[English] 日本語
Yorodumi
- PDB-4wj3: Crystal structure of the asparagine transamidosome from Pseudomon... -

+
Open data


ID or keywords:

Loading...

-
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


aspartate-tRNAAsn ligase / glutaminyl-tRNAGln biosynthesis via transamidation / aspartate-tRNA(Asn) ligase activity / asparaginyl-tRNA synthase (glutamine-hydrolyzing) 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 / aspartate-tRNA ligase activity / aspartyl-tRNA aminoacylation ...aspartate-tRNAAsn ligase / glutaminyl-tRNAGln biosynthesis via transamidation / aspartate-tRNA(Asn) ligase activity / asparaginyl-tRNA synthase (glutamine-hydrolyzing) 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 / aspartate-tRNA ligase activity / aspartyl-tRNA aminoacylation / regulation of translational fidelity / nucleic acid binding / 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, C-terminal, domain 1 / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit / GAD-like domain / Glutamyl-tRNA(Gln) amidotransferase A subunit / Aspartyl/Glutamyl-tRNA(Gln) amidotransferase, subunit B/E, catalytic / Glutamyl-tRNA(Gln) amidotransferase, subunit B, conserved site ...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, C-terminal, domain 1 / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit / GAD-like domain / Glutamyl-tRNA(Gln) amidotransferase A subunit / 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
Revision 1.4Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water00
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

-
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
Has protein modificationN
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.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
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

-
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

-
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

+
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