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- PDB-3wof: Crystal structure of P23-45 gp39 (6-132) bound to Thermus thermop... -

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Basic information

Entry
Database: PDB / ID: 3wof
TitleCrystal structure of P23-45 gp39 (6-132) bound to Thermus thermophilus RNA polymerase beta-flap domain
Components
  • DNA-directed RNA polymerase subunit beta
  • Putative uncharacterized protein
KeywordsTRANSFERASE/TRANSCRIPTION / Transcription / RNA polymerase / TRANSFERASE-TRANSCRIPTION complex
Function / homology
Function and homology information


DNA-directed RNA polymerase complex / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / DNA-templated transcription / DNA binding
Similarity search - Function
SH3 type barrels. - #1250 / Thermus phage P23-45 gp39, N-terminal domain / RNA polymerase II, Rpb2 subunit, wall domain / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase beta subunit external 1 domain / DNA-directed RNA polymerase beta subunit, bacterial-type / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit ...SH3 type barrels. - #1250 / Thermus phage P23-45 gp39, N-terminal domain / RNA polymerase II, Rpb2 subunit, wall domain / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase beta subunit external 1 domain / DNA-directed RNA polymerase beta subunit, bacterial-type / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 6 / SH3 type barrels. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Roll / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Uncharacterized protein / DNA-directed RNA polymerase subunit beta
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
Thermus phage P23-45 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.298 Å
AuthorsTagami, S. / Sekine, S. / Minakhin, L. / Esyunina, D. / Akasaka, R. / Shirouzu, M. / Kulbachinskiy, A. / Severinov, K. / Yokoyama, S.
CitationJournal: Genes Dev. / Year: 2014
Title: Structural basis for promoter specificity switching of RNA polymerase by a phage factor.
Authors: Tagami, S. / Sekine, S. / Minakhin, L. / Esyunina, D. / Akasaka, R. / Shirouzu, M. / Kulbachinskiy, A. / Severinov, K. / Yokoyama, S.
History
DepositionDec 26, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Database references / Derived calculations
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-directed RNA polymerase subunit beta
B: Putative uncharacterized protein
C: DNA-directed RNA polymerase subunit beta
D: Putative uncharacterized protein
E: DNA-directed RNA polymerase subunit beta
F: Putative uncharacterized protein
G: DNA-directed RNA polymerase subunit beta
H: Putative uncharacterized protein
I: DNA-directed RNA polymerase subunit beta
J: Putative uncharacterized protein
K: DNA-directed RNA polymerase subunit beta
L: Putative uncharacterized protein
M: DNA-directed RNA polymerase subunit beta
N: Putative uncharacterized protein
O: DNA-directed RNA polymerase subunit beta
P: Putative uncharacterized protein
Q: DNA-directed RNA polymerase subunit beta
R: Putative uncharacterized protein
S: DNA-directed RNA polymerase subunit beta
T: Putative uncharacterized protein
U: DNA-directed RNA polymerase subunit beta
V: Putative uncharacterized protein
W: DNA-directed RNA polymerase subunit beta
X: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)352,03824
Polymers352,03824
Non-polymers00
Water00
1
A: DNA-directed RNA polymerase subunit beta
B: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)29,3372
Polymers29,3372
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-6 kcal/mol
Surface area12990 Å2
MethodPISA
2
C: DNA-directed RNA polymerase subunit beta
D: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)29,3372
Polymers29,3372
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-7 kcal/mol
Surface area13030 Å2
MethodPISA
3
E: DNA-directed RNA polymerase subunit beta
F: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)29,3372
Polymers29,3372
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-8 kcal/mol
Surface area12840 Å2
MethodPISA
4
G: DNA-directed RNA polymerase subunit beta
H: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)29,3372
Polymers29,3372
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-8 kcal/mol
Surface area13100 Å2
MethodPISA
5
I: DNA-directed RNA polymerase subunit beta
J: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)29,3372
Polymers29,3372
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-8 kcal/mol
Surface area13270 Å2
MethodPISA
6
K: DNA-directed RNA polymerase subunit beta
L: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)29,3372
Polymers29,3372
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-7 kcal/mol
Surface area13050 Å2
MethodPISA
7
M: DNA-directed RNA polymerase subunit beta
N: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)29,3372
Polymers29,3372
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-8 kcal/mol
Surface area12930 Å2
MethodPISA
8
O: DNA-directed RNA polymerase subunit beta
P: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)29,3372
Polymers29,3372
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-7 kcal/mol
Surface area12890 Å2
MethodPISA
9
Q: DNA-directed RNA polymerase subunit beta
R: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)29,3372
Polymers29,3372
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-10 kcal/mol
Surface area12660 Å2
MethodPISA
10
S: DNA-directed RNA polymerase subunit beta
T: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)29,3372
Polymers29,3372
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-9 kcal/mol
Surface area13050 Å2
MethodPISA
11
U: DNA-directed RNA polymerase subunit beta
V: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)29,3372
Polymers29,3372
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-7 kcal/mol
Surface area12530 Å2
MethodPISA
12
W: DNA-directed RNA polymerase subunit beta
X: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)29,3372
Polymers29,3372
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-8 kcal/mol
Surface area13260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)213.777, 213.777, 234.598
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
DNA-directed RNA polymerase subunit beta / RNAP subunit beta / RNA polymerase subunit beta / Transcriptase subunit beta


Mass: 14481.525 Da / Num. of mol.: 12 / Fragment: beta-flap domain, UNP RESIDUES 703-830
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: rpoB, TTHA1813 / Plasmid: pGEX-6P / Production host: Escherichia coli (E. coli) / References: UniProt: Q8RQE9, DNA-directed RNA polymerase
#2: Protein
Putative uncharacterized protein / gp39


Mass: 14854.996 Da / Num. of mol.: 12 / Fragment: UNP RESIDUES 6-132
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus phage P23-45 (virus) / Strain: Thermus phage P23-45 / Gene: gp39 (P23p39), P23p39 / Plasmid: pET-47b / Production host: Escherichia coli (E. coli) / References: UniProt: A7XX65

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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: 3.81 Å3/Da / Density % sol: 67.69 %
Crystal growTemperature: 293 K / pH: 5.6
Details: 50mM MES-NaOH (pH 5.6), 6% PEG 8000, 200mM KCl, 10mM MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 11, 2012
RadiationMonochromator: NUMERICAL LINK TYPE SI(111) DOUBLE CRYSTAL MONOCHROMATOR, LIQUID NITROGEN COOLING
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.298→50 Å / Num. obs: 82014 / % possible obs: 99.9 % / Observed criterion σ(I): 5.2 / Redundancy: 10.6 % / Rsym value: 0.175 / Net I/σ(I): 14.2

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WOE
Resolution: 3.298→34.549 Å / SU ML: 0.37 / σ(F): 1.41 / Phase error: 23.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2464 4107 5.01 %
Rwork0.2191 --
obs0.2205 81938 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.298→34.549 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22026 0 0 0 22026
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00922516
X-RAY DIFFRACTIONf_angle_d1.22730539
X-RAY DIFFRACTIONf_dihedral_angle_d17.2518770
X-RAY DIFFRACTIONf_chiral_restr0.0763369
X-RAY DIFFRACTIONf_plane_restr0.0074020
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2982-3.3370.30331580.27382592X-RAY DIFFRACTION99
3.337-3.37760.32621120.27632678X-RAY DIFFRACTION100
3.3776-3.42030.30231310.27762646X-RAY DIFFRACTION100
3.4203-3.46530.34231480.28762638X-RAY DIFFRACTION100
3.4653-3.51270.28291420.26722655X-RAY DIFFRACTION100
3.5127-3.56290.29811170.25782717X-RAY DIFFRACTION100
3.5629-3.6160.27811300.252629X-RAY DIFFRACTION100
3.616-3.67240.32041490.2772644X-RAY DIFFRACTION100
3.6724-3.73260.28931280.25392675X-RAY DIFFRACTION100
3.7326-3.79690.24151360.23132643X-RAY DIFFRACTION100
3.7969-3.86580.27581490.24132658X-RAY DIFFRACTION100
3.8658-3.94010.28461590.24192632X-RAY DIFFRACTION100
3.9401-4.02040.27451420.22532662X-RAY DIFFRACTION100
4.0204-4.10770.25411380.22962668X-RAY DIFFRACTION100
4.1077-4.20310.23881270.21522691X-RAY DIFFRACTION100
4.2031-4.3080.23821520.20152645X-RAY DIFFRACTION100
4.308-4.42420.21611470.19152669X-RAY DIFFRACTION100
4.4242-4.55410.21641490.18832685X-RAY DIFFRACTION100
4.5541-4.70080.20031490.18892651X-RAY DIFFRACTION100
4.7008-4.86840.21631400.19062693X-RAY DIFFRACTION100
4.8684-5.06270.23711320.19472687X-RAY DIFFRACTION100
5.0627-5.29230.2011260.19512712X-RAY DIFFRACTION100
5.2923-5.57030.23991550.19762682X-RAY DIFFRACTION100
5.5703-5.91770.2191460.20672713X-RAY DIFFRACTION100
5.9177-6.37190.2741280.2192731X-RAY DIFFRACTION100
6.3719-7.00830.25341560.2132706X-RAY DIFFRACTION100
7.0083-8.01140.24531560.20412744X-RAY DIFFRACTION100
8.0114-10.05220.18281520.16442792X-RAY DIFFRACTION100
10.0522-34.55130.21321530.23032893X-RAY DIFFRACTION99
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)
10.0733-0.04720.07140.19930.07990.0923-0.07780.2609-0.0174-0.01310.02850.0956-0.16220.2364-0.05220.1855-0.1587-0.3010.25110.030.2791-17.9096-32.151537.1021
20.04260.0474-0.01450.1141-0.08880.0821-0.0028-0.0965-0.05240.0472-0.0841-0.012-0.02230.0323-0.18970.0963-0.2062-0.0122-0.19590.03750.0796-35.8321-20.96241.9259
30.1263-0.0847-0.15230.1871-0.02950.3482-0.08510.10150.1016-0.25540.09110.13380.232-0.3590.00290.4081-0.1257-0.03860.4210.05770.3652-94.1297-38.87258.6285
40.32410.00950.06920.1332-0.03640.02050.0308-0.11850.01780.2161-0.0013-0.00340.1591-0.14040.00510.4045-0.0787-0.01110.23250.09650.3575-81.7469-31.229324.6909
50.0491-0.06030.01470.2265-0.15480.147-0.11060.03470.273-0.2207-0.1866-0.2396-0.11340.0384-0.2260.53620.2612-0.3624-0.1304-0.03680.7731-60.023632.768919.1933
60.0853-0.053-0.02930.03390.02120.0159-0.1866-0.10110.1201-0.0293-0.07460.0247-0.1113-0.0741-0.1670.31760.3313-0.22110.0064-0.03610.4077-66.739815.125828.9362
70.0275-0.00250.00390.0183-0.00070.02360.17840.0310.1456-0.10910.017-0.02340.0970.09750.37080.0623-0.19-0.3591-0.0167-0.3602-0.232113.2559-12.367749.1596
80.0060.0082-0.029-0.0032-0.00150.08070.05980.0481-0.0375-0.04320.0283-0.02410.0520.12170.0922-0.1799-0.293-0.40840.198-0.4094-0.24828.1747-12.083233.469
90.06350.06610.05090.09290.07220.1672-0.3461-0.01270.2192-0.2371-0.00170.0653-0.1492-0.0083-0.02160.2705-0.1382-0.06390.7154-0.06280.34876.833337.690237.6299
100.04660.00990.02330.05390.01420.0183-0.0115-0.0486-0.0027-0.05190.0333-0.0143-0.00310.0095-0.00820.0194-0.25090.01590.886-0.25350.310267.564818.146134.8846
110.04890.0252-0.02330.00340.00150.03490.16960.09830.0209-0.1215-0.1478-0.0327-0.0752-0.03840.00560.59010.20440.03490.8753-0.14370.313138.43896.4036-25.6316
120.02320.01940.03150.02530.03260.04750.023-0.0562-0.12420.0112-0.07510.01890.09650.0500.25550.04620.05760.7834-0.06270.343148.23391.7234-7.1801
130.0859-0.05120.11110.0331-0.05160.16210.1212-0.22120.2049-0.14890.11120.022-0.2728-0.04830.04460.2765-0.0710.07760.1863-0.09780.2852-19.89389.70833.0933
140.12410.02290.00060.099-0.06650.08030.02490.00250.053-0.17440.0140.1377-0.1013-0.06070.00130.06480.2082-0.0038-0.17890.08210.0957-32.9764-5.281124.723
150.1133-0.02250.03040.0301-0.03590.0377-0.0831-0.0078-0.1029-0.0630.12450.3196-0.1329-0.0974-0.00330.70310.0246-0.19930.32580.09490.7434-91.858810.01563.3073
160.01260.00890.0240.0857-0.01040.0764-0.0212-0.0668-0.1877-0.08190.0634-0.0005-0.03930.02710.09090.38680.2051-0.1884-0.31460.10840.3588-71.93433.80828.9889
170.080.07380.00160.0607-0.02010.09880.2360.1323-0.20330.0564-0.1317-0.06870.13960.09140.01060.67360.0485-0.25820.2332-0.03710.993-57.541-57.039719.9159
180.0469-0.0217-0.02990.02080.00820.04720.07320.21510.00720.177-0.034-0.11560.08580.00880.00790.18750.0198-0.27850.1529-0.03990.3002-61.0937-36.884615.0313
190.13180.0581-0.04440.0775-0.02560.038-0.0352-0.0943-0.1175-0.0377-0.0468-0.13310.03330.188-0.09010.161-0.02270.07780.2530.121-0.04053.0756-9.34648.3865
200.0075-0.00350.01930.10410.01080.17610.12480.02360.0621-0.02880.1169-0.0779-0.08560.18410.31680.1892-0.11090.13950.4936-0.11780.173117.22672.937419.0127
210.0472-0.01340.03060.00610.00480.0475-0.1844-0.07640.0232-0.0921-0.008-0.0044-0.12110.154-0.01480.8635-0.41610.06450.8040.09590.50367.856730.9011-8.9692
220.04150.0090.01150.0287-0.00380.0051-0.0204-0.12640.026-0.1192-0.05310.0345-0.3250.0326-00.7245-0.2341-0.06770.7063-0.04770.321850.538323.9743-0.2075
230.07760.02540.06860.1078-0.06120.14980.1026-0.09310.1555-0.02570.1573-0.13470.11020.13850.2043-0.0739-0.03820.0130.5465-0.28420.381452.28816.801665.0913
240.03940.03410.02870.03680.04990.03840.03990.11280.088-0.13630.27750.06770.02030.06060.2713-0.0393-0.5656-0.0920.6684-0.1790.432946.959221.924244.7826
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 Q
18X-RAY DIFFRACTION18CHAIN R
19X-RAY DIFFRACTION19CHAIN S
20X-RAY DIFFRACTION20CHAIN T
21X-RAY DIFFRACTION21CHAIN U
22X-RAY DIFFRACTION22CHAIN V
23X-RAY DIFFRACTION23CHAIN W
24X-RAY DIFFRACTION24CHAIN X

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  • 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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