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- PDB-4aya: Crystal structure of ID2 HLH homodimer at 2.1A resolution -

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Basic information

Entry
Database: PDB / ID: 4aya
TitleCrystal structure of ID2 HLH homodimer at 2.1A resolution
ComponentsDNA-BINDING PROTEIN INHIBITOR ID-2
KeywordsCELL CYCLE
Function / homology
Function and homology information


: / endodermal digestive tract morphogenesis / euchromatin => GO:0000791 / bundle of His development / regulation of cell cycle => GO:0051726 / enucleate erythrocyte differentiation / negative regulation of B cell differentiation / RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / epithelial cell differentiation involved in mammary gland alveolus development / cell morphogenesis involved in neuron differentiation ...: / endodermal digestive tract morphogenesis / euchromatin => GO:0000791 / bundle of His development / regulation of cell cycle => GO:0051726 / enucleate erythrocyte differentiation / negative regulation of B cell differentiation / RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / epithelial cell differentiation involved in mammary gland alveolus development / cell morphogenesis involved in neuron differentiation / negative regulation of core promoter binding / negative regulation of muscle cell differentiation / thigmotaxis / natural killer cell differentiation / membranous septum morphogenesis / embryonic digestive tract morphogenesis / neuron fate commitment / positive regulation of macrophage differentiation / oligodendrocyte development / regulation of neural precursor cell proliferation / negative regulation of oligodendrocyte differentiation / olfactory bulb development / positive regulation of astrocyte differentiation / Peyer's patch development / positive regulation of blood pressure / metanephros development / NGF-stimulated transcription / transcription regulator inhibitor activity / mammary gland epithelial cell proliferation / regulation of neuron differentiation / cellular response to lithium ion / entrainment of circadian clock by photoperiod / regulation of G1/S transition of mitotic cell cycle / locomotor rhythm / regulation of lipid metabolic process / negative regulation of neuron differentiation / positive regulation of fat cell differentiation / mammary gland alveolus development / negative regulation of osteoblast differentiation / adipose tissue development / cell maturation / adult locomotory behavior / positive regulation of erythrocyte differentiation / positive regulation of smooth muscle cell proliferation / circadian regulation of gene expression / regulation of circadian rhythm / negative regulation of DNA-binding transcription factor activity / cellular senescence / transmembrane transporter binding / cell differentiation / protein dimerization activity / negative regulation of gene expression / negative regulation of DNA-templated transcription / positive regulation of gene expression / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein-containing complex / nucleus / cytosol / 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
ACETATE ION / : / DNA-binding protein inhibitor ID-2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.103 Å
AuthorsWong, M.V. / Jiang, S. / Palasingam, P. / Kolatkar, P.R.
CitationJournal: Plos One / Year: 2012
Title: A Divalent Ion is Crucial in the Structure and Dominant-Negative Function of Id Proteins, a Class of Helix-Loop-Helix Transcription Regulators.
Authors: Wong, M.V. / Jiang, S. / Palasingam, P. / Kolatkar, P.R.
History
DepositionJun 19, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: DNA-BINDING PROTEIN INHIBITOR ID-2
B: DNA-BINDING PROTEIN INHIBITOR ID-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8265
Polymers21,6892
Non-polymers1373
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-30.1 kcal/mol
Surface area7350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.622, 51.622, 111.474
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein DNA-BINDING PROTEIN INHIBITOR ID-2 / CLASS D BASIC HELIX-LOOP-HELIX PROTEIN 26 / CLASS B BASIC HELIX-LOOP-HELIX PROTEIN 26 / BHLHB26 / ...CLASS D BASIC HELIX-LOOP-HELIX PROTEIN 26 / CLASS B BASIC HELIX-LOOP-HELIX PROTEIN 26 / BHLHB26 / INHIBITOR OF DNA BINDING 2


Mass: 10844.563 Da / Num. of mol.: 2 / Fragment: HELIX-LOOP-HELIX DOMAIN, RESIDUES 1-82
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PDEST-565 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q02363
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFIRST RESIDUE IN SEQUENCE AFTER TEV CLEAVAGE IS A GLYCINE. ID2 SEQUENCE NUMBERING STARTS FROM ...FIRST RESIDUE IN SEQUENCE AFTER TEV CLEAVAGE IS A GLYCINE. ID2 SEQUENCE NUMBERING STARTS FROM SECOND RESIDUE, METHIONINE. RESIDUE 83 ONWARDS CONTAINS THE C-TERMINAL STABILIZER POLYPEPTIDE.

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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: 1.98 Å3/Da / Density % sol: 37.8 %
Crystal growpH: 6.5
Details: PROTEIN WAS CRYSTALLIZED FROM 0.1 M MES PH6.5, 2.0 M POTASSIUM ACETATE

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 29, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 10569 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 11.9 % / Biso Wilson estimate: 41.98 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 40.6
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 4.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: INTERNAL SELENOMETHIONINE-SUBSTITUTED ID2 STRUCTURE AT 3.0A

Resolution: 2.103→44.706 Å / SU ML: 0.23 / σ(F): 0.65 / Phase error: 27.31 / Stereochemistry target values: ML
Details: RESIDUES 1-29 ARE MISSING IN CHAIN A. RESIDUES 1-34 ARE MISSING IN CHAIN B.
RfactorNum. reflection% reflection
Rfree0.2497 987 9.8 %
Rwork0.2246 --
obs0.2271 10026 95.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 0 Å2 / ksol: 0 e/Å3
Displacement parametersBiso mean: 54.4 Å2
Refinement stepCycle: LAST / Resolution: 2.103→44.706 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms870 0 6 24 900
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007888
X-RAY DIFFRACTIONf_angle_d1.0711198
X-RAY DIFFRACTIONf_dihedral_angle_d13.029346
X-RAY DIFFRACTIONf_chiral_restr0.059141
X-RAY DIFFRACTIONf_plane_restr0.004149
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1031-2.21390.30491290.25131147X-RAY DIFFRACTION88
2.2139-2.35260.31241360.23511228X-RAY DIFFRACTION91
2.3526-2.53430.30811330.23571229X-RAY DIFFRACTION94
2.5343-2.78930.27751400.25851300X-RAY DIFFRACTION97
2.7893-3.19280.32681480.26131335X-RAY DIFFRACTION98
3.1928-4.02220.24791480.20961356X-RAY DIFFRACTION100
4.0222-44.7160.19681530.20911444X-RAY DIFFRACTION99

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