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- PDB-4zpr: Crystal Structure of the Heterodimeric HIF-1a:ARNT Complex with H... -

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Basic information

Entry
Database: PDB / ID: 4zpr
TitleCrystal Structure of the Heterodimeric HIF-1a:ARNT Complex with HRE DNA
Components
  • Aryl hydrocarbon receptor nuclear translocator
  • DNA (5'-D(*CP*AP*CP*GP*AP*CP*CP*CP*GP*CP*AP*CP*GP*TP*AP*CP*GP*CP*AP*GP*C)-3')
  • DNA (5'-D(*GP*GP*CP*TP*GP*CP*GP*TP*AP*CP*GP*TP*GP*CP*GP*GP*GP*TP*CP*GP*T)-3')
  • Hypoxia-inducible factor 1-alpha
KeywordsPROTEIN TRANSPORT/TRANSCRIPTION/DNA / ARNT / HIF-1a / HRE / bHLH-PAS / PROTEIN TRANSPORT-TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


: / PTK6 promotes HIF1A stabilization / : / : / nuclear receptor binding => GO:0016922 / Cellular response to hypoxia / regulation of thymocyte apoptotic process / Phase I - Functionalization of compounds / Xenobiotics / Aryl hydrocarbon receptor signalling ...: / PTK6 promotes HIF1A stabilization / : / : / nuclear receptor binding => GO:0016922 / Cellular response to hypoxia / regulation of thymocyte apoptotic process / Phase I - Functionalization of compounds / Xenobiotics / Aryl hydrocarbon receptor signalling / NPAS4 regulates expression of target genes / epithelial cell differentiation involved in mammary gland alveolus development / neural fold elevation formation / iris morphogenesis / hypoxia-inducible factor-1alpha signaling pathway / elastin metabolic process / Regulation of gene expression by Hypoxia-inducible Factor / Endogenous sterols / nuclear aryl hydrocarbon receptor complex / regulation of transforming growth factor beta2 production / connective tissue replacement involved in inflammatory response wound healing / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / cardiac ventricle morphogenesis / negative regulation of mesenchymal cell apoptotic process / hemoglobin biosynthetic process / positive regulation of autophagy of mitochondrion / positive regulation of hormone biosynthetic process / retina vasculature development in camera-type eye / intestinal epithelial cell maturation / aryl hydrocarbon receptor complex / negative regulation of growth / collagen metabolic process / chromatin => GO:0000785 / intracellular oxygen homeostasis / negative regulation of bone mineralization / B-1 B cell homeostasis / positive regulation of protein sumoylation / vascular endothelial growth factor production / Neddylation / camera-type eye morphogenesis / Ub-specific processing proteases / regulation of catalytic activity / dopaminergic neuron differentiation / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / lactate metabolic process / vasculature development / negative regulation of ossification / negative regulation of thymocyte apoptotic process / positive regulation of vascular endothelial growth factor receptor signaling pathway / motile cilium / cartilage development / negative regulation of TOR signaling / response to iron ion / response to muscle activity / blood vessel morphogenesis / neural crest cell migration / regulation of glycolytic process / embryonic hemopoiesis / negative regulation of vasoconstriction / regulation of aerobic respiration / digestive tract morphogenesis / histone acetyltransferase binding / muscle cell cellular homeostasis / positive regulation of neuroblast proliferation / axonal transport of mitochondrion / positive regulation of epithelial cell migration / blood vessel development / heart looping / outflow tract morphogenesis / E-box binding / positive regulation of insulin secretion involved in cellular response to glucose stimulus / aryl hydrocarbon receptor binding / transcription factor binding / positive regulation of macroautophagy / positive regulation of vascular endothelial growth factor production / negative regulation of reactive oxygen species metabolic process / embryonic placenta development / positive regulation of blood vessel endothelial cell migration / epithelial to mesenchymal transition / cellular response to interleukin-1 / cis-regulatory region sequence-specific DNA binding / positive regulation of autophagy / response to fungicide / axon cytoplasm / positive regulation of gluconeogenesis / lactation / positive regulation of erythrocyte differentiation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / positive regulation of smooth muscle cell proliferation / Hsp90 protein binding / visual learning / response to toxic substance / cerebral cortex development / positive regulation of miRNA transcription / negative regulation of inflammatory response / histone deacetylase binding / RNA polymerase II transcription regulator complex / positive regulation of angiogenesis / nuclear receptor activity / sequence-specific double-stranded DNA binding
Similarity search - Function
Hypoxia-inducible factor-1 alpha / HIF-1 alpha, transactivation domain, C-terminal / HIF-1 alpha C terminal transactivation domain / Hypoxia-inducible factor, alpha subunit-like / Hypoxia-inducible factor-1 / Nuclear translocator / PAS fold-3 / PAS fold / Helix-loop-helix DNA-binding domain / PAC motif ...Hypoxia-inducible factor-1 alpha / HIF-1 alpha, transactivation domain, C-terminal / HIF-1 alpha C terminal transactivation domain / Hypoxia-inducible factor, alpha subunit-like / Hypoxia-inducible factor-1 / Nuclear translocator / PAS fold-3 / PAS fold / Helix-loop-helix DNA-binding domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS 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. / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Aryl hydrocarbon receptor nuclear translocator / Hypoxia-inducible factor 1-alpha
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.902 Å
AuthorsWu, D. / Potluri, N. / Lu, J. / Kim, Y. / Rastinejad, F.
CitationJournal: Nature / Year: 2015
Title: Structural integration in hypoxia-inducible factors.
Authors: Wu, D. / Potluri, N. / Lu, J. / Kim, Y. / Rastinejad, F.
History
DepositionMay 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2Aug 26, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Sep 27, 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: Aryl hydrocarbon receptor nuclear translocator
B: Hypoxia-inducible factor 1-alpha
C: DNA (5'-D(*GP*GP*CP*TP*GP*CP*GP*TP*AP*CP*GP*TP*GP*CP*GP*GP*GP*TP*CP*GP*T)-3')
D: DNA (5'-D(*CP*AP*CP*GP*AP*CP*CP*CP*GP*CP*AP*CP*GP*TP*AP*CP*GP*CP*AP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)96,2294
Polymers96,2294
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10480 Å2
ΔGint-70 kcal/mol
Surface area34510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.735, 66.735, 243.644
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Aryl hydrocarbon receptor nuclear translocator / ARNT protein / Dioxin receptor / nuclear translocator / Hypoxia-inducible factor 1-beta / HIF1-beta


Mass: 43437.391 Da / Num. of mol.: 1 / Fragment: UNP residues 82-464
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Arnt / Plasmid: pMKH / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P53762
#2: Protein Hypoxia-inducible factor 1-alpha / HIF1-alpha / ARNT-interacting protein / Hypoxia inducible factor 1 / alpha subunit


Mass: 39901.574 Da / Num. of mol.: 1 / Fragment: UNP residues 13-357
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Hif1a / Plasmid: pSJ2 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q61221
#3: DNA chain DNA (5'-D(*GP*GP*CP*TP*GP*CP*GP*TP*AP*CP*GP*TP*GP*CP*GP*GP*GP*TP*CP*GP*T)-3')


Mass: 6527.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: HRE DNA sense strand / Source: (synth.) Mus musculus (house mouse)
#4: DNA chain DNA (5'-D(*CP*AP*CP*GP*AP*CP*CP*CP*GP*CP*AP*CP*GP*TP*AP*CP*GP*CP*AP*GP*C)-3')


Mass: 6363.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: HRE DNA antisense strand / Source: (synth.) Mus musculus (house mouse)

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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: 2.82 Å3/Da / Density % sol: 56.37 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM MES, pH 6.0, 100 mM calcium acetate, 15% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 26, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 3.9→50 Å / Num. obs: 9620 / % possible obs: 99.1 % / Redundancy: 3.8 % / Biso Wilson estimate: 204.78 Å2 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.027 / Rrim(I) all: 0.052 / Χ2: 1.115 / Net I/av σ(I): 24.722 / Net I/σ(I): 11.2 / Num. measured all: 36593
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.9-3.973.90.794770.6090.4650.9181.078100
3.97-4.043.90.5654550.7420.3330.6561.089100
4.04-4.123.80.4495030.8190.2670.5231.117100
4.12-4.23.80.3494740.9010.2060.4061.111100
4.2-4.293.90.2644920.930.1560.3071.172100
4.29-4.393.90.1984930.9610.1170.2311.165100
4.39-4.53.80.1624940.9720.0960.1891.255100
4.5-4.623.80.1354430.9830.0790.1571.196100
4.62-4.763.90.1235200.9850.0720.1421.164100
4.76-4.913.80.0994650.990.0580.1151.08100
4.91-5.093.80.0874910.9920.0510.1011.089100
5.09-5.293.90.084740.9940.0470.0941.223100
5.29-5.533.80.0824980.9910.0480.0951.251100
5.53-5.823.80.0754700.9920.0430.0871.125100
5.82-6.193.80.075020.9920.0410.0811.213100
6.19-6.663.80.0654860.9920.0380.0751.136100
6.66-7.333.70.0554840.9960.0330.0641.032100
7.33-8.393.70.0394920.9980.0240.0460.94799.8
8.39-10.553.70.0274880.9990.0160.0320.91399.8
10.55-503.50.0284190.9950.0180.0340.86483.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
SCALEPACKdata scaling
CORELSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4ZP4

4zp4


Resolution: 3.902→29.845 Å / SU ML: 0.84 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 43.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.341 962 10.04 %
Rwork0.2645 8616 -
obs0.2721 9578 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 252.28 Å2 / Biso mean: 194.6663 Å2 / Biso min: 175.4 Å2
Refinement stepCycle: final / Resolution: 3.902→29.845 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4187 855 0 0 5042
Num. residues----556
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055229
X-RAY DIFFRACTIONf_angle_d0.8437222
X-RAY DIFFRACTIONf_chiral_restr0.033812
X-RAY DIFFRACTIONf_plane_restr0.003767
X-RAY DIFFRACTIONf_dihedral_angle_d21.0562002
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.9019-4.10710.43861480.387212081356100
4.1071-4.36370.46091280.360512361364100
4.3637-4.69940.41061480.336412611409100
4.6994-5.17020.40421390.331412351374100
5.1702-5.91320.40111370.336612291366100
5.9132-7.4310.40491300.313112561386100
7.431-29.84570.25891320.18461191132395

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