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- PDB-4m4x: Structure and Dimerization Properties of the Aryl Hydrocarbon Rec... -

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Basic information

Entry
Database: PDB / ID: 4m4x
TitleStructure and Dimerization Properties of the Aryl Hydrocarbon Receptor (AHR) PAS-A Domain
ComponentsAryl hydrocarbon receptor
KeywordsTRANSCRIPTION / AHR / PAS-A / Dimer / interface / transcription factor / ARNT
Function / homology
Function and homology information


circumferential growth involved in left ventricle morphogenesis / negative regulation of calcium ion transmembrane transport / cellular response to 3-methylcholanthrene / regulation of heart growth / cytosolic aryl hydrocarbon receptor complex / glomerulus morphogenesis / gland development / Phase I - Functionalization of compounds / Xenobiotics / Aryl hydrocarbon receptor signalling ...circumferential growth involved in left ventricle morphogenesis / negative regulation of calcium ion transmembrane transport / cellular response to 3-methylcholanthrene / regulation of heart growth / cytosolic aryl hydrocarbon receptor complex / glomerulus morphogenesis / gland development / Phase I - Functionalization of compounds / Xenobiotics / Aryl hydrocarbon receptor signalling / kidney morphogenesis / omega-hydroxylase P450 pathway / arachidonate omega-hydroxylase activity / positive regulation of growth rate / regulation of adaptive immune response / lymphocyte homeostasis / reactive oxygen species biosynthetic process / cellular response to 2,3,7,8-tetrachlorodibenzodioxine / Endogenous sterols / nuclear aryl hydrocarbon receptor complex / cardiac left ventricle morphogenesis / prostate gland development / negative regulation of osteoblast proliferation / reproductive structure development / negative regulation of T cell mediated immune response to tumor cell / aryl hydrocarbon receptor complex / B-1 B cell homeostasis / cellular response to toxic substance / post-embryonic hemopoiesis / negative regulation of DNA biosynthetic process / vasculature development / camera-type eye development / negative regulation of systemic arterial blood pressure / blood circulation / blood vessel morphogenesis / negative regulation of vasoconstriction / branching involved in blood vessel morphogenesis / immune system process / blood vessel development / E-box binding / T cell homeostasis / aryl hydrocarbon receptor binding / B cell homeostasis / positive regulation of cell size / protein localization to nucleus / positive regulation of RNA polymerase II transcription preinitiation complex assembly / blood vessel remodeling / toxic substance binding / negative regulation of osteoblast differentiation / cis-regulatory region sequence-specific DNA binding / ovarian follicle development / spleen development / xenobiotic metabolic process / B cell differentiation / liver development / circadian regulation of gene expression / Hsp90 protein binding / cell morphogenesis / response to organic cyclic compound / nuclear receptor activity / sequence-specific double-stranded DNA binding / protein-folding chaperone binding / sequence-specific DNA binding / transcription regulator complex / transcription by RNA polymerase II / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of apoptotic process / response to xenobiotic stimulus / protein heterodimerization activity / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / DNA binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Aryl hydrocarbon receptor / Aryl hydrocarbon receptor/Aryl hydrocarbon receptor repressor / PAS fold-3 / PAS fold / Helix-loop-helix DNA-binding domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / Beta-Lactamase / helix loop helix domain ...Aryl hydrocarbon receptor / Aryl hydrocarbon receptor/Aryl hydrocarbon receptor repressor / PAS fold-3 / PAS fold / Helix-loop-helix DNA-binding domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / Beta-Lactamase / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / 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
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.551 Å
AuthorsWu, D. / Potluri, N. / Kim, Y. / Rastinejad, F.
CitationJournal: Mol.Cell.Biol. / Year: 2013
Title: Structure and dimerization properties of the aryl hydrocarbon receptor PAS-A domain.
Authors: Wu, D. / Potluri, N. / Kim, Y. / Rastinejad, F.
History
DepositionAug 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aryl hydrocarbon receptor
B: Aryl hydrocarbon receptor


Theoretical massNumber of molelcules
Total (without water)42,2592
Polymers42,2592
Non-polymers00
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-19 kcal/mol
Surface area12850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.173, 88.173, 110.014
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain: (Details: chain B and segid A)
NCS domain segments: (Selection details: chain 'B' and segid 'A ')

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Components

#1: Protein Aryl hydrocarbon receptor / Ah receptor / AhR


Mass: 21129.623 Da / Num. of mol.: 2 / Fragment: PAS-A domain, UNP residues 110-267
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: C57BL / Gene: Ahr / Plasmid: pSJ2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P30561
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.53 Å3/Da / Density % sol: 51.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM HEPES, 1.6 M Ammonium Sulfate and 2% PEG 1000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 14659 / % possible obs: 99.5 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.07 / Χ2: 1.124 / Net I/σ(I): 11.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.55-2.598.10.8377350.9751100
2.59-2.648.80.7766980.991100
2.64-2.699.30.6667211.171100
2.69-2.759.40.5517161.063199.9
2.75-2.819.40.4447181.0851100
2.81-2.879.30.3837201.0411100
2.87-2.949.40.3117271.0511100
2.94-3.029.40.2397211.0541100
3.02-3.119.40.1747211.0661100
3.11-3.219.30.1517221.0571100
3.21-3.339.30.1217341.1011100
3.33-3.469.20.1017281.192199.6
3.46-3.629.30.0747281.091199.7
3.62-3.819.20.0577271.078199.7
3.81-4.059.10.057411.058199.7
4.05-4.369.20.0467371.025199.7
4.36-4.890.0487471.229199.2
4.8-5.498.90.0557501.738199.1
5.49-6.928.70.0527581.402198.2
6.92-5080.0368100.995195.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.551→33.86 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8256 / SU ML: 0.26 / σ(F): 1.35 / Phase error: 23.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2446 736 5.04 %Random
Rwork0.2002 ---
obs0.2022 14617 99.49 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 160.61 Å2 / Biso mean: 60.8807 Å2 / Biso min: 25.76 Å2
Refinement stepCycle: LAST / Resolution: 2.551→33.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1910 0 0 39 1949
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061949
X-RAY DIFFRACTIONf_angle_d1.0982629
X-RAY DIFFRACTIONf_chiral_restr0.076291
X-RAY DIFFRACTIONf_plane_restr0.004338
X-RAY DIFFRACTIONf_dihedral_angle_d15.189696
Refine LS restraints NCSNumber: 929 / Type: POSITIONAL / Rms dev position: 12.282 Å
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5514-2.74830.27571540.22526982852100
2.7483-3.02480.28941450.204427382883100
3.0248-3.46210.261650.186727322897100
3.4621-4.36040.21111350.185827982933100
4.3604-33.86260.2471370.21012915305298
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)
14.36280.83981.1413.6332-1.0666.3766-0.0739-0.02180.1139-0.18260.10770.0430.0709-0.1545-0.01410.29420.00490.02450.25850.02740.2632.18593.161712.3033
23.47181.97010.26475.1492-0.00193.3882-0.33870.58610.0224-0.55390.45820.7741-0.3011-0.2042-0.11020.4969-0.0569-0.13580.49990.14260.53958.748-10.52476.3064
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq -10:9999)A107 - 266
2X-RAY DIFFRACTION2(chain B and resseq -10:9999)B108 - 266

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