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- PDB-9mdv: Apo form of the estrogen receptor alpha ligand binding domain of ... -

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Basic information

Entry
Database: PDB / ID: 9mdv
TitleApo form of the estrogen receptor alpha ligand binding domain of Melanotaenia fluviatilis
ComponentsEstrogen receptor
KeywordsNUCLEAR PROTEIN / transcription factor / ligand binding / endocrine signalling
Function / homology
Function and homology information


nuclear estrogen receptor activity / hormone binding / steroid binding / sequence-specific DNA binding / zinc ion binding / nucleus
Similarity search - Function
Estrogen receptor / : / Oestrogen receptor / Estrogen receptor/oestrogen-related receptor / : / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / Nuclear hormone receptors DNA-binding domain profile. ...Estrogen receptor / : / Oestrogen receptor / Estrogen receptor/oestrogen-related receptor / : / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / 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
Similarity search - Domain/homology
Biological speciesMelanotaenia fluviatilis (Murray River rainbowfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPederick, J.L. / McDougal, D.P. / Bruning, J.B.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP230100609 Australia
CitationJournal: To Be Published
Title: Apo form of the estrogen receptor alpha ligand binding domain of Melanotaenia fluviatilis
Authors: Pederick, J.L. / McDougal, D.P. / Bruning, J.B.
History
DepositionDec 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Estrogen receptor
B: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7986
Polymers57,4302
Non-polymers3684
Water5,423301
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, native MS indicated the protein is predominantly dimeric in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.374, 94.507, 60.954
Angle α, β, γ (deg.)90.00, 96.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Estrogen receptor / ER-alpha / Estradiol receptor / Nuclear receptor subfamily 3 group A member 1


Mass: 28714.871 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Melanotaenia fluviatilis (Murray River rainbowfish)
Gene: ESR1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D6N7U3
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.21 Å3/Da / Density % sol: 44.33 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M NaCl, 0.1 M PIPES pH 7, 22% PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Apr 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→39.93 Å / Num. obs: 33401 / % possible obs: 99 % / Redundancy: 6.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.062 / Rrim(I) all: 0.161 / Χ2: 1 / Net I/σ(I): 8.5 / Num. measured all: 220701
Reflection shellResolution: 2→2.05 Å / % possible obs: 98.4 % / Redundancy: 6.1 % / Rmerge(I) obs: 1.236 / Num. measured all: 14922 / Num. unique obs: 2439 / CC1/2: 0.554 / Rpim(I) all: 0.538 / Rrim(I) all: 1.352 / Χ2: 0.9 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→37.24 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2865 1686 5.06 %
Rwork0.2409 --
obs0.2432 33351 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→37.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3726 0 24 301 4051
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023871
X-RAY DIFFRACTIONf_angle_d0.5635241
X-RAY DIFFRACTIONf_dihedral_angle_d5.42516
X-RAY DIFFRACTIONf_chiral_restr0.033615
X-RAY DIFFRACTIONf_plane_restr0.004656
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.060.34941580.30812591X-RAY DIFFRACTION98
2.06-2.130.30051350.27682623X-RAY DIFFRACTION98
2.13-2.20.34031560.27592633X-RAY DIFFRACTION99
2.2-2.290.33221400.33942595X-RAY DIFFRACTION98
2.29-2.390.31941400.25862639X-RAY DIFFRACTION99
2.39-2.520.30891500.25932554X-RAY DIFFRACTION97
2.52-2.680.30261340.25582670X-RAY DIFFRACTION100
2.68-2.880.28971430.25072662X-RAY DIFFRACTION100
2.88-3.170.29871540.24042657X-RAY DIFFRACTION100
3.17-3.630.2951070.22472688X-RAY DIFFRACTION100
3.63-4.580.22461310.20542672X-RAY DIFFRACTION99
4.58-37.240.26571380.2162681X-RAY DIFFRACTION98

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