PDB-2llq: Solution nmr-derived structure of calmodulin c-lobe bound with er...

Basic information

• Entry: Database: PDB / ID: 2llq
• Title: Solution nmr-derived structure of calmodulin c-lobe bound with er alpha peptide

Components

• Calmodulin
• Estrogen receptor

• Keywords: METAL BINDING PROTEIN/HORMONE RECEPTOR / METAL BINDING PROTEIN-HORMONE RECEPTOR complex

Function / homology

Function:

regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of toll-like receptor signaling pathway / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / nuclear estrogen receptor activity / epithelial cell proliferation involved in mammary gland duct elongation / prostate epithelial cord elongation / epithelial cell development / negative regulation of smooth muscle cell apoptotic process / mammary gland branching involved in pregnancy / uterus development / vagina development / androgen metabolic process / TFIIB-class transcription factor binding / steroid hormone mediated signaling pathway / mammary gland alveolus development / intracellular estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / positive regulation of phospholipase C activity / intracellular steroid hormone receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / protein localization to chromatin / TBP-class protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / steroid binding / nitric-oxide synthase regulator activity / ESR-mediated signaling / 14-3-3 protein binding / transcription corepressor binding / negative regulation of miRNA transcription / cellular response to estradiol stimulus / transcription coregulator binding / stem cell differentiation / nuclear estrogen receptor binding / positive regulation of nitric-oxide synthase activity / euchromatin / SUMOylation of intracellular receptors / negative regulation of DNA-binding transcription factor activity / transcription coactivator binding / beta-catenin binding / Nuclear Receptor transcription pathway / response to estrogen / male gonad development / Constitutive Signaling by Aberrant PI3K in Cancer / Regulation of RUNX2 expression and activity / nuclear receptor activity / positive regulation of nitric oxide biosynthetic process / positive regulation of DNA-binding transcription factor activity / positive regulation of fibroblast proliferation / Ovarian tumor domain proteases / sequence-specific double-stranded DNA binding / response to estradiol / PIP3 activates AKT signaling / phospholipase C-activating G protein-coupled receptor signaling pathway / ATPase binding / positive regulation of cytosolic calcium ion concentration / fibroblast proliferation / regulation of inflammatory response / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / transcription regulator complex / Extra-nuclear estrogen signaling / calmodulin binding / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / signaling receptor binding / chromatin binding / calcium ion binding / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription / Golgi apparatus / negative regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm

Domain/homology:

Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor/oestrogen-related receptor / EF-hand domain pair / EF-hand, calcium binding motif / Nuclear hormone receptor / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / 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 / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair

Component:

Estrogen receptor / Calmodulin-1 / Calmodulin-2 B

• Biological species: Xenopus laevis (African clawed frog); Homo sapiens (human)
• Method: SOLUTION NMR / simulated annealing
• Model details: lowest energy, model 1
• Authors: Zhang, Y.
• Citation: Journal: J.Biol.Chem. / Year: 2012; Title: Structural basis for Ca2+-induced activation and dimerization of estrogen receptor alpha by calmodulin.; Authors: Zhang, Y. / Li, Z. / Sacks, D.B. / Ames, J.B.

History

Deposition	Nov 15, 2011	Deposition site: BMRB / Processing site: RCSB
Revision 1.0	Feb 1, 2012	Provider: repository / Type: Initial release
Revision 1.1	Aug 28, 2013	Group: Database references
Revision 1.2	May 1, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Assembly

Deposited unit

A: Calmodulin

B: Estrogen receptor

hetero molecules

Summary:

• 10 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	10,020	4
Polymers	9,940	2
Non-polymers	80	2
Water	0

1

Summary:

• Idetical with deposited unit
• defined by author

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

NMR ensembles

	Data	Criteria
Number of conformers (submitted / calculated)	10 / 200	structures with the lowest energy
Representative	Model #1	lowest energy

Components

#1: Protein

A Calmodulin / / CaM

Details:

Mass: 7737.468 Da / Num. of mol.: 1 / Fragment: EF-hand domains 3 and 4, residues 83-149
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: calm1, calm2 / Production host: Escherichia coli (E. coli) / References: UniProt: P62155, UniProt: P0DP33*PLUS

#2: Protein/peptide

B Estrogen receptor / / ER / ER-alpha / Estradiol receptor / Nuclear receptor subfamily 3 group A member 1

Details:

Mass: 2202.645 Da / Num. of mol.: 1 / Fragment: UNP residues 287-305 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P03372

#3: Chemical

A-1000 A-1001 ChemComp-CA / CALCIUM ION

Details:

Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

Experimental details

Experiment

• Experiment: Method: SOLUTION NMR

NMR experiment

Conditions-ID	Experiment-ID	Solution-ID	Type
1	1	1	2D 1H-15N HSQC
1	2	1	3D CBCA(CO)NH
1	3	1	3D HN(CA)CB

Sample preparation

• Details: Contents: 1 mM [U-100% 13C; U-100% 15N] protein, 93% H2O/7% D2O; Solvent system: 93% H2O/7% D2O
• Sample: Conc.: 1 mM / Component: entity_1-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
• Sample conditions: Ionic strength: 0.02 / pH: 7.0 / Pressure: ambient / Temperature: 310 K

NMR measurement

• NMR spectrometer: Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

Processing

NMR software

Name	Developer	Classification
NMRPipe	Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax	processing
Sparky	Goddard	chemical shift assignment
CNS	Brunger, Adams, Clore, Gros, Nilges and Read	refinement

• Refinement: Method: simulated annealing / Software ordinal: 1
• NMR representative: Selection criteria: lowest energy
• NMR ensemble: Conformer selection criteria: structures with the lowest energy; Conformers calculated total number: 200 / Conformers submitted total number: 10