08860.7428-0.0593-0.05311.0883-0.32261.183-27.757-16.142-30.735
82.79760.47320.25780.83860.47851.0056-0.08830.2408-0.1778-0.03170.05250.1180.0754-0.09260.04920.3875-0.02880.02870.762-0.03210.4996-34.79211.814-27.468
95.3080.57490.32414.5468-0.23195.0876-0.13141.0919-0.5294-1.5233-0.19320.24150.57090.11320.27260.7475-0.0086-0.06051.2111-0.14460.5752-40.0027.101-43.172
103.00110.1248-0.05217.82460.60772.61050.08040.38130.1501-0.6835-0.28560.0807-0.3064-0.2160.17110.435-0.0123-0.00140.81440.05720.5705-31.68220.493-34.728
118.7203-1.84982.06935.94651.73871.35170.31330.838-0.2686-1.0258-0.2415-1.1792-0.09870.12690.17490.7128-0.14510.22911.3631-0.240.6824-31.9135.168-43.531
124.6704-0.9331.07227.2277-0.60626.76890.53971.87870.7242-1.4586-0.4476-0.59230.38390.9796-0.22110.6452-0.17390.12161.249-0.07930.5736-24.28312.958-44.098
133.4250.5742-0.13114.0867-1.83225.0605-0.18981.5512-0.3449-0.75610.2748-0.39540.16291.2485-0.19880.736-0.09450.11831.6289-0.0690.5116-23.72913.398-41.039
141.6877-0.42250.85482.98880.15711.34430.21570.4383-0.38760.1614-0.15120.83870.5408-0.02110.08660.5541-0.02210.00720.759-0.21490.7305-19.585-18.242-26.726
152.9911-2.06350.37393.897-0.03452.7220.53380.2704-0.86040.8362-0.71330.60390.4845-0.77680.25660.936-0.2151-0.03780.8949-0.28671.2706-26.238-27.125-32.255
163.06150.92650.0354.14820.33381.5497-0.1915-0.25880.4109-0.1530.26550.4989-0.2363-0.3157-0.09840.49180.02780.02930.67710.06310.6541-18.54841.85-24.299
173.89590.92090.22321.25421.4233.5450.48330.64051.1405-1.7951-0.66940.3727-0.9854-0.7055-0.29091.09310.1246-0.16721.03360.23360.8461-14.05248.103-37.144
188.1992-4.57971.42486.2792-3.03884.45620.17560.80490.3789-0.29540.0280.1862-0.39930.1562-0.16941.33770.1576-0.13192.35480.65111.7169-9.5551.763-46.486
190.5403-1.64621.31625.3673-4.41063.7091-0.41571.15110.845-0.8189-0.2786-0.1918-0.9609-0.4280.08151.39670.17680.00461.53240.58861.0031-11.88456.734-41.383
208.34610.14542.29385.10650.33354.8673-0.69631.01810.556-0.22340.3551-1.0868-0.01480.67090.50750.8585-0.13020.10360.66970.06130.79180.96846.392-29.63
211.91840.2026-0.22681.8816-0.60910.53190.04310.1547-0.04740.034-0.0908-0.0872-0.04080.07930.05790.402-0.0229-0.00710.8483-0.04210.50911.8313.436-24.07
223.27741.2731-0.07372.26720.17061.40960.18730.2789-0.0359-0.1896-0.4302-0.4051-0.26860.23070.27950.4863-0.02560.05250.98540.13650.53320.89724.05-34.451
231.91342.9475-2.044.814-2.9212.3738-0.0766-0.86541.62611.188-0.54340.5069-1.22980.06990.52310.93440.3009-0.14151.21130.1240.799210.99631.353-36.816
246.697-0.14150.82183.67140.73366.4154-0.37911.98240.0989-1.5562-0.33240.001-0.1065-0.23280.63780.8532-0.00870.10061.46550.07380.647513.36918.915-43.898
252.95290.4630.17767.94890.51912.47930.1080.0268-0.5251-0.70230.0156-1.07850.20110.139-0.10420.4340.0982-0.01341.1006-0.12620.50954.6457.364-35.307
268.209-4.0002-2.80855.3805-0.72343.68020.4490.93031.3094-1.30640.66880.7434-0.403-0.9895-1.76660.8122-0.0558-0.09651.37980.21130.86144.95324.305-41.829
273.05261.64082.52135.4754-1.72084.17290.39962.1372-0.5855-1.4881-0.04380.5837-0.2972-0.7874-0.22990.74710.0083-0.13021.2073-0.04010.5413-2.95615.527-43.905
284.1115-1.7024-0.30074.84010.55613.63460.21610.63210.0014-1.99-0.10880.8004-0.5524-1.2541-0.03830.69190.0648-0.16061.27730.03570.5937-3.40915.671-40.133
291.9769-0.5334-0.37563.52071.05741.1854-0.0451-0.11010.33190.01050.1947-0.1206-0.30340.4143-0.1310.5378-0.02360.02190.73820.01350.5922-7.89242.095-23.162
302.8658-1.6863-0.12145.64530.22722.6050.09470.31420.8910.163-0.0707-0.7905-0.6469-0.22320.05890.895-0.09320.04680.91210.01090.9328-1.48956.847-29.742
313.195-0.206-0.0863.3214-0.39281.9446-0.1229-0.1851-0.50680.20520.12660.8592-0.157-0.4969-0.00580.4511-0.03440.11740.88880.06930.8998-41.0063.358-0.308
325.9037-0.0796-1.18881.4770.2572.56890.3687-1.9051-0.68941.0120.0641.3248-0.0905-0.7969-0.44870.8619-0.08430.31531.25050.24191.1506-43.309-3.62512.167
338.6415-4.2039-0.48817.82784.07662.59390.0131-0.45050.2980.92570.72111.2423-0.2867-1.246-0.40462.3453-0.2723-0.51141.41490.31431.6295-46.571-10.6921.02
340.4527-1.03540.82024.26720.76835.0668-0.7654-0.4058-1.02521.279-0.37960.3656-0.1139-0.79781.02730.9084-0.19040.29831.1840.10611.4803-43.842-11.61811.631
354.4482-0.17450.95085.72310.28353.43420.13710.5734-1.1931.0542-0.05690.68360.7101-0.241-0.16930.677-0.0255-0.060.92960.08411.6708-29.04-16.0260.462
361.53520.39650.00152.25270.71362.7240.13780.13980.13130.12870.0859-0.03810.05220.1764-0.22220.3767-0.0168-0.0270.54840.03510.4086-6.6015.81-0.452
375.0818-1.250.80914.685-0.42753.82870.43060.5682-0.5341-0.0127-0.1429-0.25090.55740.6546-0.30130.5345-0.0201-0.03210.704-0.10640.5404-3.96-9.339-2.185
380.77820.06790.41353.3576-0.60861.68450.1170.115-0.32020.1944-0.0341-0.06140.52150.3252-0.08420.63680.1281-0.08180.604-0.05880.5665-4.127-19.8256.443
398.0605-0.07741.45117.28810.03585.77180.0495-1.3082-0.19741.15330.08061.81060.1852-1.0163-0.10850.8870.03770.0890.62410.07510.7083-12.415-17.56715.471
403.0813-2.5399-0.18862.83661.59853.6944-0.3612-0.81280.17231.2083-0.1183-0.1182-0.15041.41850.35740.70620.0819-0.17780.8990.03840.77784.679-6.21617.888
417.75750.15441.63126.53280.17266.3423-0.5962-1.0333-0.34610.02080.09-0.5501-0.47591.10660.4140.53940.1683-0.07880.7417-0.00030.4253-2.767-3.28210.025
420.5382-0.03451.16754.003-1.21692.8893-0.2694-0.8208-0.25771.43850.6650.42290.1247-0.2506-0.44730.87970.06750.05810.83660.00850.5619-12.525-1.89616.459
433.68681.7296-2.58013.09780.76463.50020.1448-0.97021.28281.39010.6711-0.067-1.5732-0.2333-0.6340.92870.1520.15240.8208-0.16980.7765-5.9880.74623.007
446.0103-0.46612.7816.36210.11977.1396-0.0433-0.6522-0.41131.11360.25880.326-0.4884-0.7995-0.37850.86860.11240.05330.73430.00430.36-9.8371.05113.966
453.18710.3260.44490.8182-0.16981.27220.0437-0.0256-1.66330.276-0.06280.49130.7067-0.14110.23230.7655-0.15460.12850.80870.06011.3521-39.626-11.0480.781
464.49141.23240.48454.56280.75862.7227-0.01710.3375-0.31680.0693-0.1173-0.7738-0.09130.7090.16020.5041-0.1214-0.10911.03960.02670.682713.80121.0871.149
474.31071.72850.33864.4481-0.65220.6477-0.5427-0.2746-0.26991.0441-0.3566-0.4588-0.71211.48271.12441.0503-0.2487-0.38451.49460.01521.009317.14226.76714.343
480.4512-0.8231-0.81891.89271.89241.95570.349-1.0626-0.63371.10010.05410.30740.8841-0.3948-0.40771.85250.4861-0.29521.50430.00241.721120.46831.44522.69
494.41820.7062-0.54343.63320.26622.24640.2782-0.14250.02530.5976-0.5013-0.723-0.01720.09450.09320.8776-0.2765-0.26570.8593-0.00740.74577.05538.0497.047
504.1729-0.140.34611.6456-0.58522.9547-0.0809-0.46430.35970.30260.10450.1614-0.3749-0.1009-0.01310.4597-0.0040.01940.5862-0.08470.4165-22.41226.4390.3
513.0341-0.7081-0.31011.89492.71734.07170.43870.05330.031-0.1813-0.14040.16590.02620.3351-0.30052.42780.3464-0.21131.362-0.79531.4271-24.78355.47715.71
520.70420.68260.37680.63640.06930.57070.0684-0.18940.69240.76120.3524-0.3063-0.7914-0.4380.1421.55880.0589-0.13321.1765-0.78451.6331-19.36350.614.233
534.4068-2.4533-0.28221.8043-1.25624.43980.7404-1.28022.30270.2978-0.4116-0.1659-1.19360.1275-0.15940.8751-0.02770.09170.9244-0.49491.1028-22.10534.7519.468
543.8651.13971.90512.7508-0.05121.0749-0.6502-0.98050.63060.68940.59210.2467-0.39710.27840.21111.336-0.1425-0.01791.5791-0.38540.6998-23.84134.118.683
555.07780.22632.1914.63840.2015.2382-0.5987-1.82950.78270.21560.21460.5618-0.4726-0.49120.31930.68990.1112-0.06821.2576-0.21940.6533-23.4927.47711.654
561.66320.79250.95080.38750.50530.8311-0.4123-1.52060.57951.338-0.20590.37110.2293-0.15340.39891.2101-0.01-0.12822.0851-0.21210.6632-13.22726.89118.302
574.74322.16951.49212.255-1.53574.43930.5587-1.8703-0.18940.361-0.10150.6298-0.02560.6368-0.30270.8926-0.09630.0111.61370.02040.6575-20.19321.54621.392
581.8319-0.7673-1.2444.18820.71850.8672-0.0482-0.9488-0.25991.0425-0.4671-0.97050.38620.69770.01871.3342-0.221-0.01121.90390.14850.6798-21.38416.35718.363
597.957-1.5398-7.32392.2991.09626.803-0.1756-2.14420.56940.115-0.052-0.3638-0.31230.79850.12060.85570.0267-0.01481.5476-0.04930.4424-12.80124.67413.034
603.2504-0.57560.76252.04680.80430.9292-0.0950.30560.41860.40190.0407-0.7061-0.60450.49570.04240.8468-0.2997-0.14680.97670.0550.704512.97635.4543.35
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 24:36 )A24 - 36
2X-RAY DIFFRACTION2( CHAIN A AND RESID 37:91 )A37 - 91
3X-RAY DIFFRACTION3( CHAIN A AND RESID 92:100 )A92 - 100
4X-RAY DIFFRACTION4( CHAIN A AND RESID 101:109 )A101 - 109
5X-RAY DIFFRACTION5( CHAIN A AND RESID 110:126 )A110 - 126
6X-RAY DIFFRACTION6( CHAIN A AND RESID 127:131 )A127 - 131
7X-RAY DIFFRACTION7( CHAIN A AND RESID 132:152 )A132 - 152
8X-RAY DIFFRACTION8( CHAIN A AND RESID 153:309 )A153 - 309
9X-RAY DIFFRACTION9( CHAIN A AND RESID 310:330 )A310 - 330
10X-RAY DIFFRACTION10( CHAIN A AND RESID 340:356 )A340 - 356
11X-RAY DIFFRACTION11( CHAIN A AND RESID 357:369 )A357 - 369
12X-RAY DIFFRACTION12( CHAIN A AND RESID 370:385 )A370 - 385
13X-RAY DIFFRACTION13( CHAIN A AND RESID 386:402 )A386 - 402
14X-RAY DIFFRACTION14( CHAIN A AND RESID 403:437 )A403 - 437
15X-RAY DIFFRACTION15( CHAIN A AND RESID 438:450 )A438 - 450
16X-RAY DIFFRACTION16( CHAIN B AND RESID 24:93 )B24 - 93
17X-RAY DIFFRACTION17( CHAIN B AND RESID 94:110 )B94 - 110
18X-RAY DIFFRACTION18( CHAIN B AND RESID 123:125 )B123 - 125
19X-RAY DIFFRACTION19( CHAIN B AND RESID 126:131 )B126 - 131
20X-RAY DIFFRACTION20( CHAIN B AND RESID 132:143 )B132 - 143
21X-RAY DIFFRACTION21( CHAIN B AND RESID 144:264 )B144 - 264
22X-RAY DIFFRACTION22( CHAIN B AND RESID 265:309 )B265 - 309
23X-RAY DIFFRACTION23( CHAIN B AND RESID 310:313 )B310 - 313
24X-RAY DIFFRACTION24( CHAIN B AND RESID 314:330 )B314 - 330
25X-RAY DIFFRACTION25( CHAIN B AND RESID 340:356 )B340 - 356
26X-RAY DIFFRACTION26( CHAIN B AND RESID 357:369 )B357 - 369
27X-RAY DIFFRACTION27( CHAIN B AND RESID 370:386 )B370 - 386
28X-RAY DIFFRACTION28( CHAIN B AND RESID 387:402 )B387 - 402
29X-RAY DIFFRACTION29( CHAIN B AND RESID 403:432 )B403 - 432
30X-RAY DIFFRACTION30( CHAIN B AND RESID 433:450 )B433 - 450
31X-RAY DIFFRACTION31( CHAIN C AND RESID 24:92 )C24 - 92
32X-RAY DIFFRACTION32( CHAIN C AND RESID 93:110 )C93 - 110
33X-RAY DIFFRACTION33( CHAIN C AND RESID 123:126 )C123 - 126
34X-RAY DIFFRACTION34( CHAIN C AND RESID 127:138 )C127 - 138
35X-RAY DIFFRACTION35( CHAIN C AND RESID 139:152 )C139 - 152
36X-RAY DIFFRACTION36( CHAIN C AND RESID 153:215 )C153 - 215
37X-RAY DIFFRACTION37( CHAIN C AND RESID 216:253 )C216 - 253
38X-RAY DIFFRACTION38( CHAIN C AND RESID 254:309 )C254 - 309
39X-RAY DIFFRACTION39( CHAIN C AND RESID 310:322 )C310 - 322
40X-RAY DIFFRACTION40( CHAIN C AND RESID 323:341 )C323 - 341
41X-RAY DIFFRACTION41( CHAIN C AND RESID 342:358 )C342 - 358
42X-RAY DIFFRACTION42( CHAIN C AND RESID 361:379 )C361 - 379
43X-RAY DIFFRACTION43( CHAIN C AND RESID 380:389 )C380 - 389
44X-RAY DIFFRACTION44( CHAIN C AND RESID 390:402 )C390 - 402
45X-RAY DIFFRACTION45( CHAIN C AND RESID 403:450 )C403 - 450
46X-RAY DIFFRACTION46( CHAIN D AND RESID 24:93 )D24 - 93
47X-RAY DIFFRACTION47( CHAIN D AND RESID 94:110 )D94 - 110
48X-RAY DIFFRACTION48( CHAIN D AND RESID 124:129 )D124 - 129
49X-RAY DIFFRACTION49( CHAIN D AND RESID 130:152 )D130 - 152
50X-RAY DIFFRACTION50( CHAIN D AND RESID 153:271 )D153 - 271
51X-RAY DIFFRACTION51( CHAIN D AND RESID 272:278 )D272 - 278
52X-RAY DIFFRACTION52( CHAIN D AND RESID 279:298 )D279 - 298
53X-RAY DIFFRACTION53( CHAIN D AND RESID 299:311 )D299 - 311
54X-RAY DIFFRACTION54( CHAIN D AND RESID 312:343 )D312 - 343
55X-RAY DIFFRACTION55( CHAIN D AND RESID 344:357 )D344 - 357
56X-RAY DIFFRACTION56( CHAIN D AND RESID 361:373 )D361 - 373
57X-RAY DIFFRACTION57( CHAIN D AND RESID 374:386 )D374 - 386
58X-RAY DIFFRACTION58( CHAIN D AND RESID 387:394 )D387 - 394
59X-RAY DIFFRACTION59( CHAIN D AND RESID 395:403 )D395 - 403
60X-RAY DIFFRACTION60( CHAIN D AND RESID 404:450 )D404 - 450

+
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