[English] 日本語
Yorodumi
- PDB-5n9g: TFIIIB -TBP/Brf2/DNA and SANT domain of Bdp1- -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5n9g
TitleTFIIIB -TBP/Brf2/DNA and SANT domain of Bdp1-
Components
  • (Transcription factor ...) x 2
  • DNA/RNA (25-MER)
  • DNA/RNA (27-MER)
  • TATA-box-binding protein
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


transcription preinitiation complex assembly / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / TFIIIC-class transcription factor complex binding / RNA polymerase III type 3 promoter sequence-specific DNA binding / regulation of transcription by RNA polymerase III / RNA polymerase transcription factor SL1 complex / RNA polymerase III general transcription initiation factor activity / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter ...transcription preinitiation complex assembly / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / TFIIIC-class transcription factor complex binding / RNA polymerase III type 3 promoter sequence-specific DNA binding / regulation of transcription by RNA polymerase III / RNA polymerase transcription factor SL1 complex / RNA polymerase III general transcription initiation factor activity / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / RNA Polymerase III Abortive And Retractive Initiation / transcription factor TFIIA complex / female germ cell nucleus / male pronucleus / female pronucleus / RNA polymerase II general transcription initiation factor binding / transcription preinitiation complex / RNA Polymerase I Transcription Termination / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase I Transcription Initiation / aryl hydrocarbon receptor binding / RNA polymerase II transcribes snRNA genes / TFIIB-class transcription factor binding / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / transcription by RNA polymerase III / core promoter sequence-specific DNA binding / RNA polymerase II preinitiation complex assembly / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / SIRT1 negatively regulates rRNA expression / male germ cell nucleus / transcription initiation at RNA polymerase II promoter / DNA-templated transcription initiation / RNA Polymerase I Promoter Escape / euchromatin / mRNA transcription by RNA polymerase II / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / cellular response to oxidative stress / spermatogenesis / DNA-binding transcription factor binding / Estrogen-dependent gene expression / Regulation of TP53 Activity through Phosphorylation / transcription by RNA polymerase II / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / enzyme binding / protein-containing complex / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Transcription factor TFIIIB component B'', Myb domain / Myb DNA-binding like / TATA-Binding Protein / Transcription factor TFIIB / Zinc finger TFIIB-type profile. / Cyclin-like / Zinc finger, TFIIB-type / TFIIB zinc-binding / TATA-box binding protein, eukaryotic / TATA-Binding Protein ...Transcription factor TFIIIB component B'', Myb domain / Myb DNA-binding like / TATA-Binding Protein / Transcription factor TFIIB / Zinc finger TFIIB-type profile. / Cyclin-like / Zinc finger, TFIIB-type / TFIIB zinc-binding / TATA-box binding protein, eukaryotic / TATA-Binding Protein / TATA-box binding protein / TATA-box binding protein, conserved site / Transcription factor TFIID (or TATA-binding protein, TBP) / Transcription factor TFIID repeat signature. / Cyclin A; domain 1 / TBP domain superfamily / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Cyclin-like superfamily / Homeobox-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA/RNA hybrid / DNA/RNA hybrid (> 10) / Transcription factor TFIIIB component B'' homolog / TATA-box-binding protein / Transcription factor IIIB 50 kDa subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsGouge, J. / Vannini, A. / Guthertz, N.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/K014390/1 United Kingdom
Cancer Research UKC47547/A21536 United Kingdom
Wellcome Trust200818/Z/16/Z United Kingdom
CitationJournal: Nat Commun / Year: 2017
Title: Molecular mechanisms of Bdp1 in TFIIIB assembly and RNA polymerase III transcription initiation.
Authors: Gouge, J. / Guthertz, N. / Kramm, K. / Dergai, O. / Abascal-Palacios, G. / Satia, K. / Cousin, P. / Hernandez, N. / Grohmann, D. / Vannini, A.
History
DepositionFeb 24, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Aug 9, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transcription factor IIIB 50 kDa subunit
B: TATA-box-binding protein
C: Transcription factor TFIIIB component B'' homolog
D: DNA/RNA (27-MER)
E: DNA/RNA (25-MER)
F: Transcription factor IIIB 50 kDa subunit
G: TATA-box-binding protein
H: Transcription factor TFIIIB component B'' homolog
I: DNA/RNA (27-MER)
J: DNA/RNA (25-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,20111
Polymers203,17810
Non-polymers231
Water5,368298
1
A: Transcription factor IIIB 50 kDa subunit
B: TATA-box-binding protein
C: Transcription factor TFIIIB component B'' homolog
D: DNA/RNA (27-MER)
E: DNA/RNA (25-MER)


Theoretical massNumber of molelcules
Total (without water)101,5895
Polymers101,5895
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17460 Å2
ΔGint-77 kcal/mol
Surface area31990 Å2
MethodPISA
2
F: Transcription factor IIIB 50 kDa subunit
G: TATA-box-binding protein
H: Transcription factor TFIIIB component B'' homolog
I: DNA/RNA (27-MER)
J: DNA/RNA (25-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,6126
Polymers101,5895
Non-polymers231
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16890 Å2
ΔGint-92 kcal/mol
Surface area30570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.190, 124.080, 88.610
Angle α, β, γ (deg.)90.00, 99.51, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Transcription factor ... , 2 types, 4 molecules AFCH

#1: Protein Transcription factor IIIB 50 kDa subunit / hTFIIIB50 / B-related factor 2 / BRF-2 / hBRFU


Mass: 42195.645 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRF2, BRFU, PRO1470 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HAW0
#3: Protein Transcription factor TFIIIB component B'' homolog / Transcription factor IIIB 150 / TFIIIB150 / Transcription factor-like nuclear regulator


Mass: 20414.334 Da / Num. of mol.: 2 / Fragment: UNP residues 241-396
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BDP1, KIAA1241, KIAA1689, TFNR / Production host: Escherichia coli (E. coli) / References: UniProt: A6H8Y1

-
Protein , 1 types, 2 molecules BG

#2: Protein TATA-box-binding protein / TATA sequence-binding protein / TATA-binding factor / TATA-box factor / Transcription initiation ...TATA sequence-binding protein / TATA-binding factor / TATA-box factor / Transcription initiation factor TFIID TBP subunit


Mass: 22589.652 Da / Num. of mol.: 2 / Fragment: UNP residues 159-339
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TBP, GTF2D1, TF2D, TFIID / Production host: Escherichia coli (E. coli) / References: UniProt: P20226

-
DNA/RNA hybrid , 2 types, 4 molecules DIEJ

#4: DNA/RNA hybrid DNA/RNA (27-MER)


Mass: 8363.280 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: based on U6-2 promoter / Source: (synth.) Homo sapiens (human)
#5: DNA/RNA hybrid DNA/RNA (25-MER)


Mass: 8026.051 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

-
Non-polymers , 2 types, 299 molecules

#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 10-16% PEG 8000, 150-200 mM KCl, 100 mM MES pH 6.5, 10-15 mM MgCl2, 1 mM TCEP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.91976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91976 Å / Relative weight: 1
ReflectionResolution: 2.7→49.04 Å / Num. obs: 47164 / % possible obs: 99.2 % / Redundancy: 9.2 % / Biso Wilson estimate: 75.25 Å2 / CC1/2: 0.988 / Rpim(I) all: 0.161 / Net I/σ(I): 5.3
Reflection shellResolution: 2.7→2.79 Å / Redundancy: 9.3 % / Mean I/σ(I) obs: 0.7 / CC1/2: 0.257 / Rpim(I) all: 1.552 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ROC

4roc


Resolution: 2.7→49.04 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.904 / SU R Cruickshank DPI: 2.372 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.906 / SU Rfree Blow DPI: 0.308 / SU Rfree Cruickshank DPI: 0.313
RfactorNum. reflection% reflectionSelection details
Rfree0.234 2368 5.02 %RANDOM
Rwork0.194 ---
obs0.196 47140 99 %-
Displacement parametersBiso mean: 86.39 Å2
Baniso -1Baniso -2Baniso -3
1--12.8142 Å20 Å2-3.2874 Å2
2--14.6197 Å20 Å2
3----1.8054 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: 1 / Resolution: 2.7→49.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9034 2120 1 299 11454
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0111788HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0316368HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4997SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes195HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1460HARMONIC5
X-RAY DIFFRACTIONt_it11788HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.72
X-RAY DIFFRACTIONt_other_torsion3.63
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1527SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact13131SEMIHARMONIC4
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 178 5.09 %
Rwork0.2267 3319 -
all0.2288 3497 -
obs--99.57 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.3174-0.6588-1.59114.4512-1.65575.0583-0.12950.3072-0.05370.35570.08560.2675-0.4677-0.43240.04390.3150.06230.0129-0.2512-0.0126-0.2438-5.077512.80213.1564
21.2618-0.2022-1.00633.6611-1.88923.6182-0.1047-0.0942-0.153-0.36650.19470.49040.5077-0.3535-0.08990.2872-0.06680.0737-0.30340.018-0.2388-5.5595-18.310327.4105
36.2728-0.55553.64671.14271.09551.04580.0405-0.0636-0.20450.13290.01540.01240.14640.1005-0.05590.2002-0.00690.1257-0.1020.1529-0.045316.2106-12.944734.295
41.00551.0477-2.94032.6757-2.32981.9436-0.02440.1972-0.10680.0347-0.0076-0.16430.07350.15510.0319-0.15770.09030.15570.21520.1692-0.128644.4684.48963.7351
53.0898-0.2148-0.57492.0627-0.09362.0694-0.02340.27240.1775-0.2755-0.2859-0.56990.00270.59750.3093-0.03520.03260.078-0.12410.1046-0.126731.974710.247712.6404
62.05052.90640.44411.2816-0.30332.6534-0.0251-0.38160.29740.3102-0.2205-0.14460.07920.48270.24560.23540.0240.039-0.1055-0.0109-0.114616.25967.84629.2304
70.51381.9979-1.08460.8251.66990.4977-0.00370.1603-0.03660.03940.07290.0703-0.05340.0282-0.06920.2425-0.09540.2007-0.28060.0640.0014-2.5503-4.017112.4775
82.0003-2.9796-0.10958.17850.1715.44180.11070.5531-0.5488-0.1393-0.2045-0.4260.0932-0.01630.09380.16080.11280.2292-0.1042-0.0213-0.236431.474-8.4116-0.6219
90.04880.0905-0.16060.17010.56410.18050.0109-0.0172-0.0225-0.01030.00670.0156-0.0009-0.0086-0.01760.1570.02220.0026-0.0582-0.1504-0.10228.329-24.8618-6.0148
103.98540.79620.93521.5353-1.2424.3655-0.20810.540.4679-0.2959-0.12110.1176-0.02530.04720.32920.11920.03720.1289-0.3040.0011-0.232413.26428.7326.0204
111.4982-0.44830.12144.04092.87592.44470.0078-0.1181-0.081-0.12610.0184-0.0787-0.02190.0989-0.02620.2533-0.12530.1434-0.304-0.17190.353112.5895-28.90167.8344
121.5726-3.1624-3.95217.8292.42127.18060.09970.1415-0.4703-0.0061-0.1615-0.07570.0658-0.16030.06170.2129-0.05590.2045-0.304-0.0764-0.064913.0065-15.209111.165
133.88212.36422.70491.7479-0.14022.9706-0.12140.50830.43710.0452-0.25720.4277-0.36830.260.37870.26390.10890.1297-0.23170.1087-0.187214.433717.42173.9536
142.57612.0117-3.2847.64243.0833.7684-0.0625-0.03840.1030.00110.07550.38740.1173-0.2104-0.0130.0963-0.010.05310.0059-0.0333-0.1266-16.434727.784828.8184
150.73720.8848-0.76183.435-1.77131.7888-0.04620.12460.088-0.1370.13230.3011-0.024-0.2254-0.08620.29150.04060.0635-0.2129-0.0149-0.2474-6.613646.844723.672
163.22451.3483-3.61524.9351-2.46666.3386-0.12880.48230.3983-0.0505-0.25670.2376-0.26220.38670.38550.3268-0.0146-0.0203-0.21780.0543-0.29764.291566.73558.8734
171.5328-1.42052.7990.7089-0.50023.15410.1126-0.20610.37560.14890.0754-0.4494-0.29530.1955-0.188-0.0037-0.1712-0.14410.0270.1254-0.095130.536542.57949.5155
181.5187-0.37420.5152.3433-0.14083.04660.034-0.1911-0.10860.1891-0.0014-0.52020.18940.5198-0.03260.02290.00280.0105-0.15390.0312-0.155423.811533.658537.0921
191.64661.4766-1.10411.6082.96911.6644-0.0070.00890.0898-0.0761-0.03680.01580.0424-0.02510.04380.28750.09280.0813-0.12240.0275-0.150122.659636.462814.5272
20-0.03451.7750.42200.77080.3781-0.0681-0.19570.0682-0.0310.1054-0.00720.0890.0683-0.03740.34040.1073-0.0713-0.29340.0242-0.1566-4.775646.480132.5602
211.6649-0.00221.53698.3155-0.98486.7507-0.1037-0.56750.4180.2105-0.0512-0.19950.01440.10750.1549-0.0184-0.1349-0.1284-0.0666-0.1144-0.199821.207851.947755.4131
22-0.1360.13470.37010.21520.45020.4289-0.00590.00890.0011-0.00380.00620.02020.00160.0115-0.00020.0826-0.0053-0.07240.0166-0.04020.002212.52870.095856.3487
233.33110.4251-0.18493.0366-2.08234.68180.0363-0.4843-0.39290.408-0.13340.0289-0.172-0.10510.09710.19080.0592-0.0076-0.304-0.0245-0.28156.773935.486442.4912
240.30130.33920.08282.29572.6520.4015-0.00440.07480.07480.08070.0051-0.0053-0.02120.041-0.00070.33970.1625-0.1117-0.304-0.05350.22285.494673.357340.3531
252.6055-1.3342-0.05976.67372.6723.58420.0232-0.46420.48690.223-0.2746-0.1553-0.3005-0.32540.25140.34460.0993-0.0905-0.3017-0.0635-0.06289.822251.137636.4462
265.0311-3.1826-1.92555.90351.5563-0.4567-0.0027-0.5771-0.3221-0.0565-0.06770.34710.28030.16380.07040.3366-0.0864-0.0439-0.06160.1395-0.33664.922622.616848.6648
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|65 - 165}
2X-RAY DIFFRACTION2{A|166 - 311}
3X-RAY DIFFRACTION3{A|312 - 371}
4X-RAY DIFFRACTION4{A|372 - 406}
5X-RAY DIFFRACTION5{B|157 - 277}
6X-RAY DIFFRACTION6{B|278 - 334}
7X-RAY DIFFRACTION7{C|286 - 295}
8X-RAY DIFFRACTION8{C|296 - 372}
9X-RAY DIFFRACTION9{C|373 - 382}
10X-RAY DIFFRACTION10{D|2 - 23}
11X-RAY DIFFRACTION11{D|24 - 28}
12X-RAY DIFFRACTION12{E|2 - 11}
13X-RAY DIFFRACTION13{E|12 - 26}
14X-RAY DIFFRACTION14{F|65 - 91}
15X-RAY DIFFRACTION15{F|92 - 265}
16X-RAY DIFFRACTION16{F|266 - 312}
17X-RAY DIFFRACTION17{F|355 - 407}
18X-RAY DIFFRACTION18{G|157 - 322}
19X-RAY DIFFRACTION19{G|323 - 334}
20X-RAY DIFFRACTION20{H|287 - 296}
21X-RAY DIFFRACTION21{H|297 - 376}
22X-RAY DIFFRACTION22{H|377 - 384}
23X-RAY DIFFRACTION23{I|2 - 24}
24X-RAY DIFFRACTION24{I|25 - 28}
25X-RAY DIFFRACTION25{J|2 - 15}
26X-RAY DIFFRACTION26{J|16 - 26}

+
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