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- PDB-2m8s: NMR Structure of the Cytoplasmic Tail of the Membrane Form of Hep... -

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Entry
Database: PDB / ID: 2m8s
TitleNMR Structure of the Cytoplasmic Tail of the Membrane Form of Heparin-binding EGF-like Growth Factor (proHB-EGF-CT) Complexed with the Ubiquitin Homology Domain of Bcl-2-associated Athanogene 1 from Mus musculus (mBAG-1-UBH)
Components
  • BAG family molecular chaperone regulator 1
  • Proheparin-binding EGF-like growth factor
KeywordsCHAPERONE/MEMBRANE PROTEIN / mBAG-1 / proHB-EGF-CT / CHAPERONE-MEMBRANE PROTEIN complex
Function / homology
Function and homology information


: / Regulation of HSF1-mediated heat shock response / adenyl-nucleotide exchange factor activity / ERBB2-ERBB4 signaling pathway / positive regulation of smooth muscle cell apoptotic process / positive regulation of keratinocyte migration / PI3K events in ERBB4 signaling / transmembrane receptor protein tyrosine kinase activator activity / protein localization to mitochondrion / negative regulation of motor neuron apoptotic process ...: / Regulation of HSF1-mediated heat shock response / adenyl-nucleotide exchange factor activity / ERBB2-ERBB4 signaling pathway / positive regulation of smooth muscle cell apoptotic process / positive regulation of keratinocyte migration / PI3K events in ERBB4 signaling / transmembrane receptor protein tyrosine kinase activator activity / protein localization to mitochondrion / negative regulation of motor neuron apoptotic process / wound healing, spreading of epidermal cells / epidermal growth factor receptor binding / Inhibition of Signaling by Overexpressed EGFR / EGFR interacts with phospholipase C-gamma / ERBB2-EGFR signaling pathway / positive regulation of wound healing / muscle organ development / PTK6 promotes HIF1A stabilization / ERBB2 Activates PTK6 Signaling / Signaling by EGFR / regulation of heart contraction / Uptake and function of diphtheria toxin / ERBB2 Regulates Cell Motility / Signaling by ERBB4 / PI3K events in ERBB2 signaling / SHC1 events in ERBB4 signaling / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / GAB1 signalosome / Nuclear signaling by ERBB4 / Signaling by ERBB2 / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / GRB2 events in ERBB2 signaling / SHC1 events in ERBB2 signaling / cell chemotaxis / phosphoprotein binding / positive regulation of smooth muscle cell proliferation / growth factor activity / EGFR downregulation / Signaling by ERBB2 TMD/JMD mutants / clathrin-coated endocytic vesicle membrane / Signaling by ERBB2 KD Mutants / epidermal growth factor receptor signaling pathway / Downregulation of ERBB2 signaling / neuron differentiation / Constitutive Signaling by Aberrant PI3K in Cancer / endocytic vesicle membrane / positive regulation of neuron apoptotic process / Cargo recognition for clathrin-mediated endocytosis / PIP3 activates AKT signaling / heparin binding / Clathrin-mediated endocytosis / protein-folding chaperone binding / RAF/MAP kinase cascade / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / Extra-nuclear estrogen signaling / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of cell migration / receptor ligand activity / apoptotic process / positive regulation of cell population proliferation / negative regulation of apoptotic process / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Molecular chaperone regulator BAG / BAG domain superfamily / BAG domain / BAG domain / BAG domain profile. / BAG domains, present in regulator of Hsp70 proteins / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain signature 2. ...Molecular chaperone regulator BAG / BAG domain superfamily / BAG domain / BAG domain / BAG domain profile. / BAG domains, present in regulator of Hsp70 proteins / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
BAG family molecular chaperone regulator 1 / Proheparin-binding EGF-like growth factor
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model18
AuthorsHuang, H.W. / Yu, C.
CitationJournal: Biochemistry / Year: 2014
Title: Nuclear Magnetic Resonance Structure of the Cytoplasmic Tail of Heparin Binding EGF-like Growth Factor (proHB-EGF-CT) Complexed with the Ubiquitin Homology Domain of Bcl-2-Associated ...Title: Nuclear Magnetic Resonance Structure of the Cytoplasmic Tail of Heparin Binding EGF-like Growth Factor (proHB-EGF-CT) Complexed with the Ubiquitin Homology Domain of Bcl-2-Associated Athanogene 1 from Mus musculus (mBAG-1-UBH).
Authors: Hung, K.W. / Huang, H.W. / Cho, C.C. / Chang, S.C. / Yu, C.
History
DepositionJun 3, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BAG family molecular chaperone regulator 1
B: Proheparin-binding EGF-like growth factor


Theoretical massNumber of molelcules
Total (without water)13,6832
Polymers13,6832
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)18 / 5000structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein BAG family molecular chaperone regulator 1 / BAG-1 / Bcl-2-associated athanogene 1


Mass: 10799.406 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 137-233
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Bag1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q60739
#2: Protein/peptide Proheparin-binding EGF-like growth factor / Heparin-binding EGF-like growth factor / HB-EGF / HBEGF / Diphtheria toxin receptor / DT-R


Mass: 2883.185 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 185-208
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HBEGF, DTR, DTS, HEGFL / Production host: Escherichia coli (E. coli) / References: UniProt: Q99075

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D C(CO)NH
1313D HNCO
1413D HNCA
1513D HN(CA)CB
1613D HBHA(CO)NH
1713D HN(CO)CA
1813D H(CCO)NH
1913D (H)CCH-TOCSY
11013D (H)CCH-COSY

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Sample preparation

DetailsContents: 1.0 mM [U-100% 13C; U-100% 15N] ubiquitin homology domain of mouse BAG-1-1, 20 mM sodium phosphate-2, 100 mM sodium chloride-3, 5 mM DTT-4, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMubiquitin homology domain of mouse BAG-1-1[U-100% 13C; U-100% 15N]1
20 mMsodium phosphate-21
100 mMsodium chloride-31
5 mMDTT-41
Sample conditionsIonic strength: 0.1 / pH: 6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian VNMR / Manufacturer: Varian / Model: VNMR / Field strength: 700 MHz

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Processing

NMR softwareName: CNS / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 5000 / Conformers submitted total number: 18 / Representative conformer: 18

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