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- PDB-4zp4: Crystal Structure of the Heterodimeric HIF-2a:ARNT Complex -

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Basic information

Entry
Database: PDB / ID: 4zp4
TitleCrystal Structure of the Heterodimeric HIF-2a:ARNT Complex
Components
  • Aryl hydrocarbon receptor nuclear translocator
  • Endothelial PAS domain-containing protein 1
KeywordsPROTEIN TRANSPORT/TRANSCRIPTION / ARNT / HIF-2a complex / bHLH-PAS / PROTEIN TRANSPORT-TRANSCRIPTION complex
Function / homology
Function and homology information


Cellular response to hypoxia / Xenobiotics / Aryl hydrocarbon receptor signalling / Phase I - Functionalization of compounds / NPAS4 regulates expression of target genes / Regulation of gene expression by Hypoxia-inducible Factor / myoblast fate commitment / Endogenous sterols / nuclear aryl hydrocarbon receptor complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha ...Cellular response to hypoxia / Xenobiotics / Aryl hydrocarbon receptor signalling / Phase I - Functionalization of compounds / NPAS4 regulates expression of target genes / Regulation of gene expression by Hypoxia-inducible Factor / myoblast fate commitment / Endogenous sterols / nuclear aryl hydrocarbon receptor complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / positive regulation of hormone biosynthetic process / regulation of protein neddylation / positive regulation of protein sumoylation / Neddylation / norepinephrine metabolic process / surfactant homeostasis / epithelial cell maturation / aryl hydrocarbon receptor binding / hemopoiesis / positive regulation of vascular endothelial growth factor production / blood vessel remodeling / embryonic placenta development / cis-regulatory region sequence-specific DNA binding / visual perception / regulation of heart rate / lung development / positive regulation of glycolytic process / erythrocyte differentiation / mitochondrion organization / mRNA transcription by RNA polymerase II / multicellular organismal-level iron ion homeostasis / response to toxic substance / negative regulation of inflammatory response / transcription coactivator binding / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / positive regulation of cold-induced thermogenesis / response to oxidative stress / cellular response to oxidative stress / DNA-binding transcription activator activity, RNA polymerase II-specific / angiogenesis / transcription regulator complex / cellular response to hypoxia / gene expression / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / cell differentiation / response to hypoxia / nuclear speck / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein heterodimerization activity / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus / cytoplasm
Similarity search - Function
HIF-1 alpha, transactivation domain, C-terminal / HIF-1 alpha C terminal transactivation domain / : / Hypoxia-inducible factor 1-alpha bHLH domain / Hypoxia-inducible factor, alpha subunit-like / Hypoxia-inducible factor-1 / Nuclear translocator / PAS fold / Helix-loop-helix DNA-binding domain / PAC motif ...HIF-1 alpha, transactivation domain, C-terminal / HIF-1 alpha C terminal transactivation domain / : / Hypoxia-inducible factor 1-alpha bHLH domain / Hypoxia-inducible factor, alpha subunit-like / Hypoxia-inducible factor-1 / Nuclear translocator / 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 domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily
Similarity search - Domain/homology
Aryl hydrocarbon receptor nuclear translocator / Endothelial PAS domain-containing protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.355 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 7, 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 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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: Endothelial PAS domain-containing protein 1
C: Aryl hydrocarbon receptor nuclear translocator
D: Endothelial PAS domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)169,2774
Polymers169,2774
Non-polymers00
Water2,504139
1
A: Aryl hydrocarbon receptor nuclear translocator
B: Endothelial PAS domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)84,6382
Polymers84,6382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7160 Å2
ΔGint-54 kcal/mol
Surface area26350 Å2
MethodPISA
2
C: Aryl hydrocarbon receptor nuclear translocator
D: Endothelial PAS domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)84,6382
Polymers84,6382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint-51 kcal/mol
Surface area26470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.006, 76.463, 98.817
Angle α, β, γ (deg.)90.060, 90.190, 73.130
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
12chain B
22chain D

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUVALVALchain AAA98 - 46418 - 384
21GLUGLUVALVALchain CCC98 - 46418 - 384
12ARGARGGLUGLUchain BBB26 - 36025 - 359
22ARGARGGLUGLUchain DDD26 - 36025 - 359

NCS ensembles :
ID
1
2

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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.: 2 / 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 Endothelial PAS domain-containing protein 1 / EPAS-1 / HIF-1-alpha-like factor / mHLF / HIF-related factor / HRF / Hypoxia-inducible factor 2- ...EPAS-1 / HIF-1-alpha-like factor / mHLF / HIF-related factor / HRF / Hypoxia-inducible factor 2-alpha / HIF2-alpha


Mass: 41200.953 Da / Num. of mol.: 2 / Fragment: UNP residues 3-361
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Epas1, Hif2a / Plasmid: pSJ2 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P97481
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.09 Å3/Da / Density % sol: 41.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2% Tacsimate, pH 7.0, 6% PEG3350

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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: Feb 16, 2015
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
Reflection twinOperator: -h,-k,l / Fraction: 0.47
ReflectionResolution: 2.35→50 Å / Num. obs: 55780 / % possible obs: 98.4 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.046 / Rrim(I) all: 0.077 / Χ2: 0.899 / Net I/av σ(I): 11.837 / Net I/σ(I): 13 / Num. measured all: 144295
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.35-2.392.50.727510.5550.5570.90.98297.4
2.39-2.432.50.57428040.6350.4530.7360.96497.9
2.43-2.482.60.53927510.6630.4140.6840.99697.8
2.48-2.532.60.47227530.7680.3590.5960.9798
2.53-2.592.60.37828010.8420.2870.4771.00498
2.59-2.652.60.31427450.8730.2390.3971.00598
2.65-2.712.60.26628680.9040.2040.3371.00998.4
2.71-2.792.60.21827310.9320.1650.2751.00398.3
2.79-2.872.60.16728060.9590.1260.210.98798.4
2.87-2.962.60.12927730.9720.0970.1620.9598.4
2.96-3.072.60.10928370.980.0820.1370.97598.4
3.07-3.192.60.08427650.9860.0630.1060.91198.8
3.19-3.332.60.07127900.990.0530.0890.93498.6
3.33-3.512.60.05828500.9930.0430.0730.85698.9
3.51-3.732.60.05127800.9950.0380.0640.77298.9
3.73-4.022.60.04628150.9940.0340.0570.73199.1
4.02-4.422.60.04428210.9940.0330.0550.798.9
4.42-5.062.60.04327870.9940.0320.0540.67399.4
5.06-6.372.50.04328290.9950.0320.0540.6999.5
6.37-502.50.04927230.9920.0360.0610.87595.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000data scaling
Cootmodel building
PHENIXrefinement
PDB_EXTRACT3.15data extraction
PHASERphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 4F3L, 3F1P, & 4M4X

4f3l

3f1p

4m4x


Resolution: 2.355→49.408 Å / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.44 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.232 2880 5.16 %
Rwork0.2001 52891 -
obs0.2032 55769 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 170.2 Å2 / Biso mean: 63.9473 Å2 / Biso min: 33.78 Å2
Refinement stepCycle: final / Resolution: 2.355→49.408 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8924 0 0 139 9063
Biso mean---60.56 -
Num. residues----1102
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0119113
X-RAY DIFFRACTIONf_angle_d1.40312291
X-RAY DIFFRACTIONf_chiral_restr0.061392
X-RAY DIFFRACTIONf_plane_restr0.0061549
X-RAY DIFFRACTIONf_dihedral_angle_d14.8453379
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2247X-RAY DIFFRACTION9.138TORSIONAL
12C2247X-RAY DIFFRACTION9.138TORSIONAL
21B2599X-RAY DIFFRACTION9.138TORSIONAL
22D2599X-RAY DIFFRACTION9.138TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3556-2.39620.37241500.33852538268890
2.3962-2.43970.38271330.33882652278593
2.4397-2.48660.34911520.33132611276392
2.4866-2.53730.34241360.33782632276893
2.5373-2.59240.31551610.33732635279692
2.5924-2.65260.33561200.32532602272294
2.6526-2.71880.37431390.31072718285794
2.7188-2.79220.32041250.31122631275694
2.7922-2.87420.32651420.30132657279993
2.8742-2.96680.31511380.28612633277193
2.9668-3.07260.27831350.27672720285594
3.0726-3.19530.2441490.2562607275693
3.1953-3.34030.29741550.24472633278893
3.3403-3.51580.23781400.22462706284694
3.5158-3.73510.21851410.20212636277794
3.7351-4.0220.1841480.17842668281694
4.022-4.42410.18371470.14092660280794
4.4241-5.0580.17541220.12792700282295
5.058-6.34920.20551580.14962654281294
6.3492-22.6340.18881360.13862598273492
Refinement TLS params.Method: refined / Origin x: -181.5799 Å / Origin y: 80.0111 Å / Origin z: -146.6962 Å
111213212223313233
T0.3463 Å20.0204 Å20.0572 Å2-0.4344 Å20.0172 Å2--0.4306 Å2
L0.14 °20.1566 °20.327 °2-0.359 °20.2498 °2--0.7947 °2
S-0.0145 Å °-0.0485 Å °-0.0287 Å °0.0513 Å °0.0379 Å °0.0496 Å °-0.0072 Å °-0.0134 Å °-0.0188 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA98 - 464
2X-RAY DIFFRACTION1allB26 - 360
3X-RAY DIFFRACTION1allC98 - 464
4X-RAY DIFFRACTION1allD26 - 360
5X-RAY DIFFRACTION1allS1 - 212

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