[English] 日本語
Yorodumi
- PDB-2j4b: Crystal structure of Encephalitozoon cuniculi TAF5 N-terminal domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2j4b
TitleCrystal structure of Encephalitozoon cuniculi TAF5 N-terminal domain
ComponentsTRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 72/90-100 KDA
KeywordsTRANSCRIPTION / TAF5 / TFIID / WD REPEAT / INITIATION / INITIATION FACTOR
Function / homology
Function and homology information


TFIID subunit TAF5, NTD2 domain / TFIID subunit TAF5, NTD2 domain superfamily / WD40 associated region in TFIID subunit, NTD2 domain / TFIID subunit TAF5, NTD2 domain / : / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. ...TFIID subunit TAF5, NTD2 domain / TFIID subunit TAF5, NTD2 domain superfamily / WD40 associated region in TFIID subunit, NTD2 domain / TFIID subunit TAF5, NTD2 domain / : / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Transcription initiation factor TFIID subunit 5
Similarity search - Component
Biological speciesENCEPHALITOZOON CUNICULI (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsRomier, C. / James, N. / Birck, C. / Cavarelli, J. / Vivares, C. / Collart, M.A. / Moras, D.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal Structure, Biochemical and Genetic Characterization of Yeast and E. Cuniculi Taf(II)5 N-Terminal Domain: Implications for TFIID Assembly.
Authors: Romier, C. / James, N. / Birck, C. / Cavarelli, J. / Vivares, C. / Collart, M.A. / Moras, D.
History
DepositionAug 28, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 72/90-100 KDA
B: TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 72/90-100 KDA
C: TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 72/90-100 KDA
D: TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 72/90-100 KDA
E: TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 72/90-100 KDA


Theoretical massNumber of molelcules
Total (without water)83,5305
Polymers83,5305
Non-polymers00
Water5,314295
1
A: TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 72/90-100 KDA


Theoretical massNumber of molelcules
Total (without water)16,7061
Polymers16,7061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 72/90-100 KDA


Theoretical massNumber of molelcules
Total (without water)16,7061
Polymers16,7061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 72/90-100 KDA


Theoretical massNumber of molelcules
Total (without water)16,7061
Polymers16,7061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 72/90-100 KDA


Theoretical massNumber of molelcules
Total (without water)16,7061
Polymers16,7061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
E: TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 72/90-100 KDA


Theoretical massNumber of molelcules
Total (without water)16,7061
Polymers16,7061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)91.520, 91.520, 297.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein
TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 72/90-100 KDA / TAF5


Mass: 16705.953 Da / Num. of mol.: 5 / Fragment: N-TERMINAL DOMAIN, RESIDUES 16-149
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENCEPHALITOZOON CUNICULI (fungus) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8SQS4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIRST 4 RESIDUES IN EACH CHAIN REPRESENT THE THROMBIN CUTTING SITE (GS) AND THE NDEL CLONING ...THE FIRST 4 RESIDUES IN EACH CHAIN REPRESENT THE THROMBIN CUTTING SITE (GS) AND THE NDEL CLONING SITE (HM) AND ARE NOT PART OF THE FULL PROTEIN. THESE RESIDUES ARE MAPPED TO THE PDB ENTRY.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.45 %
Crystal growpH: 8 / Details: 0.1 M TRIS/HCL PH 8.0 0.2 M MGCL2 2.0 M NACL

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 30, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.5→35 Å / Num. obs: 26377 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 7.9 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 45
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 9.8 / % possible all: 99

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
SOLOMONphasing
REFMAC5.2.0019refinement
RefinementMethod to determine structure: MAD / Resolution: 2.5→28.96 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.87 / SU B: 28.534 / SU ML: 0.352 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.368 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.283 2588 9.9 %RANDOM
Rwork0.211 ---
obs0.218 23677 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 51.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å2-0.06 Å20 Å2
2---0.13 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.5→28.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5658 0 0 295 5953
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225807
X-RAY DIFFRACTIONr_bond_other_d0.0020.023915
X-RAY DIFFRACTIONr_angle_refined_deg1.0461.9457838
X-RAY DIFFRACTIONr_angle_other_deg0.71939537
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6875650
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.45824.8325
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.342151059
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4811515
X-RAY DIFFRACTIONr_chiral_restr0.0580.2832
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026332
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021250
X-RAY DIFFRACTIONr_nbd_refined0.2230.31458
X-RAY DIFFRACTIONr_nbd_other0.1950.33948
X-RAY DIFFRACTIONr_nbtor_refined0.2010.52872
X-RAY DIFFRACTIONr_nbtor_other0.0910.52760
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2840.5395
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.359
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2570.398
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2470.549
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.03924354
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.21435311
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.66323050
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.95332527
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.57 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.412 177
Rwork0.271 1688
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)
13.7763-1.5392-1.46743.40971.42962.1989-0.2244-0.42050.10140.13430.165-0.03180.2070.14260.0594-0.1890.01280.0017-0.0806-0.0046-0.244834.94749.082149.739
21.67541.52-1.12995.1444-2.29573.3372-0.1169-0.0887-0.080.15410.0851-0.1368-0.0729-0.01280.0318-0.19060.035-0.0518-0.19810.0045-0.182425.64812.498129.39
38.0759-2.9156-2.70312.6334-0.12711.67440.3650.7038-0.137-0.391-0.54520.13150.0139-0.2310.1802-0.16010.0762-0.0143-0.1135-0.2007-0.202817.55959.615126.951
42.742-1.1839-0.31484.35941.87581.9202-0.01070.15390.2106-0.3623-0.19490.029-0.1256-0.07910.2056-0.16810.0223-0.0564-0.1663-0.0204-0.20456.17610.817137.567
55.37740.4398-2.28651.8008-0.80553.56830.04490.0346-0.05-0.0387-0.1930.03540.04970.00240.148-0.18990.0227-0.0351-0.1909-0.0176-0.219164.80160.844139.689
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 148
2X-RAY DIFFRACTION2B17 - 149
3X-RAY DIFFRACTION3C16 - 148
4X-RAY DIFFRACTION4D18 - 148
5X-RAY DIFFRACTION5E18 - 147

+
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