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- PDB-6mgn: mouse Id1 (51-104) - human hE47 (348-399) complex -

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Basic information

Entry
Database: PDB / ID: 6mgn
Titlemouse Id1 (51-104) - human hE47 (348-399) complex
Components
  • DNA-binding protein inhibitor ID-1
  • Transcription factor E2-alpha
KeywordsDNA BINDING PROTEIN / DNA-binding protein inhibitor ID-1 / transcription factor E2-alpha isoform E47 [Homo sapiens]
Function / homology
Function and homology information


vitamin D response element binding / regulation of vasculature development / negative regulation of endothelial cell differentiation / Oncogene Induced Senescence / lung vasculature development / negative regulation of dendrite morphogenesis / bHLH transcription factor binding / collagen metabolic process / positive regulation of actin filament bundle assembly / endothelial cell morphogenesis ...vitamin D response element binding / regulation of vasculature development / negative regulation of endothelial cell differentiation / Oncogene Induced Senescence / lung vasculature development / negative regulation of dendrite morphogenesis / bHLH transcription factor binding / collagen metabolic process / positive regulation of actin filament bundle assembly / endothelial cell morphogenesis / immunoglobulin V(D)J recombination / endothelial cell apoptotic process / mitogen-activated protein kinase kinase kinase binding / transcription regulator inhibitor activity / negative regulation of cold-induced thermogenesis / lung morphogenesis / proteasome binding / B cell lineage commitment / Myogenesis / E-box binding / regulation of G1/S transition of mitotic cell cycle / regulation of MAPK cascade / negative regulation of osteoblast differentiation / BMP signaling pathway / regulation of angiogenesis / cis-regulatory region sequence-specific DNA binding / positive regulation of cell cycle / negative regulation of endothelial cell apoptotic process / positive regulation of B cell proliferation / positive regulation of neuron differentiation / B cell differentiation / positive regulation of epithelial cell proliferation / circadian regulation of gene expression / protein destabilization / euchromatin / DNA-binding transcription repressor activity, RNA polymerase II-specific / circadian rhythm / RNA polymerase II transcription regulator complex / : / positive regulation of DNA-binding transcription factor activity / RUNX1 regulates transcription of genes involved in differentiation of HSCs / nervous system development / heart development / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / cell differentiation / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein heterodimerization activity / response to antibiotic / negative regulation of gene expression / negative regulation of DNA-templated transcription / centrosome / apoptotic process / chromatin / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
DNA-binding protein inhibitor / Helix-loop-helix DNA-binding domain / MYOD Basic-Helix-Loop-Helix Domain, subunit B / Helix-loop-helix DNA-binding domain / 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. / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Transcription factor E2-alpha / DNA-binding protein inhibitor ID-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 Å
AuthorsBenezra, R. / Pavletich, N.P. / Gall, A.-L. / Goldgur, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)PO1 CA094060 United States
CitationJournal: Cell Rep / Year: 2019
Title: A Small-Molecule Pan-Id Antagonist Inhibits Pathologic Ocular Neovascularization.
Authors: Wojnarowicz, P.M. / Lima E Silva, R. / Ohnaka, M. / Lee, S.B. / Chin, Y. / Kulukian, A. / Chang, S.H. / Desai, B. / Garcia Escolano, M. / Shah, R. / Garcia-Cao, M. / Xu, S. / Kadam, R. / ...Authors: Wojnarowicz, P.M. / Lima E Silva, R. / Ohnaka, M. / Lee, S.B. / Chin, Y. / Kulukian, A. / Chang, S.H. / Desai, B. / Garcia Escolano, M. / Shah, R. / Garcia-Cao, M. / Xu, S. / Kadam, R. / Goldgur, Y. / Miller, M.A. / Ouerfelli, O. / Yang, G. / Arakawa, T. / Albanese, S.K. / Garland, W.A. / Stoller, G. / Chaudhary, J. / Norton, L. / Soni, R.K. / Philip, J. / Hendrickson, R.C. / Iavarone, A. / Dannenberg, A.J. / Chodera, J.D. / Pavletich, N. / Lasorella, A. / Campochiaro, P.A. / Benezra, R.
History
DepositionSep 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Transcription factor E2-alpha
B: DNA-binding protein inhibitor ID-1


Theoretical massNumber of molelcules
Total (without water)11,7272
Polymers11,7272
Non-polymers00
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-22 kcal/mol
Surface area6550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.962, 54.962, 81.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-738-

HOH

21A-753-

HOH

31A-758-

HOH

41A-780-

HOH

51B-259-

HOH

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Components

#1: Protein Transcription factor E2-alpha / Class B basic helix-loop-helix protein 21 / bHLHb21 / Immunoglobulin enhancer-binding factor ...Class B basic helix-loop-helix protein 21 / bHLHb21 / Immunoglobulin enhancer-binding factor E12/E47 / Immunoglobulin transcription factor 1 / Kappa-E2-binding factor / Transcription factor 3 / TCF-3 / Transcription factor ITF-1


Mass: 6142.190 Da / Num. of mol.: 1 / Fragment: unp residues 558-609
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TCF3, BHLHB21, E2A, ITF1 / Production host: Escherichia coli (E. coli) / References: UniProt: P15923
#2: Protein/peptide DNA-binding protein inhibitor ID-1 / Inhibitor of DNA binding 1 / Inhibitor of differentiation 1


Mass: 5584.515 Da / Num. of mol.: 1 / Fragment: unp residues 59-104
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Id1, Id, Id-1, Idb1 / Production host: Escherichia coli (E. coli) / References: UniProt: P20067
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.64 Å3/Da / Density % sol: 53.38 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M potassium phosphate (pH 6.0), 0.25 M NaCl, 22.5% PEG8000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.92 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 3, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 10249 / % possible obs: 98.7 % / Redundancy: 7 % / Rpim(I) all: 0.026 / Rsym value: 0.064 / Net I/σ(I): 29.3
Reflection shellResolution: 1.9→2 Å / Rsym value: 0.317

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T9O

5t9o
PDB Unreleased entry


Resolution: 1.901→19.432 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.86
RfactorNum. reflection% reflection
Rfree0.2175 1059 10.33 %
Rwork0.1827 --
obs0.1861 10248 98.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.901→19.432 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms817 0 0 167 984
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007823
X-RAY DIFFRACTIONf_angle_d0.7141103
X-RAY DIFFRACTIONf_dihedral_angle_d11.2525
X-RAY DIFFRACTIONf_chiral_restr0.048128
X-RAY DIFFRACTIONf_plane_restr0.004143
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9005-1.9870.32291170.23261123X-RAY DIFFRACTION99
1.987-2.09160.22351300.17861132X-RAY DIFFRACTION100
2.0916-2.22250.21071220.17221142X-RAY DIFFRACTION99
2.2225-2.39380.20321380.16941128X-RAY DIFFRACTION99
2.3938-2.63420.22971410.17511135X-RAY DIFFRACTION99
2.6342-3.01410.2111470.18721132X-RAY DIFFRACTION98
3.0141-3.79280.18481260.17461165X-RAY DIFFRACTION98
3.7928-19.4330.22931380.18981232X-RAY DIFFRACTION96

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