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- PDB-4lpz: ARNT transcription factor/coactivator complex -

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Basic information

Entry
Database: PDB / ID: 4lpz
TitleARNT transcription factor/coactivator complex
Components
  • Aryl hydrocarbon receptor nuclear translocator
  • Transforming acidic coiled-coil-containing protein 3
KeywordsTRANSCRIPTION / PAS domain coiled coil
Function / homology
Function and homology information


interkinetic nuclear migration / microtubule cytoskeleton organization involved in mitosis / nuclear aryl hydrocarbon receptor complex / Aryl hydrocarbon receptor signalling / positive regulation of hormone biosynthetic process / astral microtubule organization / aryl hydrocarbon receptor complex / metaphase/anaphase transition of mitotic cell cycle / positive regulation of protein sumoylation / Xenobiotics ...interkinetic nuclear migration / microtubule cytoskeleton organization involved in mitosis / nuclear aryl hydrocarbon receptor complex / Aryl hydrocarbon receptor signalling / positive regulation of hormone biosynthetic process / astral microtubule organization / aryl hydrocarbon receptor complex / metaphase/anaphase transition of mitotic cell cycle / positive regulation of protein sumoylation / Xenobiotics / regulation of microtubule-based process / Phase I - Functionalization of compounds / positive regulation of vascular endothelial growth factor receptor signaling pathway / Regulation of gene expression by Hypoxia-inducible Factor / aryl hydrocarbon receptor binding / hemopoiesis / centriolar satellite / positive regulation of vascular endothelial growth factor production / embryonic placenta development / Endogenous sterols / cis-regulatory region sequence-specific DNA binding / regulation of mitotic spindle organization / positive regulation of endothelial cell proliferation / NPAS4 regulates expression of target genes / positive regulation of glycolytic process / neurogenesis / mitotic spindle organization / positive regulation of erythrocyte differentiation / PPARA activates gene expression / mitotic spindle / cerebral cortex development / microtubule cytoskeleton organization / negative regulation of inflammatory response / spindle pole / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / cellular response to oxidative stress / RNA polymerase II-specific DNA-binding transcription factor binding / cell population proliferation / sequence-specific DNA binding / postsynaptic density / cell differentiation / nuclear body / response to hypoxia / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / DNA-binding transcription factor activity / protein domain specific binding / cell division / intracellular membrane-bounded organelle / centrosome / glutamatergic synapse / chromatin / regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Transforming acidic coiled-coil-containing protein, C-terminal / TACC family / Transforming acidic coiled-coil-containing protein (TACC), C-terminal / Nuclear translocator / Helix-loop-helix DNA-binding domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / PAS domain / Helix-loop-helix DNA-binding domain superfamily ...Transforming acidic coiled-coil-containing protein, C-terminal / TACC family / Transforming acidic coiled-coil-containing protein (TACC), C-terminal / Nuclear translocator / Helix-loop-helix DNA-binding domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / PAS domain / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Beta-Lactamase / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Aryl hydrocarbon receptor nuclear translocator / Transforming acidic coiled-coil-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsGuo, Y. / Scheuermann, T.H. / Gardner, K.H.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Coiled-coil coactivators play a structural role mediating interactions in hypoxia-inducible factor heterodimerization.
Authors: Guo, Y. / Scheuermann, T.H. / Partch, C.L. / Tomchick, D.R. / Gardner, K.H.
History
DepositionJul 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 22, 2021Group: Database references
Category: citation / citation_author ...citation / citation_author / database_2 / struct_ref_seq_dif
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.2Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aryl hydrocarbon receptor nuclear translocator
B: Aryl hydrocarbon receptor nuclear translocator
C: Transforming acidic coiled-coil-containing protein 3
D: Transforming acidic coiled-coil-containing protein 3


Theoretical massNumber of molelcules
Total (without water)38,0834
Polymers38,0834
Non-polymers00
Water0
1
A: Aryl hydrocarbon receptor nuclear translocator

B: Aryl hydrocarbon receptor nuclear translocator
C: Transforming acidic coiled-coil-containing protein 3
D: Transforming acidic coiled-coil-containing protein 3


Theoretical massNumber of molelcules
Total (without water)38,0834
Polymers38,0834
Non-polymers00
Water0
TypeNameSymmetry operationNumber
crystal symmetry operation4_445-x-1/2,y-1/2,-z1
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-39 kcal/mol
Surface area13380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.846, 59.816, 73.510
Angle α, β, γ (deg.)90.00, 97.85, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A104 - 359
2010B104 - 359
Detailsthe biological assembly is contained in the asymmetric unit

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Components

#1: Protein Aryl hydrocarbon receptor nuclear translocator / ARNT protein / Class E basic helix-loop-helix protein 2 / bHLHe2 / Dioxin receptor / nuclear ...ARNT protein / Class E basic helix-loop-helix protein 2 / bHLHe2 / Dioxin receptor / nuclear translocator / Hypoxia-inducible factor 1-beta / HIF-1-beta / HIF1-beta


Mass: 13956.701 Da / Num. of mol.: 2 / Fragment: PAS 2 and PAC domain residues 356-470
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARNT, BHLHE2 / Production host: Escherichia coli (E. coli) / References: UniProt: P27540
#2: Protein/peptide Transforming acidic coiled-coil-containing protein 3


Mass: 5084.926 Da / Num. of mol.: 2 / Mutation: D622A, E629A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9JJ11*PLUS

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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: 3.34 Å3/Da / Density % sol: 63.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1M Succinic acid, 30% w/v D-Sorbitol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97912 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 18, 2012
RadiationMonochromator: custom / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 3.15→50 Å / Num. all: 8354 / Num. obs: 8354 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 73.64 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 14.8
Reflection shellResolution: 3.15→3.2 Å / % possible all: 65.1

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4EQ1

4eq1


Resolution: 3.15→44.268 Å / SU ML: 0.31 / σ(F): 1.38 / Phase error: 30.03 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2718 832 9.99 %random
Rwork0.2445 ---
obs0.2472 8332 94.17 %-
all-8332 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.15→44.268 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2108 0 0 0 2108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042144
X-RAY DIFFRACTIONf_angle_d0.7592882
X-RAY DIFFRACTIONf_dihedral_angle_d16.661798
X-RAY DIFFRACTIONf_chiral_restr0.032328
X-RAY DIFFRACTIONf_plane_restr0.002364
Refine LS restraints NCS

Ens-ID: 1 / Number: 15881 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1504-3.34770.31231060.2793954X-RAY DIFFRACTION73
3.3477-3.60610.35891340.27991207X-RAY DIFFRACTION93
3.6061-3.96880.28361440.23421320X-RAY DIFFRACTION99
3.9688-4.54250.23881470.20661320X-RAY DIFFRACTION100
4.5425-5.72120.27241480.2371328X-RAY DIFFRACTION100
5.7212-44.27270.25221530.26271371X-RAY DIFFRACTION100

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