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- PDB-5fur: Structure of human TFIID-IIA bound to core promoter DNA -

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Entry
Database: PDB / ID: 5fur
TitleStructure of human TFIID-IIA bound to core promoter DNA
Components
  • (SUPER CORE PROMOTER) x 2
  • (TRANSCRIPTION INITIATION FACTOR IIA SUBUNIT ...) x 3
  • (TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT ...) x 5
  • TATA-BOX-BINDING PROTEIN
KeywordsTRANSCRIPTION / TFIID / TFIIA / RNA POLYMERASE II / GENERAL TRANSCRIPTION FACTORS / PREINITIATION COMPLEX / CORE PROMOTER / DNA BINDING
Function / homology
Function and homology information


spermine transport / negative regulation of MHC class I biosynthetic process / DNA-templated transcription open complex formation / TFIIH-class transcription factor complex binding / negative regulation of protein autoubiquitination / transcription factor TFTC complex / negative regulation of MHC class II biosynthetic process / RNA polymerase transcription factor SL1 complex / regulation of cell cycle G1/S phase transition / RNA polymerase I general transcription initiation factor activity ...spermine transport / negative regulation of MHC class I biosynthetic process / DNA-templated transcription open complex formation / TFIIH-class transcription factor complex binding / negative regulation of protein autoubiquitination / transcription factor TFTC complex / negative regulation of MHC class II biosynthetic process / RNA polymerase transcription factor SL1 complex / regulation of cell cycle G1/S phase transition / RNA polymerase I general transcription initiation factor activity / SLIK (SAGA-like) complex / RNA polymerase III general transcription initiation factor activity / maintenance of protein location in nucleus / 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 / positive regulation of androgen receptor activity / RNA Polymerase III Abortive And Retractive Initiation / transcription factor TFIIA complex / female germ cell nucleus / male pronucleus / transcription regulator inhibitor activity / female pronucleus / SAGA complex / nuclear vitamin D receptor binding / RNA polymerase II general transcription initiation factor binding / nuclear thyroid hormone receptor binding / transcription preinitiation complex / cellular response to ATP / RNA Polymerase I Transcription Termination / regulation of fat cell differentiation / inner cell mass cell proliferation / histone acetyltransferase binding / midbrain development / 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 / ubiquitin conjugating enzyme activity / MLL1 complex / RNA Polymerase I Transcription Initiation / transcription initiation at RNA polymerase I promoter / aryl hydrocarbon receptor binding / RNA polymerase II transcribes snRNA genes / TFIIB-class transcription factor binding / P-TEFb complex binding / negative regulation of cell cycle / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / intracellular estrogen receptor signaling pathway / regulation of DNA repair / transcription by RNA polymerase III / positive regulation of intrinsic apoptotic signaling pathway / core promoter sequence-specific DNA binding / histone acetyltransferase activity / RNA polymerase II preinitiation complex assembly / negative regulation of ubiquitin-dependent protein catabolic process / histone acetyltransferase / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / SIRT1 negatively regulates rRNA expression / regulation of signal transduction by p53 class mediator / male germ cell nucleus / nuclear receptor binding / transcription initiation at RNA polymerase II promoter / DNA-templated transcription initiation / RNA Polymerase I Promoter Escape / peptidyl-threonine phosphorylation / negative regulation of protein kinase activity / lysine-acetylated histone binding / euchromatin / mRNA transcription by RNA polymerase II / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / response to organic cyclic compound / protein polyubiquitination / cellular response to UV / G2/M transition of mitotic cell cycle / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / p53 binding / cell junction / positive regulation of protein binding / kinase activity / ubiquitin-dependent protein catabolic process / spermatogenesis / peptidyl-serine phosphorylation / DNA-binding transcription factor binding / Estrogen-dependent gene expression / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription by RNA polymerase II / protein autophosphorylation / cell differentiation
Similarity search - Function
TAFII55 protein, conserved region / Transcription initiation factor TFIID subunit 7 / TAFII55 protein conserved region / TAFII55 protein conserved region / Transcription initiation factor TFIID subunit 2 / Transcription initiation factor TFIID subunit 8 / Transcription factor TFIID complex subunit 8 C-term / Transcription factor TFIID, subunit 8, C-terminal / Bromodomain associated / Bromodomain transcription factors and PHD domain containing proteins ...TAFII55 protein, conserved region / Transcription initiation factor TFIID subunit 7 / TAFII55 protein conserved region / TAFII55 protein conserved region / Transcription initiation factor TFIID subunit 2 / Transcription initiation factor TFIID subunit 8 / Transcription factor TFIID complex subunit 8 C-term / Transcription factor TFIID, subunit 8, C-terminal / Bromodomain associated / Bromodomain transcription factors and PHD domain containing proteins / Bromodomain associated domain / TAF6, C-terminal HEAT repeat domain superfamily / TATA box binding protein associated factor (TAF) / Transcription initiation factor TFIID subunit 6 / TAF6 C-terminal HEAT repeat domain / TAF6, C-terminal HEAT repeat domain / TAFII-230 TBP-binding / Transcription initiation factor TFIID subunit 1, animal / TAFII-230 TBP-binding domain superfamily / TATA box-binding protein binding / Zinc knuckle / Zinc knuckle / Transcription initiation factor TFIID subunit 1, histone acetyltransferase domain / Transcription initiation factor TFIID subunit 1 / Protein of unknown function (DUF3591) / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription initiation factor IIA, gamma subunit / Transcription factor IIA, alpha-helical domain / Transcription factor IIA, beta-barrel / Transcription initiation factor IIA, gamma subunit, C-terminal / Transcription initiation factor IIA, gamma subunit, N-terminal / Transcription initiation factor IIA, gamma subunit, helical domain / Transcription initiation factor IIA, gamma subunit / TATA-box binding protein, eukaryotic / TATA-box binding protein / TATA-box binding protein, conserved site / Transcription factor TFIID (or TATA-binding protein, TBP) / Transcription factor TFIID repeat signature. / Aminopeptidase N-like , N-terminal domain superfamliy / TBP domain superfamily / Peptidase M4/M1, CTD superfamily / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone-fold / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Armadillo-type fold
Similarity search - Domain/homology
DNA / DNA (> 10) / TATA-box-binding protein / Transcription initiation factor TFIID subunit 1 / Transcription initiation factor TFIID subunit 6 / Transcription initiation factor IIA subunit 1 / Transcription initiation factor IIA subunit 2 / Transcription initiation factor TFIID subunit 7 / Transcription initiation factor TFIID subunit 2 / Transcription initiation factor TFIID subunit 8
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.5 Å
AuthorsLouder, R.K. / He, Y. / Lopez-Blanco, J.R. / Fang, J. / Chacon, P. / Nogales, E.
CitationJournal: Nature / Year: 2016
Title: Structure of promoter-bound TFIID and model of human pre-initiation complex assembly.
Authors: Robert K Louder / Yuan He / José Ramón López-Blanco / Jie Fang / Pablo Chacón / Eva Nogales /
Abstract: The general transcription factor IID (TFIID) plays a central role in the initiation of RNA polymerase II (Pol II)-dependent transcription by nucleating pre-initiation complex (PIC) assembly at the ...The general transcription factor IID (TFIID) plays a central role in the initiation of RNA polymerase II (Pol II)-dependent transcription by nucleating pre-initiation complex (PIC) assembly at the core promoter. TFIID comprises the TATA-binding protein (TBP) and 13 TBP-associated factors (TAF1-13), which specifically interact with a variety of core promoter DNA sequences. Here we present the structure of human TFIID in complex with TFIIA and core promoter DNA, determined by single-particle cryo-electron microscopy at sub-nanometre resolution. All core promoter elements are contacted by subunits of TFIID, with TAF1 and TAF2 mediating major interactions with the downstream promoter. TFIIA bridges the TBP-TATA complex with lobe B of TFIID. We also present the cryo-electron microscopy reconstruction of a fully assembled human TAF-less PIC. Superposition of common elements between the two structures provides novel insights into the general role of TFIID in promoter recognition, PIC assembly, and transcription initiation.
History
DepositionJan 29, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2016Group: Database references
Revision 1.2Aug 2, 2017Group: Data collection / Category: em_software
Item: _em_software.fitting_id / _em_software.image_processing_id / _em_software.name
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN **-STRANDED BARREL THIS IS REPRESENTED BY A **-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-3305
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  • EMDB-3305
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Assembly

Deposited unit
A: TATA-BOX-BINDING PROTEIN
B: TRANSCRIPTION INITIATION FACTOR IIA SUBUNIT 1
C: TRANSCRIPTION INITIATION FACTOR IIA SUBUNIT 1
D: TRANSCRIPTION INITIATION FACTOR IIA SUBUNIT 2
E: SUPER CORE PROMOTER
F: SUPER CORE PROMOTER
G: TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 1
H: TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 7
I: TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 2
J: TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 6
K: TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 6
L: TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 8


Theoretical massNumber of molelcules
Total (without water)688,28912
Polymers688,28912
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

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Protein , 1 types, 1 molecules A

#1: 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: 37729.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P20226

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TRANSCRIPTION INITIATION FACTOR IIA SUBUNIT ... , 3 types, 3 molecules BCD

#2: Protein/peptide TRANSCRIPTION INITIATION FACTOR IIA SUBUNIT 1 / GENERAL TRANSCRIPTION FACTOR IIA SUBUNIT 1 / TFIIAL / TRANSCRIPTION INITIATION FACTOR TFIIA 42 KDA ...GENERAL TRANSCRIPTION FACTOR IIA SUBUNIT 1 / TFIIAL / TRANSCRIPTION INITIATION FACTOR TFIIA 42 KDA SUBUNIT / TFIIA-42


Mass: 5098.864 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HELA / References: UniProt: P52655
#3: Protein/peptide TRANSCRIPTION INITIATION FACTOR IIA SUBUNIT 1 / GENERAL TRANSCRIPTION FACTOR IIA SUBUNIT 1 / TFIIAL / TRANSCRIPTION INITIATION FACTOR TFIIA 42 KDA ...GENERAL TRANSCRIPTION FACTOR IIA SUBUNIT 1 / TFIIAL / TRANSCRIPTION INITIATION FACTOR TFIIA 42 KDA SUBUNIT / TFIIA-42


Mass: 5594.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HELA / References: UniProt: P52655
#4: Protein TRANSCRIPTION INITIATION FACTOR IIA SUBUNIT 2 / GENERAL TRANSCRIPTION FACTOR IIA SUBUNIT 2 / TFIIA P12 SUBUNIT / TFIIAS / TRANSCRIPTION INITIATION ...GENERAL TRANSCRIPTION FACTOR IIA SUBUNIT 2 / TFIIA P12 SUBUNIT / TFIIAS / TRANSCRIPTION INITIATION FACTOR IIA GAMMA CHAIN / TFIIA- GAMMA


Mass: 11275.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HELA / References: UniProt: P52657

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DNA chain , 2 types, 2 molecules EF

#5: DNA chain SUPER CORE PROMOTER


Mass: 27664.635 Da / Num. of mol.: 1 / Fragment: NONTEMPLATE STRAND / Source method: isolated from a natural source
Details: A COMPOSITE SEQUENCE COMBINING SEVERAL PROMOTER MOTIFS FROM HUMANS A
Source: (natural) HOMO SAPIENS (human) / Cell line: HELA
#6: DNA chain SUPER CORE PROMOTER


Mass: 28485.129 Da / Num. of mol.: 1 / Fragment: TEMPLATE STRAND / Source method: isolated from a natural source
Details: A COMPOSITE SEQUENCE COMBINING SEVERAL PROMOTER MOTIFS FROM HUMANS A
Source: (natural) HOMO SAPIENS (human) / Cell line: HELA

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TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT ... , 5 types, 6 molecules GHIJKL

#7: Protein TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 1 / CELL CYCLE GENE 1 PROTEIN / TBP-ASSOCIATED FACTOR 250 KDA / P250 / TRANSCRIPTION INITIATION FACTOR ...CELL CYCLE GENE 1 PROTEIN / TBP-ASSOCIATED FACTOR 250 KDA / P250 / TRANSCRIPTION INITIATION FACTOR TFIID 250 KDA SUBUNIT / TAFII250


Mass: 215152.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HELA
References: UniProt: P21675, histone acetyltransferase, non-specific serine/threonine protein kinase
#8: Protein TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 7 / RNA POLYMERASE II TBP-ASSOCIATED FACTOR SUBUNIT F / TRANSCRIPTION INITIATION FACTOR TFIID 55 KDA ...RNA POLYMERASE II TBP-ASSOCIATED FACTOR SUBUNIT F / TRANSCRIPTION INITIATION FACTOR TFIID 55 KDA SUBUNIT / TAFII55


Mass: 40325.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HELA / References: UniProt: Q15545
#9: Protein TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 2 / 150 KDA COFACTOR OF INITIATOR FUNCTION / RNA POLYMERASE II TBP-ASSOCIATED FACTOR SUBUNIT B / TBP- ...150 KDA COFACTOR OF INITIATOR FUNCTION / RNA POLYMERASE II TBP-ASSOCIATED FACTOR SUBUNIT B / TBP-ASSOCIATED FACTOR 150 KDA / TRANSCRIPTION INITIATION FACTOR TFIID 150 KDA SUBUNIT / TAFII150


Mass: 137159.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HELA / References: UniProt: Q6P1X5
#10: Protein TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 6 / RNA POLYMERASE II TBP-ASSOCIATED FACTOR SUBUNIT E / TRANSCRIPTION INITIATION FACTOR TFIID 70 KDA ...RNA POLYMERASE II TBP-ASSOCIATED FACTOR SUBUNIT E / TRANSCRIPTION INITIATION FACTOR TFIID 70 KDA SUBUNIT / TAFII70 / TRANSCRIPTION INITIATION FACTOR TFIID 80 KDA SUBUNIT / TAFII80


Mass: 72749.297 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HELA / References: UniProt: P49848
#11: Protein TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 8 / PROTEIN TAUBE NUSS / TBP-ASSOCIATED FACTOR 43 KDA / TBP-ASSOCIATED FACTOR 8 / TRANSCRIPTION ...PROTEIN TAUBE NUSS / TBP-ASSOCIATED FACTOR 43 KDA / TBP-ASSOCIATED FACTOR 8 / TRANSCRIPTION INITIATION FACTOR TFIID 43 KDA SUBUNIT / HTAFII43


Mass: 34304.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HELA / References: UniProt: Q7Z7C8

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Details

Sequence detailsTHE SUPER CORE PROMOTER SEQUENCE IS DESCRIBED IN JUVEN- GERSHON. ET AL. (2006) NATURE METHODS, 3, P.917-922.

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: HUMAN TFIID-TFIIA COMPLEX BOUND TO SUPER CORE PROMOTER DNA
Type: COMPLEX
Buffer solutionName: 10 MM HEPES, 10 MM MGCL2, 50 MM KCL, 3% TREHALOSE 1 MM DTT, 0.0125% NP-40
pH: 7.9
Details: 10 MM HEPES, 10 MM MGCL2, 50 MM KCL, 3% TREHALOSE 1 MM DTT, 0.0125% NP-40
SpecimenConc.: 0.05 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: CARBON
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Details: LIQUID ETHANE

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Electron microscopy imaging

MicroscopyModel: FEI TITAN / Date: Aug 11, 2014
Details: THE CAMERA WAS OPERATED IN COUNTING MODE WITH A DOSE RATE OF 8 ELECTRONS PER PIXEL PER SECOND, WITH A TOTAL EXPOSURE TIME OF 10 SECONDS FRACTIONATED OVER 20 FRAMES.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Calibrated magnification: 37879 X / Nominal defocus max: 4000 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm
Image recordingElectron dose: 46 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansNum. digital images: 1253

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Processing

EM software
IDNameVersionCategory
1CTFFIND4CTF correction
2UCSF Chimeramodel fitting
3Bsoft3D reconstruction
4RELION3D reconstruction
CTF correctionDetails: EACH PARTICLE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 8.5 Å / Num. of particles: 22050 / Actual pixel size: 1.32 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3305. (DEPOSITION ID: 14001).
Symmetry type: POINT
Atomic model buildingSpace: REAL
RefinementHighest resolution: 8.5 Å
Refinement stepCycle: LAST / Highest resolution: 8.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18205 3280 0 0 21485

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