[English] 日本語
Yorodumi
- PDB-6p3a: Crystal Structure Analysis of TAF1 Bromodomain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6p3a
TitleCrystal Structure Analysis of TAF1 Bromodomain
ComponentsTranscription initiation factor TFIID subunit 1
KeywordsTRANSFERASE / kinase / bromodomain / inhibitor / TRANSCRIPTION
Function / homology
Function and homology information


negative regulation of protein autoubiquitination / regulation of cell cycle G1/S phase transition / RNA polymerase I general transcription initiation factor activity / positive regulation of androgen receptor activity / transcription regulator inhibitor activity / RNA polymerase II general transcription initiation factor binding / cellular response to ATP / midbrain development / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape ...negative regulation of protein autoubiquitination / regulation of cell cycle G1/S phase transition / RNA polymerase I general transcription initiation factor activity / positive regulation of androgen receptor activity / transcription regulator inhibitor activity / RNA polymerase II general transcription initiation factor binding / cellular response to ATP / midbrain development / 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 / transcription initiation at RNA polymerase I promoter / ubiquitin conjugating enzyme activity / transcription factor TFIID complex / MLL1 complex / RNA polymerase II general transcription initiation factor activity / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / histone acetyltransferase activity / RNA polymerase II preinitiation complex assembly / histone acetyltransferase / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / negative regulation of ubiquitin-dependent protein catabolic process / regulation of signal transduction by p53 class mediator / nuclear receptor binding / transcription initiation at RNA polymerase II promoter / peptidyl-threonine phosphorylation / lysine-acetylated histone binding / mRNA transcription by RNA polymerase II / protein polyubiquitination / cellular response to UV / p53 binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of protein binding / kinase activity / ubiquitin-dependent protein catabolic process / peptidyl-serine phosphorylation / RNA polymerase II-specific DNA-binding transcription factor binding / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / sequence-specific DNA binding / transcription by RNA polymerase II / protein autophosphorylation / protein stabilization / non-specific serine/threonine protein kinase / protein kinase activity / cell cycle / protein heterodimerization activity / protein phosphorylation / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus
Similarity search - Function
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) / Bromodomain-like ...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) / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-NQP / Transcription initiation factor TFIID subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsSeo, H.-S. / Dhe-Paganon, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: To Be Published
Title: Crystal Structure Analysis of TAF1 Bromodomain
Authors: Seo, H.-S. / Dhe-Paganon, S.
History
DepositionMay 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transcription initiation factor TFIID subunit 1
B: Transcription initiation factor TFIID subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8914
Polymers31,7662
Non-polymers1,1252
Water362
1
A: Transcription initiation factor TFIID subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4462
Polymers15,8831
Non-polymers5631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcription initiation factor TFIID subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4462
Polymers15,8831
Non-polymers5631
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.430, 92.430, 117.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1522 through 1546 or resid 1548...
21(chain B and (resid 1522 through 1546 or resid 1548...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPSERSER(chain A and (resid 1522 through 1546 or resid 1548...AA1522 - 15463 - 27
12PROPROASNASN(chain A and (resid 1522 through 1546 or resid 1548...AA1548 - 155429 - 35
13LYSLYSLYSLYS(chain A and (resid 1522 through 1546 or resid 1548...AA1555 - 155636 - 37
14METMETNQPNQP(chain A and (resid 1522 through 1546 or resid 1548...AA - C1521 - 40002
15METMETNQPNQP(chain A and (resid 1522 through 1546 or resid 1548...AA - C1521 - 40002
16METMETNQPNQP(chain A and (resid 1522 through 1546 or resid 1548...AA - C1521 - 40002
17METMETNQPNQP(chain A and (resid 1522 through 1546 or resid 1548...AA - C1521 - 40002
21ASPASPSERSER(chain B and (resid 1522 through 1546 or resid 1548...BB1522 - 15463 - 27
22PROPROTYRTYR(chain B and (resid 1522 through 1546 or resid 1548...BB1548 - 156229 - 43
23VALVALVALVAL(chain B and (resid 1522 through 1546 or resid 1548...BB1564 - 160145 - 82
24TYRTYRSERSER(chain B and (resid 1522 through 1546 or resid 1548...BB1603 - 160884 - 89
25TYRTYRGLUGLU(chain B and (resid 1522 through 1546 or resid 1548...BB1610 - 163691 - 117
26ASPASPNQPNQP(chain B and (resid 1522 through 1546 or resid 1548...BB - D1522 - 40003
27ASPASPNQPNQP(chain B and (resid 1522 through 1546 or resid 1548...BB - D1522 - 40003
28ASPASPNQPNQP(chain B and (resid 1522 through 1546 or resid 1548...BB - D1522 - 40003
29ASPASPNQPNQP(chain B and (resid 1522 through 1546 or resid 1548...BB - D1522 - 40003
210ASPASPNQPNQP(chain B and (resid 1522 through 1546 or resid 1548...BB - D1522 - 40003
211ASPASPNQPNQP(chain B and (resid 1522 through 1546 or resid 1548...BB - D1522 - 40003

-
Components

#1: 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: 15882.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAF1, BA2R, CCG1, CCGS, TAF2A / Production host: Escherichia coli (E. coli)
References: UniProt: P21675, histone acetyltransferase, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-NQP / 4-{[(3R)-1-(but-3-en-1-yl)-3-methyl-4-(oxan-4-yl)-2-oxo-1,2,3,4-tetrahydropyrido[2,3-b]pyrazin-6-yl]amino}-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide


Mass: 562.703 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H42N6O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.95 Å3/Da / Density % sol: 68.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG8000, Tris pH 8.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.99→58.72 Å / Num. obs: 10768 / % possible obs: 99.6 % / Redundancy: 12.4 % / Biso Wilson estimate: 87.985 Å2 / Rpim(I) all: 0.07 / Rrim(I) all: 0.242 / Net I/σ(I): 9.1 / Num. measured all: 133276
Reflection shellResolution: 2.99→3.04 Å / Redundancy: 13.7 % / Mean I/σ(I) obs: 0.9 / Num. measured all: 7079 / Num. unique obs: 518 / Rpim(I) all: 0.868 / Rrim(I) all: 3.236 / % possible all: 98.3

-
Processing

Software
NameVersionClassification
XDSdata reduction
xia2data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UV5

3uv5


Resolution: 2.99→57.108 Å / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 38.71
RfactorNum. reflection% reflection
Rfree0.2862 532 4.97 %
Rwork0.2548 --
obs0.2564 10713 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 195.89 Å2 / Biso mean: 103.9829 Å2 / Biso min: 59.94 Å2
Refinement stepCycle: final / Resolution: 2.99→57.108 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2040 0 82 2 2124
Biso mean--114.89 69.4 -
Num. residues----254
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A784X-RAY DIFFRACTION4.904TORSIONAL
12B784X-RAY DIFFRACTION4.904TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 99 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.9902-3.29110.4551360.385124602596
3.2911-3.76730.37441140.338225112625
3.7673-4.7460.32351290.252225332662
4.746-57.11890.22561530.209326772830
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)
16.29030.2755-0.15922.78571.28015.2867-0.3203-1.135-0.97121.21680.0415-0.6074-1.1492-0.0845-0.05821.28890.1294-0.04921.15490.0380.8827-40.5763-17.736622.1945
24.15542.5444-1.50164.4182-0.09283.92660.33690.06511.4422-0.44930.0772-0.0243-1.68650.2541-0.20281.1670.1931-0.03241.3143-0.02120.6559-43.9294-7.53375.5802
34.99910.4977-1.75490.5578-0.1740.72440.36050.82920.9160.39640.2780.2555-1.2539-1.24-0.22161.2246-0.0276-0.04171.49380.09330.7663-58.4771-12.4430.7271
47.4845-1.4601-0.8074.5003-3.46454.3760.771-0.5014-0.626-1.08990.3129-0.84790.4002-2.2981-0.27071.25380.02270.0371.35690.15811.0727-54.6599-21.19290.6264
53.10420.94351.58722.5096-0.5492.8062-0.4002-0.1174-0.37070.12050.47140.27291.2481-0.8113-0.12861.0528-0.0492-0.0361.0970.03410.8021-45.756-21.03099.051
64.5652-0.5049-0.71422.9314-3.26785.2371-0.9328-0.00190.4866-0.43740.2467-1.039-0.8520.41290.05260.9684-0.14170.06950.8563-0.05850.7071-37.8677-13.82861.7763
75.64451.6593-1.64736.5268-2.69096.4137-0.0971-0.1406-1.85331.3538-0.6598-0.71880.96530.01940.13631.54560.12720.04151.3545-0.10591.0811-34.5867-28.84323.6342
84.7828-0.5434-0.06173.4633-1.59664.414-0.0219-0.60210.71620.1615-0.4691-0.05440.0449-1.1085-0.16331.0935-0.14120.21071.0746-0.02470.8282-32.60513.87592.6186
93.4247-0.0596-0.01176.28261.32922.40460.4975-0.46730.2463-0.95020.6271-0.2105-0.2799-1.0338-0.1161.047-0.159-0.02951.2998-0.27950.9306-33.9624-11.8196-12.2486
103.12751.94740.64174.13721.90514.2623-0.27960.67630.0244-0.19740.2802-0.1043-0.40210.5797-0.08051.3759-0.05990.05511.44650.01830.837-28.09992.1534-7.848
114.54711.36820.47023.7791-0.7274.37580.2758-0.03720.72140.192-1.0213-0.54221.54220.69260.1371.7645-0.15760.02861.3349-0.09641.1009-16.982411.72149.7092
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1521 through 1538 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1539 through 1549 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1550 through 1560 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1561 through 1570 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 1571 through 1604 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 1605 through 1627 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 1628 through 1648 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid 1522 through 1549 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 1550 through 1560 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 1561 through 1627 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 1628 through 1647 )B0

+
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://pdbjlvh1.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