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- PDB-2nxp: Structure of NTD2 domain of the human TAF5 subunit of TFIID -

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Basic information

Entry
Database: PDB / ID: 2nxp
TitleStructure of NTD2 domain of the human TAF5 subunit of TFIID
ComponentsTranscription initiation factor TFIID subunit 5
KeywordsTRANSCRIPTION / Transcription factor / TFIID subunit / TAF5
Function / homology
Function and homology information


transcription factor TFTC 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 II transcribes snRNA genes / transcription factor TFIID complex ...transcription factor TFTC 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 II transcribes snRNA genes / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / positive regulation of transcription initiation by RNA polymerase II / regulation of DNA repair / RNA polymerase II preinitiation complex assembly / RNA Polymerase II Pre-transcription Events / DNA-templated transcription initiation / transcription initiation at RNA polymerase II promoter / mRNA transcription by RNA polymerase II / actin cytoskeleton / Regulation of TP53 Activity through Phosphorylation / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
TFIID subunit TAF5, NTD2 domain / TFIID subunit TAF5, NTD2 domain superfamily / WD40 associated region in TFIID subunit, NTD2 domain / TFIID subunit TAF5, NTD2 domain / LIS1 homology (LisH) motif profile. / LIS1 homology motif / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / G-protein beta WD-40 repeat / WD40 repeat, conserved site ...TFIID subunit TAF5, NTD2 domain / TFIID subunit TAF5, NTD2 domain superfamily / WD40 associated region in TFIID subunit, NTD2 domain / TFIID subunit TAF5, NTD2 domain / LIS1 homology (LisH) motif profile. / LIS1 homology motif / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.17 Å
AuthorsBhattacharya, S. / Takada, S. / Jacobson, R.H.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structural analysis and dimerization potential of the human TAF5 subunit of TFIID.
Authors: Bhattacharya, S. / Takada, S. / Jacobson, R.H.
History
DepositionNov 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription initiation factor TFIID subunit 5
B: Transcription initiation factor TFIID subunit 5
C: Transcription initiation factor TFIID subunit 5
D: Transcription initiation factor TFIID subunit 5
E: Transcription initiation factor TFIID subunit 5
F: Transcription initiation factor TFIID subunit 5
G: Transcription initiation factor TFIID subunit 5
H: Transcription initiation factor TFIID subunit 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,06016
Polymers150,7398
Non-polymers3218
Water9,386521
1
A: Transcription initiation factor TFIID subunit 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8832
Polymers18,8421
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcription initiation factor TFIID subunit 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8832
Polymers18,8421
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Transcription initiation factor TFIID subunit 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8832
Polymers18,8421
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Transcription initiation factor TFIID subunit 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8832
Polymers18,8421
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Transcription initiation factor TFIID subunit 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8832
Polymers18,8421
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Transcription initiation factor TFIID subunit 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8832
Polymers18,8421
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Transcription initiation factor TFIID subunit 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8832
Polymers18,8421
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Transcription initiation factor TFIID subunit 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8832
Polymers18,8421
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.620, 61.829, 133.357
Angle α, β, γ (deg.)90.00, 105.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Transcription initiation factor TFIID subunit 5 / Transcription initiation factor TFIID 100 kDa subunit / TAFII / 100 / TAFII-100 / TAFII100


Mass: 18842.436 Da / Num. of mol.: 8 / Fragment: N-terminal conserved domain 2 (NTD2)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAF5 / Plasmid: pDEST15 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15542
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 521 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.22 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7.1
Details: 0.1M Tris-HCl, 0.6M calcium chloride, 20% PEG 4000, pH 7.1, VAPOR DIFFUSION, temperature 295K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.9797, 1.0199
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 25, 2005 / Details: KOHZU: Double Crystal Si(111)
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97971
21.01991
ReflectionResolution: 2.2→64.4 Å / Num. all: 78392 / Num. obs: 76736 / % possible obs: 97.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 38.2 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 9.3
Reflection shellHighest resolution: 2.2 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.065 / Mean I/σ(I) obs: 2.5 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCQUANTUMdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
MLPHAREphasing
RefinementMethod to determine structure: MAD / Resolution: 2.17→64.42 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.908 / SU B: 6.224 / SU ML: 0.161 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.238 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26252 3837 5 %RANDOM
Rwork0.21257 ---
obs0.21507 72912 97.89 %-
all-76736 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.522 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.297 Å
Refinement stepCycle: LAST / Resolution: 2.17→64.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9986 0 8 521 10515
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.02210237
X-RAY DIFFRACTIONr_bond_other_d00.028691
X-RAY DIFFRACTIONr_angle_refined_deg0.7221.93413792
X-RAY DIFFRACTIONr_angle_other_deg0.6320326
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.37951167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.44124.57604
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.129151844
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.5971548
X-RAY DIFFRACTIONr_chiral_restr0.0470.21413
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0211387
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022221
X-RAY DIFFRACTIONr_nbd_refined0.2120.32490
X-RAY DIFFRACTIONr_nbd_other0.1760.38712
X-RAY DIFFRACTIONr_nbtor_refined0.1930.55047
X-RAY DIFFRACTIONr_nbtor_other0.090.55202
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2120.5838
X-RAY DIFFRACTIONr_metal_ion_refined0.1270.532
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2340.321
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2210.387
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2210.540
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1180.51
LS refinement shellResolution: 2.17→2.226 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 264 -
Rwork0.261 5309 -
obs--96.5 %

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