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- PDB-4j24: Estrogen Receptor in complex with proline-flanked LXXLL peptides -

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Basic information

Entry
Database: PDB / ID: 4j24
TitleEstrogen Receptor in complex with proline-flanked LXXLL peptides
Components
  • 19-mer peptide
  • Estrogen receptor beta
KeywordsHORMONE RECEPTOR/PEPTIDE / Estrogen Receptor / Proline / LXXLL / Alpha-helix / Structure stabilization / HORMONE RECEPTOR-PEPTIDE complex
Function / homology
Function and homology information


receptor antagonist activity / nuclear steroid receptor activity / nuclear estrogen receptor activity / estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / steroid binding / ESR-mediated signaling / cellular response to estradiol stimulus / negative regulation of cell growth ...receptor antagonist activity / nuclear steroid receptor activity / nuclear estrogen receptor activity / estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / steroid binding / ESR-mediated signaling / cellular response to estradiol stimulus / negative regulation of cell growth / positive regulation of DNA-binding transcription factor activity / Nuclear Receptor transcription pathway / Constitutive Signaling by Aberrant PI3K in Cancer / nuclear receptor activity / PIP3 activates AKT signaling / cell-cell signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Extra-nuclear estrogen signaling / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / intracellular membrane-bounded organelle / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Estrogen receptor beta-like, N-terminal / Estrogen receptor beta/gamma / Estrogen receptor beta / Estrogen receptor/oestrogen-related receptor / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type ...Estrogen receptor beta-like, N-terminal / Estrogen receptor beta/gamma / Estrogen receptor beta / Estrogen receptor/oestrogen-related receptor / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ESTRADIOL / Estrogen receptor beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsFuchs, S. / Nguyen, H.D. / Phan, T. / Burton, M. / Nieto, L. / de Vries-van Leeuwen, I. / Schmidt, A. / Goodarzifard, M. / Agten, S. / Rose, R. ...Fuchs, S. / Nguyen, H.D. / Phan, T. / Burton, M. / Nieto, L. / de Vries-van Leeuwen, I. / Schmidt, A. / Goodarzifard, M. / Agten, S. / Rose, R. / Ottmann, C. / Milroy, L.G. / Brunsveld, L.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: Proline primed helix length as a modulator of the nuclear receptor-coactivator interaction
Authors: Fuchs, S. / Nguyen, H.D. / Phan, T.T. / Burton, M.F. / Nieto, L. / de Vries-van Leeuwen, I.J. / Schmidt, A. / Goodarzifard, M. / Agten, S.M. / Rose, R. / Ottmann, C. / Milroy, L.G. / Brunsveld, L.
History
DepositionFeb 4, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: Estrogen receptor beta
B: Estrogen receptor beta
C: Estrogen receptor beta
D: Estrogen receptor beta
K: 19-mer peptide
I: 19-mer peptide
J: 19-mer peptide
L: 19-mer peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,26812
Polymers117,1798
Non-polymers1,0904
Water9,566531
1
A: Estrogen receptor beta
I: 19-mer peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5673
Polymers29,2952
Non-polymers2721
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-10 kcal/mol
Surface area11550 Å2
MethodPISA
2
B: Estrogen receptor beta
J: 19-mer peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5673
Polymers29,2952
Non-polymers2721
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-9 kcal/mol
Surface area11360 Å2
MethodPISA
3
C: Estrogen receptor beta
K: 19-mer peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5673
Polymers29,2952
Non-polymers2721
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-9 kcal/mol
Surface area11540 Å2
MethodPISA
4
D: Estrogen receptor beta
L: 19-mer peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5673
Polymers29,2952
Non-polymers2721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-10 kcal/mol
Surface area11000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.980, 53.490, 131.390
Angle α, β, γ (deg.)90.00, 120.47, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A264 - 324
2113C264 - 324
1213A326 - 408
2213C326 - 408
1313A424 - 488
2313C424 - 488
1413A490 - 497
2413C490 - 497
1123B262 - 284
2123D262 - 284
1223B290 - 324
2223D290 - 324
1323B326 - 408
2323D326 - 408
1423B424 - 497
2423D424 - 497

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.999691, -0.004783, 0.024387), (-0.00476, -0.999988, -0.000969), (0.024391, 0.000853, -0.999702)0.27787, 49.46939, -3.50827

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Components

#1: Protein
Estrogen receptor beta / ER-beta / Nuclear receptor subfamily 3 group A member 2


Mass: 27109.143 Da / Num. of mol.: 4 / Fragment: Ligand Binding Domain, UNP residue 261-500'
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR2 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q92731
#2: Protein/peptide
19-mer peptide


Mass: 2185.529 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Phage display derived sequence.
#3: Chemical
ChemComp-EST / ESTRADIOL


Mass: 272.382 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H24O2 / Comment: hormone*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 531 / 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: 2.49 Å3/Da / Density % sol: 50.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 4.5
Details: 0.2M Magnesium acetate, 20%(w/v) PEG3350, pH 4.5, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 16, 2010 / Details: mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 68190 / Num. obs: 67629 / % possible obs: 99.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 29.8 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 23.69
Reflection shellResolution: 2.1→2.3 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 5.17 / Num. unique all: 15989 / Rsym value: 0.3 / % possible all: 99.1

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U9E

1u9e


Resolution: 2.1→19.74 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.939 / SU B: 10.722 / SU ML: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.209 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22385 3382 5 %RANDOM
Rwork0.19007 ---
all0.19174 64244 --
obs0.19174 64244 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.147 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20.01 Å2
2---0.04 Å2-0 Å2
3---0.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0 Å0 Å
Luzzati d res low-0 Å
Luzzati sigma a0 Å0 Å
Refinement stepCycle: LAST / Resolution: 2.1→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7409 0 80 531 8020
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0197867
X-RAY DIFFRACTIONr_bond_other_d0.0010.027921
X-RAY DIFFRACTIONr_angle_refined_deg1.212.00310691
X-RAY DIFFRACTIONr_angle_other_deg0.785318273
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2745987
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.24124.271288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.934151497
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7151537
X-RAY DIFFRACTIONr_chiral_restr0.0660.21282
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218535
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021640
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2088LOOSE POSITIONAL0.035
1A1244TIGHT THERMAL1.780.5
1A2088LOOSE THERMAL1.9710
2B2016LOOSE POSITIONAL0.035
2B1215TIGHT THERMAL6.830.5
2B2016LOOSE THERMAL710
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 246 -
Rwork0.262 4663 -
obs-289 98.85 %
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)
10.2723-0.07470.09610.89360.38850.6456-0.0557-0.02740.0516-0.0018-0.0114-0.07720.0448-0.12490.06720.1121-00.00210.1472-0.03030.1416-24.69525.3167-17.18
26.82185.58445.415612.38459.77.8611-0.65330.5063-0.08750.64220.46990.3480.29080.44750.18340.30010.00740.1060.15420.01080.2122-20.042834.6712-44.5277
30.35860.273-0.08130.8261-0.05990.4237-0.0130.07590.01240.00150.00610.03780.0104-0.0270.00680.1301-0.00830.00390.1625-0.01180.1186-26.133626.023-43.7104
49.97794.7553-12.03832.2665-5.737214.5312-0.59880.3214-0.3793-0.28180.141-0.18680.6709-0.41230.45770.25870.07830.00230.207-0.04150.1981-25.498935.7215-16.2028
50.24150.1392-0.1481.08050.08550.8129-0.04960.0244-0.04440.0313-0.0308-0.0325-0.046-0.10240.08040.10520.0157-0.02080.1364-0.03540.1429-25.240424.162613.0688
64.2658-0.83471.79930.2024-0.38910.79420.0630.22370.0669-0.049-0.02520.05690.06050.0733-0.03770.19170.001-0.0270.17520.00560.1438-20.54514.779640.0308
70.3701-0.33740.03651.3441-0.62651.07270.0608-0.0225-0.05640.3985-0.07430.0264-0.17570.02450.01350.2269-0.0243-0.01450.1207-0.00030.0687-26.100523.29839.561
810.5168-11.384614.656612.3405-15.887120.4928-0.2251-0.0421-0.01090.35750.0764-0.0084-0.3765-0.10530.14870.6972-0.19450.11780.2274-0.10670.3339-26.028213.907512.0559
96.40269.908-4.760116.1069-7.57463.6024-0.10860.0081-0.9645-0.0685-0.4891-1.23270.02130.10430.59770.10590.00310.07350.356-0.06160.3968-5.524822.06468.3726
103.2188-2.09780.867917.5684-1.75930.3294-0.4245-0.30660.6139-0.05110.2433-1.3953-0.0745-0.11330.18110.0767-0.0155-0.09570.1789-0.00860.4549-4.948727.9896-12.3807
1112.62348.20777.95228.15453.07016.6370.0995-0.55121.2411-0.5959-0.89820.58870.6083-0.00230.79870.17880.09250.00140.21470.0240.4389-41.303839.4117-46.6078
1216.3977-3.2461-9.94177.22631.6586.12270.3739-0.1406-0.63050.0358-0.39520.9584-0.33170.12630.02130.0728-0.05850.18050.0932-0.09480.9592-41.936910.306842.9761
130.03230.0354-0.0330.0882-0.04190.5863-0.02860.00740.01150.0141-0.0262-0.01660.0231-0.03990.05490.11060.0118-0.00420.147-0.02660.1642-24.029324.81-11.5597
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A262 - 498
2X-RAY DIFFRACTION2B600
3X-RAY DIFFRACTION3B261 - 498
4X-RAY DIFFRACTION4A600
5X-RAY DIFFRACTION5C262 - 498
6X-RAY DIFFRACTION6D600
7X-RAY DIFFRACTION7D264 - 497
8X-RAY DIFFRACTION8C600
9X-RAY DIFFRACTION9K4 - 15
10X-RAY DIFFRACTION10I4 - 15
11X-RAY DIFFRACTION11J4 - 14
12X-RAY DIFFRACTION12L4 - 13
13X-RAY DIFFRACTION13A701 - 869
14X-RAY DIFFRACTION13B701 - 855
15X-RAY DIFFRACTION13C701 - 847
16X-RAY DIFFRACTION13D701 - 756
17X-RAY DIFFRACTION13I101
18X-RAY DIFFRACTION13J101 - 102
19X-RAY DIFFRACTION13K101

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