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- PDB-4wg0: Crystal structure of a tridecameric superhelix -

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Basic information

Entry
Database: PDB / ID: 4wg0
TitleCrystal structure of a tridecameric superhelix
ComponentsNuclear receptor coactivator 2
KeywordsTRANSCRIPTION / TIF2 co-activator peptide / arcimboldo molecular replacement / superhelix / glucocorticoid receptor
Function / homology
Function and homology information


RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / locomotor rhythm / aryl hydrocarbon receptor binding / regulation of lipid metabolic process / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol ...RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / locomotor rhythm / aryl hydrocarbon receptor binding / regulation of lipid metabolic process / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / regulation of cellular response to insulin stimulus / Recycling of bile acids and salts / cellular response to hormone stimulus / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / Regulation of lipid metabolism by PPARalpha / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / response to progesterone / nuclear receptor binding / circadian regulation of gene expression / Heme signaling / mRNA transcription by RNA polymerase II / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / Transcriptional regulation of white adipocyte differentiation / RNA polymerase II transcription regulator complex / Circadian Clock / HATs acetylate histones / Estrogen-dependent gene expression / transcription regulator complex / transcription coactivator activity / nuclear body / protein dimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / chromatin binding / regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain ...Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / PAS domain / Nuclear receptor coactivator, interlocking / 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. / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily
Similarity search - Domain/homology
CHOLIC ACID / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsRudolph, M.G. / Uson, I. / Schoch, G.
CitationJournal: Iucrj / Year: 2015
Title: Structure of a 13-fold superhelix (almost) determined from first principles.
Authors: Schoch, G.A. / Sammito, M. / Millan, C. / Uson, I. / Rudolph, M.G.
History
DepositionSep 17, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nuclear receptor coactivator 2
B: Nuclear receptor coactivator 2
C: Nuclear receptor coactivator 2
D: Nuclear receptor coactivator 2
E: Nuclear receptor coactivator 2
F: Nuclear receptor coactivator 2
G: Nuclear receptor coactivator 2
H: Nuclear receptor coactivator 2
I: Nuclear receptor coactivator 2
J: Nuclear receptor coactivator 2
K: Nuclear receptor coactivator 2
L: Nuclear receptor coactivator 2
M: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,64950
Polymers21,03313
Non-polymers7,61737
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27470 Å2
ΔGint-327 kcal/mol
Surface area10030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.869, 37.784, 101.430
Angle α, β, γ (deg.)90.00, 96.84, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11L-13-

ASP

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Components

#1: Protein/peptide
Nuclear receptor coactivator 2 / NCoA-2 / Class E basic helix-loop-helix protein 75 / bHLHe75 / Transcriptional intermediary factor ...NCoA-2 / Class E basic helix-loop-helix protein 75 / bHLHe75 / Transcriptional intermediary factor 2 / hTIF2 / ACE-GLU-LYS-ASN-ALA-LEU-LEU-ARG-TYR-LEU-LEU-ASP-LYS-ASP-NH2


Mass: 1617.889 Da / Num. of mol.: 13 / Fragment: UNP Residues 740-752 / Source method: obtained synthetically
Details: The sequence is supposed to be (ACE)KENALLRYLLDKD(NH2), but during synthesis of the peptide, the first two residues were swapped.
Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CHD / CHOLIC ACID


Mass: 408.571 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C24H40O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 4.34 Å3/Da / Density % sol: 71.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: 2M ammonium sulfate, 5-10% glycerol, 0.1 M citric acid pH 3.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9722 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 17, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9722 Å / Relative weight: 1
ReflectionResolution: 1.82→45.2 Å / Num. obs: 32046 / % possible obs: 97.5 % / Redundancy: 4.1 % / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.1
Reflection shellResolution: 1.82→1.89 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.558 / Mean I/σ(I) obs: 3 / % possible all: 93.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
PHENIX(phenix.refine: dev_1769)refinement
Cootmodel building
Arcimboldophasing
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ideal alpha-helix

Resolution: 1.82→45.158 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.31 / Stereochemistry target values: ML
Details: The occupancy of the C-terminal two residues was set to 0.5 based on weak electron density and clashes between equivalent residues of different chains if they had full occupancy. The peptide ...Details: The occupancy of the C-terminal two residues was set to 0.5 based on weak electron density and clashes between equivalent residues of different chains if they had full occupancy. The peptide crystallized was therefore probably a mixture of full-length and C-terminally truncated peptide. It is not known at which stage (synthesis or crystallization at acidic pH) the partial hydrolysis occurred.
RfactorNum. reflection% reflectionSelection details
Rfree0.2176 1605 5.01 %random
Rwork0.1849 ---
obs0.1866 32008 97.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.7 Å2
Refinement stepCycle: LAST / Resolution: 1.82→45.158 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1495 0 497 127 2119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122070
X-RAY DIFFRACTIONf_angle_d1.5252891
X-RAY DIFFRACTIONf_dihedral_angle_d12.656708
X-RAY DIFFRACTIONf_chiral_restr0.08371
X-RAY DIFFRACTIONf_plane_restr0.005308
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / % reflection Rfree: 5 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.82-1.87880.2851360.2571262193
1.8788-1.94590.27581270.2267265795
1.9459-2.02380.24141320.2133270896
2.0238-2.11590.23611650.1851274097
2.1159-2.22750.23151490.1659274698
2.2275-2.3670.2271590.1638277199
2.367-2.54980.19341460.1881281599
2.5498-2.80630.23291290.1942814100
2.8063-3.21230.23111490.20132872100
3.2123-4.04680.19961490.17582849100
4.0468-45.17180.20271640.1734281096
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)
12.52090.6982-1.61442.55913.19516.934-0.0659-0.61730.23640.21260.0258-0.20510.20070.13370.08480.13420.0151-0.01550.1703-0.01350.2679-1.147620.57535.2021
29.33-0.8362-2.25298.4841-1.56495.5754-0.011-0.57090.07020.6698-0.0170.2495-0.2706-0.0447-0.05450.1609-0.0021-0.00160.1613-0.0170.203812.241620.29956.8889
34.8663-2.7372-0.58242.6718-0.33555.06180.00320.1448-0.242-0.00640.10410.49770.1676-0.4365-0.10960.1326-0.02620.00240.09990.00390.220311.542913.3929-1.3208
47.2494-0.353-2.42566.6665-1.98795.6822-0.0654-0.73030.23050.55090.0277-0.0582-0.39610.2157-0.1470.22040.0179-0.02360.1622-0.01580.153422.33912.74811.3306
57.8727-3.0404-1.26022.22750.55367.54460.0724-0.0826-0.2573-0.0759-0.02590.3886-0.021-0.70560.03150.13980.00780.02190.15080.01550.214515.79374.91428.3448
65.9164-1.4404-2.67124.98320.73299.2273-0.1967-0.77180.08640.67830.1684-0.35070.07020.6829-0.08480.28870.0288-0.01430.31440.02610.158526.6384.247620.9114
79.65942.8363-2.54825.78360.35455.408-0.0269-0.1030.1618-0.22690.0480.30050.1275-0.8432-0.06280.29870.0040.01190.31770.03950.160915.97642.25321.4046
87.46962.4496-3.80747.91260.37718.58540.425-0.6378-0.37180.7001-0.203-0.67510.54820.4719-0.10070.3935-0.0191-0.0350.52540.10930.242926.32242.351934.171
97.40122.439-3.91349.2471-1.56886.20470.15070.05630.2697-0.1252-0.32160.64-0.1169-1.5041-0.06420.35910.00240.01120.6098-0.01590.234117.03917.566133.8992
100.64340.1106-1.35276.32590.20952.89610.2973-1.20710.21910.4718-0.2119-0.26960.5323-0.22430.08510.3844-0.16170.04080.90340.02370.205627.11128.042646.2786
116.16411.9515-0.79494.89445.31588.6155-0.0265-0.27980.9002-0.6486-0.20670.8661-0.9316-0.82140.30850.3210.0491-0.0080.5997-0.0380.400624.038917.124641.0666
122.75720.537-1.66764.64661.51116.02420.2241-1.38830.62720.1934-0.23790.1508-0.0364-0.08220.03890.2578-0.03860.04850.6333-0.12130.35834.21417.424153.5368
132.3088-0.7550.08648.80240.00115.73560.00170.91870.9683-0.5452-0.3196-0.1016-0.0685-0.04190.24530.21260.04370.0610.57270.0040.515436.743520.960743.9586
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 16 )
2X-RAY DIFFRACTION2chain 'B' and (resid 2 through 16 )
3X-RAY DIFFRACTION3chain 'C' and (resid 2 through 16 )
4X-RAY DIFFRACTION4chain 'D' and (resid 2 through 16 )
5X-RAY DIFFRACTION5chain 'E' and (resid 2 through 16 )
6X-RAY DIFFRACTION6chain 'F' and (resid 2 through 16 )
7X-RAY DIFFRACTION7chain 'G' and (resid 2 through 16 )
8X-RAY DIFFRACTION8chain 'H' and (resid 2 through 16 )
9X-RAY DIFFRACTION9chain 'I' and (resid 2 through 16 )
10X-RAY DIFFRACTION10chain 'J' and (resid 2 through 16 )
11X-RAY DIFFRACTION11chain 'K' and (resid 2 through 16 )
12X-RAY DIFFRACTION12chain 'L' and (resid 2 through 16 )
13X-RAY DIFFRACTION13chain 'M' and (resid 2 through 16 )

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