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- PDB-1tfw: How CCA is added to the 3' end of immature tRNA without the use o... -

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Basic information

Entry
Database: PDB / ID: 1tfw
TitleHow CCA is added to the 3' end of immature tRNA without the use of an oligonucleotide template
Components
  • 5'-R(*CP*GP*CP*GP*GP*AP*UP*CP*CP*GP*CP*AP*C)-3'
  • 5'-R(*GP*CP*GP*GP*AP*CP*CP*CP*GP*CP*AP*C)-3'
  • 5'-R(*GP*CP*GP*GP*AP*UP*CP*CP*GP*CP*AP*C)-3'
  • 5'-R(*GP*CP*GP*GP*AP*UP*CP*CP*GP*CP*AP*CP*C)-3'
  • tRNA nucleotidyltransferase
KeywordsTRANSFERASE/RNA / CCA-adding Complex / TRANSFERASE-RNA COMPLEX
Function / homology
Function and homology information


tRNA surveillance / CCACCA tRNA nucleotidyltransferase activity / CCA tRNA nucleotidyltransferase / tRNA 3'-terminal CCA addition / RNA repair / tRNA binding / magnesium ion binding / ATP binding
Similarity search - Function
CCA tRNA nucleotidyltransferase, domain 2 / Archaeal tRNA CCA-adding enzyme catalytic domain / tRNA nucleotidyltransferase, archaea / tRNA nucleotidyltransferase, substrate binding / tRNA nucleotidyltransferase, domain 2 / : / tRNA nucleotidyltransferase, second domain / Archaeal CCA-adding enzyme, C-terminal domain / Poly(A) polymerase predicted RNA binding domain / Nucleotidyltransferase, class I-like, C-terminal ...CCA tRNA nucleotidyltransferase, domain 2 / Archaeal tRNA CCA-adding enzyme catalytic domain / tRNA nucleotidyltransferase, archaea / tRNA nucleotidyltransferase, substrate binding / tRNA nucleotidyltransferase, domain 2 / : / tRNA nucleotidyltransferase, second domain / Archaeal CCA-adding enzyme, C-terminal domain / Poly(A) polymerase predicted RNA binding domain / Nucleotidyltransferase, class I-like, C-terminal / 2-5OAS/ClassI-CCAase, nucleotidyltransferase domain / Poly(a)-polymerase, middle domain / Polymerase, nucleotidyl transferase domain / Nucleotidyltransferase domain / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / CCA-adding enzyme
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsXiong, Y. / Steitz, T.A.
CitationJournal: Nature / Year: 2004
Title: Mechanism of transfer RNA maturation by CCA-adding enzyme without using an oligonucleotide template.
Authors: Xiong, Y. / Steitz, T.A.
History
DepositionMay 27, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_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_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_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: 5'-R(*GP*CP*GP*GP*AP*UP*CP*CP*GP*CP*AP*C)-3'
H: 5'-R(*GP*CP*GP*GP*AP*UP*CP*CP*GP*CP*AP*CP*C)-3'
F: 5'-R(*GP*CP*GP*GP*AP*CP*CP*CP*GP*CP*AP*C)-3'
I: 5'-R(*GP*CP*GP*GP*AP*UP*CP*CP*GP*CP*AP*CP*C)-3'
G: 5'-R(*GP*CP*GP*GP*AP*UP*CP*CP*GP*CP*AP*CP*C)-3'
J: 5'-R(*CP*GP*CP*GP*GP*AP*UP*CP*CP*GP*CP*AP*C)-3'
A: tRNA nucleotidyltransferase
B: tRNA nucleotidyltransferase
C: tRNA nucleotidyltransferase
D: tRNA nucleotidyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,11714
Polymers230,05410
Non-polymers1,0634
Water19,0781059
1
E: 5'-R(*GP*CP*GP*GP*AP*UP*CP*CP*GP*CP*AP*C)-3'
H: 5'-R(*GP*CP*GP*GP*AP*UP*CP*CP*GP*CP*AP*CP*C)-3'
G: 5'-R(*GP*CP*GP*GP*AP*UP*CP*CP*GP*CP*AP*CP*C)-3'
J: 5'-R(*CP*GP*CP*GP*GP*AP*UP*CP*CP*GP*CP*AP*C)-3'
A: tRNA nucleotidyltransferase
B: tRNA nucleotidyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,6918
Polymers119,1596
Non-polymers5312
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: 5'-R(*GP*CP*GP*GP*AP*CP*CP*CP*GP*CP*AP*C)-3'
I: 5'-R(*GP*CP*GP*GP*AP*UP*CP*CP*GP*CP*AP*CP*C)-3'
C: tRNA nucleotidyltransferase
D: tRNA nucleotidyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,4276
Polymers110,8954
Non-polymers5312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.641, 84.770, 135.813
Angle α, β, γ (deg.)90.00, 104.66, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21D
12A
22C
32A
42C
13A
23B
33C
43D
14E
24F

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETLYSLYS5BH1 - 1351 - 135
211METMETLYSLYS5DJ1 - 1351 - 135
112METMETTYRTYR2AG1 - 901 - 90
212METMETTYRTYR2CI1 - 901 - 90
322HISHISLYSLYS5AG101 - 135101 - 135
422HISHISLYSLYS5CI101 - 135101 - 135
113TRPTRPASPASP5AG136 - 437136 - 437
213TRPTRPASPASP5BH136 - 437136 - 437
313TRPTRPASPASP5CI136 - 437136 - 437
413TRPTRPASPASP5DJ136 - 437136 - 437
114GGCC5EA1 - 121 - 12
214GGCC5FC1 - 121 - 12

NCS ensembles :
ID
1
2
3
4

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Components

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RNA chain , 4 types, 6 molecules EHIGFJ

#1: RNA chain 5'-R(*GP*CP*GP*GP*AP*UP*CP*CP*GP*CP*AP*C)-3'


Mass: 3826.352 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: RNA chain 5'-R(*GP*CP*GP*GP*AP*UP*CP*CP*GP*CP*AP*CP*C)-3'


Mass: 4131.534 Da / Num. of mol.: 3 / Source method: obtained synthetically
#3: RNA chain 5'-R(*GP*CP*GP*GP*AP*CP*CP*CP*GP*CP*AP*C)-3'


Mass: 3825.368 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: RNA chain 5'-R(*CP*GP*CP*GP*GP*AP*UP*CP*CP*GP*CP*AP*C)-3'


Mass: 4131.533 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Protein , 1 types, 4 molecules ABCD

#5: Protein
tRNA nucleotidyltransferase / / 2.7.7.25 / tRNA adenylyltransferase / tRNA CCA-pyrophosphorylase / CCA-adding enzyme


Mass: 51469.137 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: CCA, AF2156 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O28126, EC: 2.7.7.25

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Non-polymers , 3 types, 1063 molecules

#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1059 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.1→47.7 Å / Num. obs: 122568 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Rmerge(I) obs: 0.072

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1R89
Resolution: 2.2→47.7 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 11.938 / SU ML: 0.164 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.245 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24168 6447 5 %RANDOM
Rwork0.19207 ---
obs0.19454 122568 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 45.443 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å2-0.3 Å2
2--0.21 Å20 Å2
3----0.75 Å2
Refinement stepCycle: LAST / Resolution: 2.2→47.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14520 1598 64 1059 17241
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02216697
X-RAY DIFFRACTIONr_bond_other_d0.0010.0214375
X-RAY DIFFRACTIONr_angle_refined_deg1.1652.09622820
X-RAY DIFFRACTIONr_angle_other_deg0.956333528
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.46551744
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.43122.784776
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.543152780
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.81315160
X-RAY DIFFRACTIONr_chiral_restr0.0660.22454
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217182
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023372
X-RAY DIFFRACTIONr_nbd_refined0.1870.23237
X-RAY DIFFRACTIONr_nbd_other0.1840.214494
X-RAY DIFFRACTIONr_nbtor_refined0.1840.27693
X-RAY DIFFRACTIONr_nbtor_other0.0770.29024
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2833
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0320.21
X-RAY DIFFRACTIONr_metal_ion_refined0.070.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.120.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2120.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0970.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.2722.511403
X-RAY DIFFRACTIONr_mcbond_other0.2922.53540
X-RAY DIFFRACTIONr_mcangle_it1.45414056
X-RAY DIFFRACTIONr_scbond_it2.4559912
X-RAY DIFFRACTIONr_scangle_it3.32988764
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
21A531tight positional0.030.05
11B795medium positional0.250.5
21A1137medium positional0.350.5
31A1781medium positional0.290.5
32B1781medium positional0.190.5
33C1781medium positional0.360.5
34D1781medium positional0.390.5
11B1378loose positional0.775
21A336loose positional0.65
31A3110loose positional0.65
32B3110loose positional0.595
33C3110loose positional0.715
34D3110loose positional0.765
41E322loose positional0.285
21A531tight thermal0.090.5
11B795medium thermal0.252
21A1137medium thermal0.482
31A1781medium thermal0.562
32B1781medium thermal0.582
33C1781medium thermal0.692
34D1781medium thermal0.622
11B1378loose thermal0.7110
21A336loose thermal0.9110
31A3110loose thermal1.5510
32B3110loose thermal1.610
33C3110loose thermal1.7310
34D3110loose thermal1.8410
41E322loose thermal1.8310
LS refinement shellResolution: 2.2→2.352 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.287 1125 -
Rwork0.246 21803 -
obs--97.73 %
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)
112.5969-3.792-1.07733.5513-0.58114.38720.1841-0.68540.9710.0023-0.1097-0.5199-0.15880.343-0.0744-0.1479-0.04570.0799-0.07290.08050.012177.744532.616535.4538
21.9808-0.1528-0.56992.38211.03462.96760.1060.25810.1501-0.1784-0.22910.0134-0.0077-0.43620.1231-0.3102-0.0331-0.0207-0.12160.0211-0.235554.030233.495945.9387
31.5268-0.1312-0.96230.56030.25523.15540.0632-0.06970.15690.01160.0746-0.2299-0.33910.1507-0.1378-0.2184-0.0557-0.0627-0.22990.0149-0.072563.005753.351877.4628
47.18720.63532.62053.22770.381210.3753-0.1788-0.80340.08120.99910.4790.8453-0.2771-1.2438-0.30020.47170.38650.34380.49210.34640.183125.927439.5329131.3273
52.6131-0.36990.32463.678-1.95034.9382-0.1856-0.5374-0.00040.95440.2163-0.08-0.455-0.0516-0.03070.24610.1793-0.07280.12810.1112-0.254349.593837.3197123.6952
62.0524-0.3845-0.94750.92860.27023.0665-0.0674-0.1660.06210.26890.1405-0.0055-0.3854-0.225-0.0731-0.17130.0798-0.0248-0.16820.07-0.195141.339954.387190.8262
73.5768-3.8411-1.911710.48863.25683.4552-0.2565-0.31170.177-0.15770.4167-0.88710.02960.4126-0.1602-0.08070.0714-0.00090.13280.09280.028867.400524.166797.8409
83.4851-0.8419-1.01343.11030.57752.7692-0.2476-0.1953-0.63190.39450.08460.44640.3184-0.22240.163-0.2175-0.02730.0914-0.24210.11840.045669.04064.602581.1417
91.3355-0.2265-0.07551.11290.3031.44780.08270.01690.13910.0449-0.1075-0.22230.04480.20750.0248-0.283-0.00210.0068-0.3360.0623-0.101898.342718.596260.8408
100.31210.5024-1.66877.22280.662810.67140.02710.9176-0.5259-0.61460.1033-0.34641.2371-0.0684-0.13040.62030.3039-0.00270.5651-0.05480.304798.8265-2.1139-2.7093
112.3524-0.71230.95392.811-1.02716.19370.30730.86740.2747-0.6757-0.3329-0.25550.66110.63430.02550.12510.32780.17220.33790.3226-0.120496.059219.148310.0893
121.1760.0313-0.67542.1143-1.2933.4860.10020.3179-0.0214-0.7398-0.3123-0.17410.78840.43940.21210.05140.22610.0307-0.17060.0714-0.1252102.1581.017742.7292
134.20540.22523.2444.3356-3.34497.01870.11490.2741-0.6683-0.73120.42520.45851.4569-0.4038-0.54010.1624-0.0385-0.00420.15080.13580.04330.115734.105397.9671
143.58371.696-1.29738.4797-5.895815.32980.53190.1692-0.0475-0.35710.46340.98291.2071-1.519-0.99530.4309-0.0672-0.20590.11730.09340.109784.3061-5.026427.94
152.2497-2.03230.37418.8305-4.00292.0124-0.1493-0.17650.0916-0.0635-0.0912-0.48340.18420.30390.2405-0.235-0.021-0.0319-0.19370.0362-0.141675.586529.628668.2222
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AG17 - 12417 - 124
2X-RAY DIFFRACTION2AG125 - 258125 - 258
3X-RAY DIFFRACTION2AG1 - 161 - 16
4X-RAY DIFFRACTION3AG259 - 437259 - 437
5X-RAY DIFFRACTION4BH17 - 12417 - 124
6X-RAY DIFFRACTION5BH125 - 258125 - 258
7X-RAY DIFFRACTION5BH1 - 161 - 16
8X-RAY DIFFRACTION6BH259 - 437259 - 437
9X-RAY DIFFRACTION7CI17 - 12417 - 124
10X-RAY DIFFRACTION8CI125 - 258125 - 258
11X-RAY DIFFRACTION8CI1 - 161 - 16
12X-RAY DIFFRACTION9CI259 - 437259 - 437
13X-RAY DIFFRACTION10DJ17 - 12417 - 124
14X-RAY DIFFRACTION11DJ125 - 258125 - 258
15X-RAY DIFFRACTION11DJ1 - 161 - 16
16X-RAY DIFFRACTION12DJ259 - 437259 - 437
17X-RAY DIFFRACTION13EA1 - 121 - 12
18X-RAY DIFFRACTION13HB63 - 751 - 13
19X-RAY DIFFRACTION14FC1 - 121 - 12
20X-RAY DIFFRACTION14ID63 - 751 - 13
21X-RAY DIFFRACTION15GE2 - 141 - 13
22X-RAY DIFFRACTION15JF61 - 731 - 13

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