phosphatidylinositol-5-phosphate binding / nucleotide-excision repair factor 3 complex / phosphatidylinositol-3-phosphate binding / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape ...phosphatidylinositol-5-phosphate binding / nucleotide-excision repair factor 3 complex / phosphatidylinositol-3-phosphate binding / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / TP53 Regulates Transcription of DNA Repair Genes / 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 II Pre-transcription Events / Formation of TC-NER Pre-Incision Complex / RNA Polymerase I Promoter Escape / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription by RNA polymerase I / Dual incision in TC-NER / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / transcription by RNA polymerase II / DNA repair / nucleus / cytosol Similarity search - Function
Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999
SEQUENCE THE FRAGMENT OF TFB1 STUDIED IN THIS CASE CONTAINS TWO EXTRA RESIDUES (GLY SER) AT THE N- ...SEQUENCE THE FRAGMENT OF TFB1 STUDIED IN THIS CASE CONTAINS TWO EXTRA RESIDUES (GLY SER) AT THE N-TERMINUS AND FOUR EXTRA RESIDUES (GLY ASN SER SER) AT THE C-TERMINUS AS A CONSEQUENCE OF CLONING ARTIFACTS. THESE EXTRA AMINO ACIDS WERE NOT INCLUDED IN THE STRUCTURE CALCULATIONS AND THEREFORE THEY ARE NOT PRESENT IN DEPOSITED STRUCTURES
THE SUBMITTED MODELS ARE THE 20 STRUCTURES WITH NO UPPER BOUND VIOLATION GREATER THAN 0.2 ARMSTRONG, NO DIHEDRAL ANGLE RESTRAINT VIOLATION GREATER THAN 2 DEGREES AND WITH THE LOWEST ENERGIES.
Method: SIMULATED ANNEALING, WITH A COMBINATION OF TORSION ANGLE DYNAMICS, CARTESIAN DYNAMICS. Software ordinal: 1 Details: THE THREE-DIMENSIONAL STRUCTURES OF THE AMINO-TERMINAL DOMAIN OF TFB1 WERE DETERMINED USING A SET OF 1208 NOE-DERIVED DISTANCE RESTRAINTS, 124 BACKBONE DIHEDRAL ANGLE (PHI AND PSI) ...Details: THE THREE-DIMENSIONAL STRUCTURES OF THE AMINO-TERMINAL DOMAIN OF TFB1 WERE DETERMINED USING A SET OF 1208 NOE-DERIVED DISTANCE RESTRAINTS, 124 BACKBONE DIHEDRAL ANGLE (PHI AND PSI) RESTRAINTS AND 20 DISTANCE RESTRAINTS FROM HYDROGEN BONDS.
NMR ensemble
Conformer selection criteria: THE SUBMITTED MODELS ARE THE 20 STRUCTURES WITH NO UPPER BOUND VIOLATION GREATER THAN 0.2 ARMSTRONG, NO DIHEDRAL ANGLE RESTRAINT VIOLATION GREATER THAN 2 DEGREES AND ...Conformer selection criteria: THE SUBMITTED MODELS ARE THE 20 STRUCTURES WITH NO UPPER BOUND VIOLATION GREATER THAN 0.2 ARMSTRONG, NO DIHEDRAL ANGLE RESTRAINT VIOLATION GREATER THAN 2 DEGREES AND WITH THE LOWEST ENERGIES. Conformers calculated total number: 62 / Conformers submitted total number: 20
+
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.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
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
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