[English] 日本語
Yorodumi
- PDB-4gkk: Structure of the Thermus thermophilus 30S ribosomal subunit compl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4gkk
TitleStructure of the Thermus thermophilus 30S ribosomal subunit complexed with a human mitochondrial anticodon stem loop (ASL) of transfer RNA Methionine (TRNAMET) bound to an mRNA with an AUA-codon in the A-site and paromomycin
Components
  • (30S ribosomal protein ...) x 20
  • 16S rRNA
  • mRNA A-site fragment
  • tRNA ASL human mitochondrial Met
KeywordsRIBOSOME/ANTIBIOTIC / Translation initiation / 5-formylcytidine / RIBOSOME-ANTIBIOTIC complex
Function / homology
Function and homology information


ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / ribosome / translation ...ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / zinc ion binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
S16 Ribosomal Protein; Chain: A; / Ribosomal protein S16 / Ribosomal protein S18 / 30s Ribosomal Protein S18 / 30s ribosomal protein s13; domain 2 / Ribosomal protein S13/S18, C-terminal domain / Ribosomal protein S20 / 30s Ribosomal Protein S19; Chain A / Ribosomal protein S19/S15 / Ribosomal protein S3, C-terminal domain ...S16 Ribosomal Protein; Chain: A; / Ribosomal protein S16 / Ribosomal protein S18 / 30s Ribosomal Protein S18 / 30s ribosomal protein s13; domain 2 / Ribosomal protein S13/S18, C-terminal domain / Ribosomal protein S20 / 30s Ribosomal Protein S19; Chain A / Ribosomal protein S19/S15 / Ribosomal protein S3, C-terminal domain / Ribosomal Protein S14/S29 / 30s Ribosomal Protein S14; Chain N / Ribosomal protein S4/S9, N-terminal domain / Ribosomal Protein S4 Delta 41; Chain A, domain 1 / Ribosomal Protein S8; Chain: A, domain 1 - #30 / Ribosomal protein S3 C-terminal domain / Ribosomal protein S6/Translation elongation factor EF1B / Dna Ligase; domain 1 - #10 / Ribosomal protein S11/S14 / Ribosomal protein S10 / S15/NS1, RNA-binding / Helix hairpin bin / Ribosomal Protein S7 / Ribosomal protein S7/S5 / RNA-binding S4 domain / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / K homology (KH) domain / Helicase, Ruva Protein; domain 3 - #50 / Double Stranded RNA Binding Domain - #20 / Glucose-6-phosphate isomerase like protein; domain 1 / Ribosomal Protein S8; Chain: A, domain 1 / Ribosomal Protein S5; domain 2 - #10 / 30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / GMP Synthetase; Chain A, domain 3 / Ribosomal Protein S5; domain 2 / Ribosomal protein S14, type Z / Double Stranded RNA Binding Domain / Helicase, Ruva Protein; domain 3 / Nucleic acid-binding proteins / Dna Ligase; domain 1 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / : / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / Ribosomal protein S5, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S14/S29 / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Few Secondary Structures / Irregular / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / K Homology domain / K homology RNA-binding domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleotidyltransferase; domain 5 / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / Helix Hairpins / Ribosomal protein S2 signature 1. / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S10 / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily
Similarity search - Domain/homology
PAROMOMYCIN / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS7 ...PAROMOMYCIN / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS19 / 30S ribosomal protein S17 / 30S ribosomal protein S14 type Z / 30S ribosomal protein S8 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein bTHX / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
Synthetic (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsCantara, W.A. / Murphy IV, F.V. / Spears, J.L. / Demirci, H. / Agris, P.F.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Expanded use of sense codons is regulated by modified cytidines in tRNA.
Authors: Cantara, W.A. / Murphy, F.V. / Demirci, H. / Agris, P.F.
History
DepositionAug 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Structure summary
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Jul 3, 2013Group: Database references
Revision 1.4Jul 17, 2013Group: Database references
Revision 1.5Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 16S rRNA
B: 30S ribosomal protein S2
C: 30S ribosomal protein S3
D: 30S ribosomal protein S4
E: 30S ribosomal protein S5
F: 30S ribosomal protein S6
G: 30S ribosomal protein S7
H: 30S ribosomal protein S8
I: 30S ribosomal protein S9
J: 30S ribosomal protein S10
K: 30S ribosomal protein S11
L: 30S ribosomal protein S12
M: 30S ribosomal protein S13
N: 30S ribosomal protein S14 type Z
O: 30S ribosomal protein S15
P: 30S ribosomal protein S16
Q: 30S ribosomal protein S17
R: 30S ribosomal protein S18
S: 30S ribosomal protein S19
T: 30S ribosomal protein S20
V: 30S ribosomal protein Thx
W: mRNA A-site fragment
X: tRNA ASL human mitochondrial Met
hetero molecules


Theoretical massNumber of molelcules
Total (without water)777,310212
Polymers772,04323
Non-polymers5,267189
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area56390 Å2
ΔGint-515 kcal/mol
Surface area243500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)402.370, 402.370, 175.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

-
RNA chain , 3 types, 3 molecules AWX

#1: RNA chain 16S rRNA


Mass: 491166.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: 48256
#22: RNA chain mRNA A-site fragment


Mass: 1907.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic (others)
#23: RNA chain tRNA ASL human mitochondrial Met


Mass: 5405.279 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic (others)

-
30S ribosomal protein ... , 20 types, 20 molecules BCDEFGHIJKLMNOPQRSTV

#2: Protein 30S ribosomal protein S2


Mass: 26987.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80371
#3: Protein 30S ribosomal protein S3


Mass: 22862.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80372
#4: Protein 30S ribosomal protein S4


Mass: 24242.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80373
#5: Protein 30S ribosomal protein S5


Mass: 16331.079 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ5
#6: Protein 30S ribosomal protein S6


Mass: 11988.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SLP8
#7: Protein 30S ribosomal protein S7


Mass: 17919.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P17291
#8: Protein 30S ribosomal protein S8


Mass: 15868.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ2, UniProt: A0A0M9AFS9*PLUS
#9: Protein 30S ribosomal protein S9


Mass: 14298.466 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80374
#10: Protein 30S ribosomal protein S10


Mass: 11299.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN7
#11: Protein 30S ribosomal protein S11


Mass: 12606.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80376
#12: Protein 30S ribosomal protein S12


Mass: 13804.311 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN3
#13: Protein 30S ribosomal protein S13


Mass: 14207.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80377
#14: Protein 30S ribosomal protein S14 type Z


Mass: 7027.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ1, UniProt: A0A0N0BLP2*PLUS
#15: Protein 30S ribosomal protein S15


Mass: 10447.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SJ76
#16: Protein 30S ribosomal protein S16


Mass: 9924.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SJH3
#17: Protein 30S ribosomal protein S17


Mass: 12193.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP7, UniProt: A0A0N0BLS5*PLUS
#18: Protein 30S ribosomal protein S18


Mass: 8483.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SLQ0
#19: Protein 30S ribosomal protein S19


Mass: 9203.743 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP2
#20: Protein 30S ribosomal protein S20


Mass: 10907.060 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80380
#21: Protein/peptide 30S ribosomal protein Thx


Mass: 2960.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SIH3

-
Non-polymers , 3 types, 189 molecules

#24: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 186 / Source method: obtained synthetically / Formula: Mg
#25: Chemical ChemComp-PAR / PAROMOMYCIN / PAROMOMYCIN I / AMMINOSIDIN / CATENULIN / CRESTOMYCIN / MONOMYCIN A / NEOMYCIN E


Mass: 615.628 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H45N5O14 / Comment: Antimicrobial, medication*YM
#26: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.6 Å3/Da / Density % sol: 73.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: MPD, NH4Cl, KCl, CaCl2, magnesium acetate, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K, temperature 277.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 11, 2010
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.2→73.5 Å / Num. obs: 230910 / % possible obs: 47.9 % / Observed criterion σ(I): -3
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.91-3.050.0170.15178.6
3.05-3.210.0170.46184.3
3.21-3.410.0171.28199.3
3.41-3.640.0172.16199.3
3.64-3.930.0173.64199.1
3.93-4.310.0175.42199
4.31-4.820.0177.41198.9
4.82-5.560.0179.01198.6
5.56-6.810.01710.14197.6
6.81-9.640.01711.44195.6
9.640.01712.17189.6

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
Consoledata collection
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→73.466 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.41 / σ(F): 0.78 / Phase error: 22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2359 11785 5.11 %
Rwork0.1952 --
obs0.1973 230816 98.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 96.1629 Å2
Refinement stepCycle: LAST / Resolution: 3.2→73.466 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19231 32727 230 0 52188
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00856211
X-RAY DIFFRACTIONf_angle_d1.34783434
X-RAY DIFFRACTIONf_dihedral_angle_d18.42726124
X-RAY DIFFRACTIONf_chiral_restr0.06810488
X-RAY DIFFRACTIONf_plane_restr0.0064915
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.23640.35713700.32967262X-RAY DIFFRACTION99
3.2364-3.27440.3433800.31837315X-RAY DIFFRACTION99
3.2744-3.31440.34743760.30187312X-RAY DIFFRACTION99
3.3144-3.35630.32613710.29567325X-RAY DIFFRACTION99
3.3563-3.40050.31553820.28387323X-RAY DIFFRACTION99
3.4005-3.44710.30144180.26727319X-RAY DIFFRACTION99
3.4471-3.49630.29734120.26117249X-RAY DIFFRACTION99
3.4963-3.54850.2924300.25657250X-RAY DIFFRACTION99
3.5485-3.6040.28474120.23777325X-RAY DIFFRACTION99
3.604-3.6630.26843950.22647331X-RAY DIFFRACTION99
3.663-3.72620.24964340.22077262X-RAY DIFFRACTION99
3.7262-3.79390.25064060.19937276X-RAY DIFFRACTION99
3.7939-3.86690.22123820.19017327X-RAY DIFFRACTION99
3.8669-3.94580.23244190.18277264X-RAY DIFFRACTION99
3.9458-4.03160.22073880.17887334X-RAY DIFFRACTION99
4.0316-4.12540.22573850.187341X-RAY DIFFRACTION99
4.1254-4.22860.21014180.17297291X-RAY DIFFRACTION99
4.2286-4.34290.20643720.16257363X-RAY DIFFRACTION99
4.3429-4.47070.2143910.1647350X-RAY DIFFRACTION99
4.4707-4.61490.2033910.16177327X-RAY DIFFRACTION99
4.6149-4.77990.19113930.16247338X-RAY DIFFRACTION99
4.7799-4.97120.213760.16127357X-RAY DIFFRACTION99
4.9712-5.19740.19713780.15737358X-RAY DIFFRACTION99
5.1974-5.47130.20774150.15287331X-RAY DIFFRACTION98
5.4713-5.8140.22423880.15767344X-RAY DIFFRACTION98
5.814-6.26270.20653470.16377360X-RAY DIFFRACTION98
6.2627-6.89250.21554120.16397281X-RAY DIFFRACTION97
6.8925-7.88880.20343720.15967294X-RAY DIFFRACTION96
7.8888-9.93520.22253970.18157219X-RAY DIFFRACTION95
9.9352-73.4850.26723750.25197003X-RAY DIFFRACTION88
Refinement TLS params.Method: refined / Origin x: 175.1675 Å / Origin y: 105.6748 Å / Origin z: -8.2091 Å
111213212223313233
T0.5307 Å20.0309 Å20.0982 Å2-0.5236 Å2-0.1768 Å2--0.6049 Å2
L0.613 °20.1467 °2-0.1512 °2-0.2438 °2-0.0649 °2--0.236 °2
S0.1218 Å °-0.1903 Å °0.1699 Å °0.1493 Å °0.0097 Å °0.0287 Å °-0.0269 Å °0.1536 Å °-0.1114 Å °
Refinement TLS groupSelection details: all

+
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