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- PDB-4wj3: Crystal structure of the asparagine transamidosome from Pseudomon... -

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Basic information

Entry
Database: PDB / ID: 4wj3
TitleCrystal structure of the asparagine transamidosome from Pseudomonas aeruginosa
Components
  • 76mer-tRNA
  • Aspartate--tRNA(Asp/Asn) ligase
  • Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
  • Glutamyl-tRNA(Gln) amidotransferase subunit A
  • Glutamyl-tRNA(Gln) amidotransferase subunit C
KeywordsLIGASE/RNA / transamidosome / aminoacyl-tRNA synthetase / GatCAB / tRNA / LIGASE-RNA complex
Function / homology
Function and homology information


glutaminyl-tRNAGln biosynthesis via transamidation / aspartate-tRNAAsn ligase / aspartate-tRNA(Asn) ligase activity / glutaminyl-tRNA synthase (glutamine-hydrolysing) / glutamyl-tRNA(Gln) amidotransferase complex / Ligases; Forming carbon-nitrogen bonds; Carbon-nitrogen ligases with glutamine as amido-N-donor / glutaminyl-tRNA synthase (glutamine-hydrolyzing) activity / aspartyl-tRNA aminoacylation / aspartate-tRNA ligase activity / regulation of translational fidelity ...glutaminyl-tRNAGln biosynthesis via transamidation / aspartate-tRNAAsn ligase / aspartate-tRNA(Asn) ligase activity / glutaminyl-tRNA synthase (glutamine-hydrolysing) / glutamyl-tRNA(Gln) amidotransferase complex / Ligases; Forming carbon-nitrogen bonds; Carbon-nitrogen ligases with glutamine as amido-N-donor / glutaminyl-tRNA synthase (glutamine-hydrolyzing) activity / aspartyl-tRNA aminoacylation / aspartate-tRNA ligase activity / regulation of translational fidelity / nucleic acid binding / hydrolase activity / translation / ATP binding / cytoplasm
Similarity search - Function
Glu-tRNAGln amidotransferase C subunit / Glu-tRNAGln amidotransferase superfamily, subunit C / Glu-tRNAGln amidotransferase C subunit / Glu-tRNAGln amidotransferase C subunit, N-terminal domain / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit / GAD-like domain / Glutamyl-tRNA(Gln) amidotransferase A subunit / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C-terminal, domain 1 / : / : ...Glu-tRNAGln amidotransferase C subunit / Glu-tRNAGln amidotransferase superfamily, subunit C / Glu-tRNAGln amidotransferase C subunit / Glu-tRNAGln amidotransferase C subunit, N-terminal domain / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit / GAD-like domain / Glutamyl-tRNA(Gln) amidotransferase A subunit / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C-terminal, domain 1 / : / : / Aspartyl/Glutamyl-tRNA(Gln) amidotransferase, subunit B/E, catalytic / Glutamyl-tRNA(Gln) amidotransferase, subunit B, conserved site / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, subunit B /E / GatB/GatE catalytic domain / Glutamyl-tRNA(Gln) amidotransferase subunit B signature. / Asn/Gln amidotransferase / GatB domain / GatB domain / Aspartyl/glutamyl-tRNA amidotransferase subunit B-like / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C-terminal, domain 2 / Aspartate-tRNA ligase, type 1 / GAD domain / GAD domain / GAD-like domain superfamily / Amidase / Aspartyl/Asparaginyl-tRNA synthetase, class IIb / Amidase, conserved site / Amidases signature. / Amidase signature (AS) enzymes / Amidase signature (AS) domain / Amidase signature domain / Amidase signature (AS) superfamily / Amidase / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / Glutamine synthetase/guanido kinase, catalytic domain / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Histone, subunit A / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Gyrase A; domain 2 / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Alpha-Beta Complex / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / RNA / RNA (> 10) / Aspartate--tRNA(Asp/Asn) ligase / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B / Glutamyl-tRNA(Gln) amidotransferase subunit A / Glutamyl-tRNA(Gln) amidotransferase subunit C
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.705 Å
AuthorsSuzuki, T. / Nakamura, A. / Kato, K. / Tanaka, I. / Yao, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology of Japan21370041 Japan
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structure of the Pseudomonas aeruginosa transamidosome reveals unique aspects of bacterial tRNA-dependent asparagine biosynthesis
Authors: Suzuki, T. / Nakamura, A. / Kato, K. / Soll, D. / Tanaka, I. / Sheppard, K. / Yao, M.
History
DepositionSep 29, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references / Structure summary
Revision 1.2Jan 28, 2015Group: Database references
Revision 1.3Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_entity_src_syn / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamyl-tRNA(Gln) amidotransferase subunit A
B: Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
C: Glutamyl-tRNA(Gln) amidotransferase subunit C
D: Glutamyl-tRNA(Gln) amidotransferase subunit A
E: Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
F: Glutamyl-tRNA(Gln) amidotransferase subunit C
G: Glutamyl-tRNA(Gln) amidotransferase subunit A
H: Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
I: Glutamyl-tRNA(Gln) amidotransferase subunit C
J: Glutamyl-tRNA(Gln) amidotransferase subunit A
K: Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
L: Glutamyl-tRNA(Gln) amidotransferase subunit C
M: Aspartate--tRNA(Asp/Asn) ligase
N: Aspartate--tRNA(Asp/Asn) ligase
O: Aspartate--tRNA(Asp/Asn) ligase
P: Aspartate--tRNA(Asp/Asn) ligase
Q: 76mer-tRNA
R: 76mer-tRNA
S: 76mer-tRNA
T: 76mer-tRNA


Theoretical massNumber of molelcules
Total (without water)825,96220
Polymers825,96220
Non-polymers00
Water0
1
A: Glutamyl-tRNA(Gln) amidotransferase subunit A
B: Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
C: Glutamyl-tRNA(Gln) amidotransferase subunit C
J: Glutamyl-tRNA(Gln) amidotransferase subunit A
K: Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
L: Glutamyl-tRNA(Gln) amidotransferase subunit C
M: Aspartate--tRNA(Asp/Asn) ligase
N: Aspartate--tRNA(Asp/Asn) ligase
Q: 76mer-tRNA
R: 76mer-tRNA


Theoretical massNumber of molelcules
Total (without water)412,98110
Polymers412,98110
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area45070 Å2
ΔGint-258 kcal/mol
Surface area155120 Å2
MethodPISA
2
D: Glutamyl-tRNA(Gln) amidotransferase subunit A
E: Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
F: Glutamyl-tRNA(Gln) amidotransferase subunit C
G: Glutamyl-tRNA(Gln) amidotransferase subunit A
H: Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
I: Glutamyl-tRNA(Gln) amidotransferase subunit C
O: Aspartate--tRNA(Asp/Asn) ligase
P: Aspartate--tRNA(Asp/Asn) ligase
S: 76mer-tRNA
T: 76mer-tRNA


Theoretical massNumber of molelcules
Total (without water)412,98110
Polymers412,98110
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area45460 Å2
ΔGint-257 kcal/mol
Surface area154920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.140, 185.675, 290.359
Angle α, β, γ (deg.)90.00, 92.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glutamyl-tRNA(Gln) amidotransferase subunit A / Glu-ADT subunit A / aspartyl-tRNA(Asn)/glutamyl-tRNA(Gln) amidotransferase subunit A


Mass: 51912.508 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: gatA, PA4483 / Plasmid: pET28b / Production host: Escherichia coli (E. coli)
References: UniProt: Q9HVT8, glutaminyl-tRNA synthase (glutamine-hydrolysing)
#2: Protein
Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B / Asp/Glu-ADT subunit B / aspartyl-tRNA(Asn)/glutamyl-tRNA(Gln) amidotransferase subunit B


Mass: 51236.820 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: gatB, PA4484 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(de3)
References: UniProt: Q9HVT7, Ligases; Forming carbon-nitrogen bonds; Carbon-nitrogen ligases with glutamine as amido-N-donor
#3: Protein
Glutamyl-tRNA(Gln) amidotransferase subunit C / Glu-ADT subunit C / aspartyl-tRNA(Asn)/glutamyl-tRNA(Gln) amidotransferase subunit C


Mass: 11557.967 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: gatC, PA4482 / Plasmid: pET28b / Production host: Escherichia coli (E. coli)
References: UniProt: Q9HVT9, Ligases; Forming carbon-nitrogen bonds; Carbon-nitrogen ligases with glutamine as amido-N-donor
#4: Protein
Aspartate--tRNA(Asp/Asn) ligase / Aspartyl-tRNA synthetase / AspRS / Non-discriminating aspartyl-tRNA synthetase / ND-AspRS


Mass: 67311.672 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: aspS, PA0963 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(de3) / References: UniProt: Q51422, aspartate-tRNAAsn ligase
#5: RNA chain
76mer-tRNA


Mass: 24471.504 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Pseudomonas aeruginosa PAO1 (bacteria) / References: GenBank: 110227054
Sequence detailsTHE C-TERMINAL RESIDUES FOR CHAINS B, E, H AND K HAVE ONLY WEAK ELECTRON DENSITY SO IT WAS NOT ...THE C-TERMINAL RESIDUES FOR CHAINS B, E, H AND K HAVE ONLY WEAK ELECTRON DENSITY SO IT WAS NOT POSSIBLE TO ACCURATELY ASSIGN THE SIDE CHAINS. THE C-TERMINI WERE MODELED AS ALA, BUT THE SEQUENCE ALIGNMENT IS UNKNOWN, AND WERE THEREFORE CHANGED TO UNK IN THIS ENTRY. THE UNK CORRESPOND TO RESIDUES WITHIN THE SEQUENCE DQIIEAKGLKQVTDSGAIEKMLDEVLAANAEQVEQYRAADEAKRGKMFGFFVGQAM KASKGKANPQQVNELLKKKLEA BUT CANNOT BE NUMBERED FOR CERTAINTY SINCE THEY ARE NOT SURE OF THE FRAME. SO THE RESIDUE NUMBERS OF UNK IS MEANINGLESS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: MES, lithium sulfate, PEG3350, hexammine cobalt(III) chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jan 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.7→48.12 Å / Num. obs: 96512 / % possible obs: 92.1 % / Redundancy: 2.6 % / Net I/σ(I): 6.36

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementResolution: 3.705→46.769 Å / SU ML: 0.64 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 35.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3286 4823 5 %
Rwork0.2923 --
obs0.2941 96481 92.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.705→46.769 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49557 6488 0 0 56045
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00357725
X-RAY DIFFRACTIONf_angle_d0.83679683
X-RAY DIFFRACTIONf_dihedral_angle_d14.50122409
X-RAY DIFFRACTIONf_chiral_restr0.0349157
X-RAY DIFFRACTIONf_plane_restr0.0049393
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7047-3.74680.40081260.36742132X-RAY DIFFRACTION65
3.7468-3.79080.39511640.3553068X-RAY DIFFRACTION93
3.7908-3.83710.33151440.35363074X-RAY DIFFRACTION93
3.8371-3.88560.39951770.35073107X-RAY DIFFRACTION93
3.8856-3.93670.38271430.33553066X-RAY DIFFRACTION94
3.9367-3.99060.36221690.33013095X-RAY DIFFRACTION94
3.9906-4.04760.30391680.32863147X-RAY DIFFRACTION93
4.0476-4.1080.33271630.32393051X-RAY DIFFRACTION94
4.108-4.17210.33391530.32833087X-RAY DIFFRACTION94
4.1721-4.24050.38111740.31533172X-RAY DIFFRACTION94
4.2405-4.31350.34081540.31533069X-RAY DIFFRACTION94
4.3135-4.39190.35451650.29933060X-RAY DIFFRACTION93
4.3919-4.47630.34981790.30063090X-RAY DIFFRACTION93
4.4763-4.56760.33791590.29743055X-RAY DIFFRACTION94
4.5676-4.66690.30121560.28993145X-RAY DIFFRACTION93
4.6669-4.77530.31581750.28993077X-RAY DIFFRACTION94
4.7753-4.89460.32621590.30053129X-RAY DIFFRACTION94
4.8946-5.02680.31391760.29123057X-RAY DIFFRACTION94
5.0268-5.17450.33491510.29483175X-RAY DIFFRACTION94
5.1745-5.34130.34411610.29113050X-RAY DIFFRACTION94
5.3413-5.5320.3331590.29423118X-RAY DIFFRACTION94
5.532-5.75310.34281600.29373119X-RAY DIFFRACTION93
5.7531-6.01440.35021640.30063072X-RAY DIFFRACTION94
6.0144-6.33080.33211580.29993126X-RAY DIFFRACTION93
6.3308-6.72630.35131640.28093116X-RAY DIFFRACTION93
6.7263-7.24390.3371610.27933068X-RAY DIFFRACTION93
7.2439-7.96970.29921690.2553054X-RAY DIFFRACTION92
7.9697-9.11550.28831540.23913048X-RAY DIFFRACTION91
9.1155-11.45660.25751530.21833069X-RAY DIFFRACTION91
11.4566-46.77320.27871650.25192962X-RAY DIFFRACTION87
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)
10.2056-0.1189-0.00120.13930.010.05730.1171-0.0580.0097-0.1367-0.1827-0.13690.12830.1960.23750.09540.60150.0530.68470.31590.32474.4237-106.9762430.288
20.01940.017-0.04290.1364-0.13860.1267-0.059-0.2586-0.0515-0.166-0.0183-0.02530.00920.0510.02750.28970.13710.10690.4403-0.07340.382-15.078-65.8631401.656
30.0049-0.0020.02110.0541-0.04620.06650.0449-0.01170.0523-0.11980.015-0.06220.01660.01220.01380.35320.1920.12080.81340.05880.25817.2615-94.5023410.7376
40.1843-0.13480.10970.46420.0130.39530.1864-0.1422-0.1854-0.17150.0765-0.02630.16130.07690.2301-0.06550.0082-0.01950.27050.122-0.0218-0.7629-195.4985433.5066
50.0829-0.03340.04190.153-0.1970.1299-0.11380.02970.113-0.2345-0.27320.038-0.1213-0.0351-0.51470.34380.3288-0.16690.0179-0.06840.3628-25.2788-159.0579403.3095
60.0169-0.05070.05650.098-0.12690.1723-0.1538-0.0022-0.04230.0075-0.1675-0.0183-0.08030.0918-0.08770.2716-0.04220.09880.2651-0.10140.38170.1239-184.0533413.2669
70.0095-0.0045-0.00330.0001-0.00350.01640.0050.10250.0037-0.2686-0.14190.0031-0.2031-0.1623-0.00771.39660.4842-0.05141.49460.00740.601-45.5981-157.6205308.0415
80.2107-0.025-0.18860.0238-0.04780.20730.09810.2411-0.2479-0.244-0.0556-0.0384-0.3253-0.2150.03630.67570.1214-0.05910.5795-0.28680.6436-5.8092-180.6519334.8225
90.0101-0.01050.02760.0071-0.02390.03580.1376-0.00650.08530.00110.0328-0.0753-0.1369-0.019501.20520.1185-0.10051.0641-0.06870.7825-32.6346-156.1324327.5371
100.0073-0.00670.01780.0141-0.01550.03410.16760.1672-0.026-0.27940.0294-0.0018-0.1928-0.03630.00021.56820.5255-0.31581.4855-0.33420.9492-35.9769-65.6143306.6256
110.0772-0.02870.01450.04640.02950.02410.13040.2173-0.1546-0.2195-0.00680.1735-0.265-0.06950.0270.88920.0656-0.13510.8242-0.21690.63393.9681-88.6955333.8453
120.00990.00470.00040.0004-0.00190.00120.0161-0.03810.0483-0.13080.01370.0369-0.1608-0.0584-01.1090.06970.16191.04390.04370.8452-23.0588-64.0736326.0308
130.1875-0.00250.01340.26350.08440.1667-0.03760.3398-0.0812-0.195-0.07920.1054-0.02130.2665-0.01010.53440.134-0.07610.4795-0.0850.359131.6923-46.7658348.5665
140.19890.113-0.1020.0706-0.00420.2946-0.0346-0.10490.08590.0944-0.13930.1218-0.1740.0703-0.10650.40260.0625-0.02270.2448-0.22210.518728.7298-44.1785386.7127
150.1726-0.1267-0.05830.19530.17980.15220.06620.2996-0.0382-0.2662-0.10360.097-0.2547-0.1118-0.17650.69740.4678-0.03140.3968-0.22090.477521.3253-139.2103349.9969
160.3344-0.0928-0.20140.3220.25770.2896-0.1696-0.1982-0.21720.1751-0.04930.1807-0.2516-0.1407-0.29120.3430.45870.1029-0.0251-0.28790.297819.064-136.3206387.9926
170.0986-0.0249-0.05010.01480.01340.0750.0307-0.09480.0153-0.11780.0312-0.1889-0.2820.02170.0010.85860.2566-0.01330.6652-0.19050.9492-7.2977-31.7093390.2059
180.03540.01310.03840.0317-0.03250.19680.0470.11720.00010.0188-0.0556-0.072-0.1040.1252-0.02570.40790.1141-0.00590.2987-0.13930.564929.0153-175.9721345.0294
190.0268-0.0189-0.01080.0732-0.01690.0744-0.02370.0514-0.0490.11130.02610.017-0.0409-0.0705-00.70850.17510.1070.8336-0.18820.990238.8931-84.4714344.432
200.0334-0.0374-0.09680.00750.02410.0998-0.012-0.0750.0064-0.0771-0.0337-0.1097-0.0096-0.0627-0.09681.14290.3165-0.15340.3692-0.27650.9402-18.5028-125.1797392.2974
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1Chain A
2X-RAY DIFFRACTION2Chain B
3X-RAY DIFFRACTION3Chain C
4X-RAY DIFFRACTION4Chain D
5X-RAY DIFFRACTION5Chain E
6X-RAY DIFFRACTION6Chain F
7X-RAY DIFFRACTION7Chain G
8X-RAY DIFFRACTION8Chain H
9X-RAY DIFFRACTION9Chain I
10X-RAY DIFFRACTION10Chain J
11X-RAY DIFFRACTION11Chain K
12X-RAY DIFFRACTION12Chain L
13X-RAY DIFFRACTION13Chain M
14X-RAY DIFFRACTION14Chain N
15X-RAY DIFFRACTION15Chain O
16X-RAY DIFFRACTION16Chain P
17X-RAY DIFFRACTION17Chain R
18X-RAY DIFFRACTION18Chain S
19X-RAY DIFFRACTION19Chain Q
20X-RAY DIFFRACTION20Chain T

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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

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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

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