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- PDB-1tfy: 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: 1tfy
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*C)-3'
  • 5'-R(*CP*GP*GP*AP*UP*CP*CP*GP*CP*AP*C)-3'
  • 5'-R(*GP*CP*GP*GP*AP*UP*AP*UP*CP*CP*GP*CP*AP*C)-3'
  • 5'-R(*GP*CP*GP*GP*AP*UP*AP*UP*CP*CP*GP*CP*G)-3'
  • tRNA nucleotidyltransferase
KeywordsTRANSFERASE/RNA / CCA-adding Complex / CTP / 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
CYTIDINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / CCA-adding enzyme
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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*AP*UP*CP*CP*GP*CP*G)-3'
H: 5'-R(*GP*CP*GP*GP*AP*UP*AP*UP*CP*CP*GP*CP*AP*C)-3'
F: 5'-R(*GP*CP*GP*GP*AP*UP*AP*UP*CP*CP*GP*CP*G)-3'
I: 5'-R(*GP*CP*GP*GP*AP*UP*AP*UP*CP*CP*GP*CP*AP*C)-3'
G: 5'-R(*CP*GP*GP*AP*UP*CP*CP*GP*CP*AP*C)-3'
J: 5'-R(*CP*GP*CP*GP*GP*AP*UP*C)-3'
A: tRNA nucleotidyltransferase
B: tRNA nucleotidyltransferase
C: tRNA nucleotidyltransferase
D: tRNA nucleotidyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,19818
Polymers229,16810
Non-polymers2,0308
Water0
1
E: 5'-R(*GP*CP*GP*GP*AP*UP*AP*UP*CP*CP*GP*CP*G)-3'
H: 5'-R(*GP*CP*GP*GP*AP*UP*AP*UP*CP*CP*GP*CP*AP*C)-3'
G: 5'-R(*CP*GP*GP*AP*UP*CP*CP*GP*CP*AP*C)-3'
J: 5'-R(*CP*GP*CP*GP*GP*AP*UP*C)-3'
A: tRNA nucleotidyltransferase
B: tRNA nucleotidyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,61010
Polymers117,5956
Non-polymers1,0154
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: 5'-R(*GP*CP*GP*GP*AP*UP*AP*UP*CP*CP*GP*CP*G)-3'
I: 5'-R(*GP*CP*GP*GP*AP*UP*AP*UP*CP*CP*GP*CP*AP*C)-3'
C: tRNA nucleotidyltransferase
D: tRNA nucleotidyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,5878
Polymers111,5734
Non-polymers1,0154
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.092, 84.023, 134.561
Angle α, β, γ (deg.)90.00, 102.38, 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:

Refine code: 2

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETLYSLYSBH1 - 1351 - 135
211METMETLYSLYSDJ1 - 1351 - 135
112METMETTYRTYRAG1 - 901 - 90
212METMETTYRTYRCI1 - 901 - 90
322HISHISLYSLYSAG101 - 135101 - 135
422HISHISLYSLYSCI101 - 135101 - 135
113TRPTRPASPASPAG136 - 437136 - 437
213TRPTRPASPASPBH136 - 437136 - 437
313TRPTRPASPASPCI136 - 437136 - 437
413TRPTRPASPASPDJ136 - 437136 - 437
114GGGGEA1 - 131 - 13
214GGGGFC1 - 131 - 13

NCS ensembles :
ID
1
2
3
4

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Components

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RNA chain , 4 types, 6 molecules EFHIGJ

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


Mass: 4172.542 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: RNA chain 5'-R(*GP*CP*GP*GP*AP*UP*AP*UP*CP*CP*GP*CP*AP*C)-3'


Mass: 4461.723 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: RNA chain 5'-R(*CP*GP*GP*AP*UP*CP*CP*GP*CP*AP*C)-3'


Mass: 3481.146 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: RNA chain 5'-R(*CP*GP*CP*GP*GP*AP*UP*C)-3'


Mass: 2541.577 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 , 2 types, 8 molecules

#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE / Cytidine triphosphate


Mass: 483.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H16N3O14P3

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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: 3.2→50 Å / Num. obs: 38861 / % possible obs: 99 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.098
Reflection shellResolution: 3.2→3.42 Å / % possible all: 99.4

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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: 3.2→44.28 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.901 / SU B: 85.655 / SU ML: 0.636 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.612
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.29043 2053 5 %RANDOM
Rwork0.23521 ---
obs0.23801 38861 99.13 %-
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: 131.197 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.2→44.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14520 1540 120 0 16180
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02216689
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1212.09622811
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.31251744
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.67522.784776
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.338152780
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8415160
X-RAY DIFFRACTIONr_chiral_restr0.070.22447
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0212151
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.27464
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.211143
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2430
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0270.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.0932.58932
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.118414056
X-RAY DIFFRACTIONr_scbond_it0.21859202
X-RAY DIFFRACTIONr_scangle_it0.35488755
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
11B540tight positional0.040.05
21A500tight positional0.060.05
31A1208tight positional0.070.05
32B1208tight positional0.060.05
33C1208tight positional0.10.05
34D1208tight positional0.120.05
11B573medium positional0.750.5
21A523medium positional0.580.5
31A1339medium positional0.620.5
32B1339medium positional0.60.5
33C1339medium positional0.720.5
34D1339medium positional0.740.5
41E571medium positional0.450.5
11B540tight thermal0.060.5
21A500tight thermal0.080.5
31A1208tight thermal0.090.5
32B1208tight thermal0.090.5
33C1208tight thermal0.110.5
34D1208tight thermal0.120.5
11B573medium thermal0.492
21A523medium thermal0.692
31A1339medium thermal0.852
32B1339medium thermal0.832
33C1339medium thermal0.962
34D1339medium thermal1.052
41E571medium thermal0.592
LS refinement shellResolution: 3.2→3.42 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.373 394 -
Rwork0.336 6899 -
obs--99.9 %
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)
112.9413-6.09080.56738.835-0.32962.5354-0.0919-0.48610.95780.4833-0.2224-0.49710.0626-0.32820.3143-0.4651-0.18220.1277-0.4674-0.0637-0.498276.934932.419835.3471
24.122-0.8385-1.20484.23510.65725.92290.06780.21480.0949-0.5372-0.1864-0.00680.1028-0.63620.1186-0.6783-0.1930.0322-0.2766-0.1372-0.66554.32531.967845.6181
32.20470.5476-1.37091.0916-0.2986.9791-0.15740.21340.1324-0.08450.159-0.2221-0.88230.5072-0.0016-0.6151-0.1702-0.0455-0.4313-0.0317-0.460865.218651.95476.2718
412.39413.28640.95685.6265-0.43813.034-0.56210.33110.9073-0.18120.69991.5283-0.4551-0.79-0.13780.0760.44860.24520.36040.3855-0.18530.725838.9361130.9873
54.6967-0.0736-0.46444.5772-2.26297.652-0.1779-0.5087-0.05110.96440.168-0.001-0.6874-0.10870.0099-0.39960.2148-0.0528-0.30020.0643-0.834553.580936.0892123.1809
62.3918-0.7645-0.95481.29380.73456.1761-0.1694-0.04870.0830.28260.22460.0279-0.9411-0.4518-0.0552-0.4620.09380.0258-0.45480.088-0.604944.145953.282190.7542
76.0618-4.45970.79814.11650.86933.1166-0.12470.32810.0172-0.4446-0.2992-0.4282-0.04520.03970.4239-0.677-0.10080.1485-0.3195-0.0045-0.483570.363822.626596.5206
84.6752-0.8455-1.47274.9340.74464.8877-0.1615-0.3402-0.45940.173-0.07030.56910.561-0.36110.2318-0.7-0.15140.1308-0.5329-0.0351-0.32570.64313.665780.6475
91.60920.1455-1.04871.7750.66886.10790.1221-0.11020.22250.1137-0.1494-0.1373-0.21030.2230.0273-0.6207-0.0195-0.0282-0.88440.0145-0.482498.674218.91259.8999
105.58232.6552.062610.08931.74573.33890.5211-0.0196-1.1040.2208-0.2627-0.58640.9932-0.0071-0.25850.24330.3893-0.04510.1089-0.0011-0.301298.0857-2.2254-2.0949
114.6124-0.68560.94594.427-0.96747.05780.18870.66740.135-0.5115-0.2696-0.18170.06840.32450.0809-0.4310.20130.1158-0.33190.2082-0.737694.95218.85119.4827
121.7792-0.9128-2.16411.88770.21066.97770.0140.2155-0.0505-0.2462-0.24150.07870.5680.27340.2275-0.4480.0779-0.0755-0.74850.0162-0.5661102.8461.335541.7711
1312.5113-0.52988.1826.666-2.89876.3312-0.49481.4969-0.1749-1.70310.21090.47281.6608-0.32310.28390.20850.02670.0690.30980.0168-0.359533.576733.415294.7563
146.49132.12141.593810.2985-8.76599.37010.6177-0.649-0.44920.97970.00610.79530.8498-2.2103-0.62380.0308-0.2752-0.04840.11510.0343-0.111283.9134-5.51131.9069
159.18551.07563.107826.3759-21.461721.8992-1.22771.54770.7371-0.2394-0.1887-1.92082.15571.87941.4164-0.35920.13790.1904-0.0151-0.07180.082775.402329.575666.4529
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AG17 - 12417 - 124
2X-RAY DIFFRACTION1AO5011
3X-RAY DIFFRACTION1AK6011
4X-RAY DIFFRACTION2AG125 - 258125 - 258
5X-RAY DIFFRACTION2AG1 - 161 - 16
6X-RAY DIFFRACTION3AG259 - 437259 - 437
7X-RAY DIFFRACTION4BH17 - 12417 - 124
8X-RAY DIFFRACTION4BP5021
9X-RAY DIFFRACTION4BL6021
11X-RAY DIFFRACTION5BH125 - 258125 - 258
12X-RAY DIFFRACTION5BH1 - 161 - 16
13X-RAY DIFFRACTION6BH259 - 437259 - 437
14X-RAY DIFFRACTION7CI17 - 12417 - 124
15X-RAY DIFFRACTION7CQ5031
16X-RAY DIFFRACTION7CM6031
17X-RAY DIFFRACTION8CI125 - 258125 - 258
18X-RAY DIFFRACTION8CI1 - 161 - 16
19X-RAY DIFFRACTION9CI259 - 437259 - 437
20X-RAY DIFFRACTION10DJ17 - 12417 - 124
21X-RAY DIFFRACTION10DR5041
22X-RAY DIFFRACTION10DN6041
23X-RAY DIFFRACTION10ID7414
24X-RAY DIFFRACTION11DJ125 - 258125 - 258
25X-RAY DIFFRACTION11DJ1 - 161 - 16
26X-RAY DIFFRACTION12DJ259 - 437259 - 437
27X-RAY DIFFRACTION13EA1 - 131 - 13
28X-RAY DIFFRACTION13HB61 - 731 - 13
29X-RAY DIFFRACTION14FC1 - 131 - 13
30X-RAY DIFFRACTION14ID61 - 731 - 13
31X-RAY DIFFRACTION15GE3 - 131 - 11
32X-RAY DIFFRACTION15JF61 - 681 - 8

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