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- PDB-6hkp: Factor Inhibiting HIF (FIH) in complex with zinc, NOG and ASPP2 (... -

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Basic information

Entry
Database: PDB / ID: 6hkp
TitleFactor Inhibiting HIF (FIH) in complex with zinc, NOG and ASPP2 (970-992)
Components
  • Apoptosis-stimulating of p53 protein 2
  • Hypoxia-inducible factor 1-alpha inhibitor
KeywordsGENE REGULATION / NON-HEME / DIOXYGENASE / OXYGENASE / METAL-BINDING / TRANSCRIPTION / DOUBLE STRANDED BETA-HELIX / DSBH / FACIAL TRIAD / ASPARAGINYL/ASPARTYL HYDROXYLASE / EPIGENETIC REGULATION / SIGNALING / ARD / BETA-HYDROXYLATION / ACTIVATOR-INHIBITOR / OXIDOREDUCTASE-PEPTIDE COMPLEX / OXIDOREDUCTASE / ANKYRIN REPEAT DOMAIN / APOPTOSIS / P53 BINDING PROTEIN / ANK REPEAT / SH3 DOMAIN / ANKYRIN REPEATS
Function / homology
Function and homology information


hypoxia-inducible factor-asparagine dioxygenase / : / [protein]-asparagine 3-dioxygenase activity / peptidyl-histidine dioxygenase activity / peptidyl-aspartic acid 3-dioxygenase activity / regulation of vascular endothelial growth factor receptor signaling pathway / Cellular response to hypoxia / carboxylic acid binding / positive regulation of vasculogenesis / ankyrin repeat binding ...hypoxia-inducible factor-asparagine dioxygenase / : / [protein]-asparagine 3-dioxygenase activity / peptidyl-histidine dioxygenase activity / peptidyl-aspartic acid 3-dioxygenase activity / regulation of vascular endothelial growth factor receptor signaling pathway / Cellular response to hypoxia / carboxylic acid binding / positive regulation of vasculogenesis / ankyrin repeat binding / Notch binding / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / oxygen sensor activity / Regulation of TP53 Activity through Association with Co-factors / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of execution phase of apoptosis / negative regulation of cell cycle / negative regulation of Notch signaling pathway / NF-kappaB binding / positive regulation of myoblast differentiation / ferrous iron binding / SH3 domain binding / transcription corepressor activity / p53 binding / cell junction / perinuclear region of cytoplasm / signal transduction / protein homodimerization activity / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / : / : / Apoptosis-stimulating of p53 protein 2-like, N-terminal RA domain / Clavaminate synthase-like / Hypoxia-inducible factor 1-alpha inhibitor, domain II / Cupin-like domain 8 / Cupin-like domain / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain ...: / : / : / Apoptosis-stimulating of p53 protein 2-like, N-terminal RA domain / Clavaminate synthase-like / Hypoxia-inducible factor 1-alpha inhibitor, domain II / Cupin-like domain 8 / Cupin-like domain / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Jelly Rolls / SH3 domain / RmlC-like jelly roll fold / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Helix Hairpins / Ubiquitin-like domain superfamily / Jelly Rolls / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
N-OXALYLGLYCINE / Apoptosis-stimulating of p53 protein 2 / Hypoxia-inducible factor 1-alpha inhibitor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLeissing, T.M. / Clifton, I.J. / Lu, X. / Schofield, C.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilP/G03706X/1 United Kingdom
CitationJournal: To Be Published
Title: Factor Inhibiting HIF (FIH) in complex with zinc, NOG and ASPP2 (970-992)
Authors: Leissing, T.M. / Clifton, I.J. / Lu, X. / Schofield, C.J.
History
DepositionSep 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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: Hypoxia-inducible factor 1-alpha inhibitor
S: Apoptosis-stimulating of p53 protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,08415
Polymers42,8352
Non-polymers1,24913
Water3,189177
1
A: Hypoxia-inducible factor 1-alpha inhibitor
S: Apoptosis-stimulating of p53 protein 2
hetero molecules

A: Hypoxia-inducible factor 1-alpha inhibitor
S: Apoptosis-stimulating of p53 protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,16930
Polymers85,6704
Non-polymers2,49926
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area11910 Å2
ΔGint-263 kcal/mol
Surface area29440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.020, 86.020, 148.508
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AS

#1: Protein Hypoxia-inducible factor 1-alpha inhibitor / Factor inhibiting HIF-1 / FIH-1 / Hypoxia-inducible factor asparagine hydroxylase


Mass: 40415.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIF1AN, FIH1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NWT6, hypoxia-inducible factor-asparagine dioxygenase, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one ...References: UniProt: Q9NWT6, hypoxia-inducible factor-asparagine dioxygenase, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor
#2: Protein/peptide Apoptosis-stimulating of p53 protein 2 / Bcl2-binding protein / Bbp / Renal carcinoma antigen NY-REN-51 / Tumor suppressor p53-binding ...Bcl2-binding protein / Bbp / Renal carcinoma antigen NY-REN-51 / Tumor suppressor p53-binding protein 2 / p53BP2


Mass: 2419.645 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13625

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Non-polymers , 5 types, 190 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 3.21 Å3/Da / Density % sol: 61.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Hepes pH = 7.5, 2.0 M ammonium sulfate, 5.5% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.9→86.02 Å / Num. obs: 44748 / % possible obs: 100 % / Redundancy: 16 % / Biso Wilson estimate: 38.9 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.18 / Rpim(I) all: 0.046 / Rrim(I) all: 0.186 / Net I/σ(I): 8.3
Reflection shellResolution: 1.9→2 Å / Redundancy: 15.6 % / Rmerge(I) obs: 1.923 / Num. unique obs: 6404 / CC1/2: 0.605 / Rpim(I) all: 0.496 / Rrim(I) all: 1.987 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H2K

1h2k


Resolution: 1.9→56.287 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1948 2270 5.08 %
Rwork0.1755 --
obs0.1765 44648 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→56.287 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2790 0 71 177 3038
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052955
X-RAY DIFFRACTIONf_angle_d0.6844021
X-RAY DIFFRACTIONf_dihedral_angle_d12.7011707
X-RAY DIFFRACTIONf_chiral_restr0.048409
X-RAY DIFFRACTIONf_plane_restr0.005526
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94130.30121350.30842575X-RAY DIFFRACTION100
1.9413-1.98650.2721420.29052610X-RAY DIFFRACTION100
1.9865-2.03620.27561540.25652581X-RAY DIFFRACTION100
2.0362-2.09120.28021330.24172623X-RAY DIFFRACTION100
2.0912-2.15270.26991180.21832625X-RAY DIFFRACTION100
2.1527-2.22220.22761260.19742614X-RAY DIFFRACTION100
2.2222-2.30170.22191410.18782618X-RAY DIFFRACTION100
2.3017-2.39380.2141420.17712625X-RAY DIFFRACTION100
2.3938-2.50280.17661560.1692612X-RAY DIFFRACTION100
2.5028-2.63470.20371480.1722629X-RAY DIFFRACTION100
2.6347-2.79980.1951330.1792644X-RAY DIFFRACTION100
2.7998-3.01590.20941400.17692652X-RAY DIFFRACTION100
3.0159-3.31940.19251490.17662673X-RAY DIFFRACTION100
3.3194-3.79970.1741430.15872694X-RAY DIFFRACTION100
3.7997-4.78680.14221640.13322714X-RAY DIFFRACTION100
4.7868-56.31160.21841460.18832889X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6992-0.60780.36112.6886-1.40122.0957-0.0030.0761-0.0797-0.00120.1124-0.06720.1303-0.0728-0.09610.44380.001-0.09030.2293-0.0220.316418.110171.839710.4267
22.5702-0.5942-0.51675.62191.70363.03950.11920.26460.0682-0.2766-0.0068-0.23710.44810.1494-0.14680.4090.051-0.03820.47060.09870.38775.439593.1751-4.8833
32.47080.32561.45992.2037-1.13771.71060.0249-0.0212-0.2914-0.22520.36550.31050.234-0.0799-0.39171.0858-0.1086-0.00720.991-0.00320.96345.619372.9595.214
40.3589-0.0367-0.10060.0570.00960.087-0.2353-0.40020.03160.6399-0.1699-0.821-0.23760.41710.33980.70870.0134-0.2390.4230.04390.68532.390872.850722.8324
51.8273-0.14520.41162.4709-1.13981.85160.09860.4141-0.1247-0.5444-0.1314-0.33670.35430.30390.02870.66440.1136-0.03020.3725-0.07380.422126.876163.27564.7199
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 150 through 330 )
2X-RAY DIFFRACTION2chain 'A' and (resid 331 through 349 )
3X-RAY DIFFRACTION3chain 'S' and (resid 975 through 987 )
4X-RAY DIFFRACTION4chain 'A' and (resid 12 through 49 )
5X-RAY DIFFRACTION5chain 'A' and (resid 50 through 149 )

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