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- PDB-6ha6: Factor Inhibiting HIF (FIH) in complex with zinc, NOG and TRPV3 (... -

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Basic information

Entry
Database: PDB / ID: 6ha6
TitleFactor Inhibiting HIF (FIH) in complex with zinc, NOG and TRPV3 (220-246)
Components
  • Hypoxia-inducible factor 1-alpha inhibitor
  • Transient receptor potential cation channel subfamily V member 3
KeywordsGENE REGULATION / NON-HEME / DIOXYGENASE / OXYGENASE / METAL-BINDING / TRANSCRIPTION / DSBH / FACIAL TRIAD / ASPARAGINYL/ASPARTYL HYDROXYLASE / SIGNALING / ARD / BETA-HYDROXYLATION / ACTIVATOR-INHIBITOR / OXIDOREDUCTASE-PEPTIDE COMPLEX / OXIDOREDUCTASE ANKYRIN / CHANNEL / PROTEIN BINDING / ION CHANNEL / TRPV CHANNEL / MEMBRANE PROTEIN
Function / homology
Function and homology information


hypoxia-inducible factor-asparagine dioxygenase / : / [protein]-asparagine 3-dioxygenase activity / peptidyl-histidine dioxygenase activity / negative regulation of hair cycle / peptidyl-aspartic acid 3-dioxygenase activity / 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 / negative regulation of hair cycle / peptidyl-aspartic acid 3-dioxygenase activity / Cellular response to hypoxia / carboxylic acid binding / positive regulation of vasculogenesis / ankyrin repeat binding / oxygen sensor activity / Notch binding / TRP channels / response to temperature stimulus / negative regulation of Notch signaling pathway / positive regulation of calcium ion import / NF-kappaB binding / positive regulation of myoblast differentiation / ferrous iron binding / calcium ion transmembrane transport / calcium channel activity / transcription corepressor activity / receptor complex / perinuclear region of cytoplasm / protein homodimerization activity / zinc ion binding / nucleoplasm / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Clavaminate synthase-like / Hypoxia-inducible factor 1-alpha inhibitor, domain II / Cupin-like domain 8 / Cupin-like domain / Transient receptor potential cation channel subfamily V member 1-4 / Transient receptor potential cation channel subfamily V / A domain family that is part of the cupin metalloenzyme superfamily. / Jelly Rolls / JmjC domain / JmjC domain profile. ...Clavaminate synthase-like / Hypoxia-inducible factor 1-alpha inhibitor, domain II / Cupin-like domain 8 / Cupin-like domain / Transient receptor potential cation channel subfamily V member 1-4 / Transient receptor potential cation channel subfamily V / A domain family that is part of the cupin metalloenzyme superfamily. / Jelly Rolls / JmjC domain / JmjC domain profile. / Ankyrin repeat / 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 / Ion transport domain / Ion transport protein / Helix Hairpins / Jelly Rolls / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
N-OXALYLGLYCINE / Transient receptor potential cation channel subfamily V member 3 / Hypoxia-inducible factor 1-alpha inhibitor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsLeissing, T.M. / Clifton, I.J. / Saward, B.G. / Lu, X. / Hopkinson, R.J. / 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 TRPV3 (220-246)
Authors: Leissing, T.M. / Clifton, I.J. / Saward, B.G. / Lu, X. / Hopkinson, R.J. / Schofield, C.J.
History
DepositionAug 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 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
D: Transient receptor potential cation channel subfamily V member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,97711
Polymers43,1042
Non-polymers8739
Water2,108117
1
A: Hypoxia-inducible factor 1-alpha inhibitor
D: Transient receptor potential cation channel subfamily V member 3
hetero molecules

A: Hypoxia-inducible factor 1-alpha inhibitor
D: Transient receptor potential cation channel subfamily V member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,95522
Polymers86,2094
Non-polymers1,74618
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area10390 Å2
ΔGint-222 kcal/mol
Surface area29440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.080, 87.080, 149.360
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 AD

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


Mass: 40328.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIF1AN, FIH1 / Plasmid: pET28 / 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 Transient receptor potential cation channel subfamily V member 3 / TrpV3 / Vanilloid receptor-like 3 / VRL-3


Mass: 2776.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q8NET8

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Non-polymers , 5 types, 126 molecules

#3: Chemical ChemComp-OGA / N-OXALYLGLYCINE / N-Oxalylglycine


Mass: 147.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#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 / Water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 3.28 Å3/Da / Density % sol: 62.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Hepes pH = 7.5, 1.7 M ammonium sulfate, 5.5% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.98→74.68 Å / Num. obs: 40834 / % possible obs: 100 % / Redundancy: 19 % / Rrim(I) all: 0.085 / Net I/σ(I): 18
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 20.2 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2001 / Rrim(I) all: 2.821 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H2K

1h2k


Resolution: 1.98→61.575 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.28
RfactorNum. reflection% reflection
Rfree0.2028 2027 4.97 %
Rwork0.1806 --
obs0.1818 40754 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.98→61.575 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2786 0 49 117 2952
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032966
X-RAY DIFFRACTIONf_angle_d0.5914043
X-RAY DIFFRACTIONf_dihedral_angle_d12.6541729
X-RAY DIFFRACTIONf_chiral_restr0.046413
X-RAY DIFFRACTIONf_plane_restr0.004533
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9801-2.02960.29831710.27252690X-RAY DIFFRACTION100
2.0296-2.08450.28391340.25122728X-RAY DIFFRACTION100
2.0845-2.14580.24681480.23282684X-RAY DIFFRACTION100
2.1458-2.21510.31671150.22922762X-RAY DIFFRACTION100
2.2151-2.29420.29771350.25852740X-RAY DIFFRACTION100
2.2942-2.38610.24951460.20782700X-RAY DIFFRACTION100
2.3861-2.49470.23771420.18992752X-RAY DIFFRACTION100
2.4947-2.62620.24141380.19092751X-RAY DIFFRACTION100
2.6262-2.79080.2181350.20032753X-RAY DIFFRACTION100
2.7908-3.00620.2231430.20122773X-RAY DIFFRACTION100
3.0062-3.30870.21251360.19882778X-RAY DIFFRACTION100
3.3087-3.78750.19871580.17432795X-RAY DIFFRACTION100
3.7875-4.77150.16281610.13572821X-RAY DIFFRACTION100
4.7715-61.60460.1871650.17753000X-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)
18.9773-4.26778.30381.6826-3.79197.3348-0.29821.33121.0468-0.1891-0.5964-0.36-0.26970.73490.95110.5516-0.0116-0.05410.76260.32020.9064-12.621336.9814-21.4502
27.33521.80194.47684.60740.26495.46610.10711.0123-0.0143-0.575-0.10990.03510.3470.2703-0.02080.4740.11910.08570.8170.15830.4292-14.884218.3107-26.6368
34.2696-0.61933.05013.1391.16223.5658-0.3511-0.72320.56730.38180.11340.6716-0.2012-0.81760.26710.45310.13220.13660.81460.0990.7043-31.657128.5767-9.4282
44.1512-2.80060.71884.1566-1.49993.7124-0.7168-0.82890.31661.29910.42450.0282-0.8787-0.70580.24250.77120.17450.01050.9866-0.08880.6896-18.927628.87144.8267
54.88620.15692.58640.89081.36696.6777-0.0064-1.2520.28960.6176-0.07420.24160.1233-1.30320.18650.53360.16310.09160.97140.07570.6163-29.965926.9608-5.675
64.8695-0.1332.35711.8310.11163.24470.1849-0.2119-0.10280.16210.08540.35030.206-0.3954-0.26150.39720.02220.0440.65710.18260.5056-22.012218.128-13.2047
74.8168-1.77932.2482.9105-1.93734.9773-0.01440.23210.5730.0708-0.01170.0549-0.06090.2520.03220.3497-0.00920.01930.50370.07820.4746-5.068721.4878-7.0855
86.522-0.3772.44811.0117-0.32632.35620.0180.24950.51930.0575-0.08580.0498-0.1465-0.06710.06350.36370.01520.02980.5780.13720.4922-10.922224.373-12.9367
97.0889-1.85521.97115.5307-2.88293.90430.41620.2678-0.8343-0.4898-0.08930.30740.7609-0.0684-0.36520.512-0.0164-0.12550.43790.0380.5564-6.1432.6507-7.1199
102.2398-2.558-2.64356.3372-0.58436.30750.0491-0.2852-0.36080.5596-0.19220.0219-0.5705-0.5425-0.0950.59390.0163-0.10680.5117-0.01230.40757.50245.83834.9512
112.5583-4.26672.25987.5682-3.6222.02970.8305-0.4141-2.3538-1.13990.06811.71151.5314-1.8815-0.80731.2064-0.30650.04081.8811-0.3231.4332-6.625-2.3793-7.3692
129.2912-0.14335.0934.6893-5.54279.2301-0.6487-0.5636-2.36920.92891.03121.5232-0.8706-1.0895-0.15480.78190.03030.27551.1059-0.10281.7481-16.230112.1522-3.4695
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 37 )
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 64 )
3X-RAY DIFFRACTION3chain 'A' and (resid 65 through 95 )
4X-RAY DIFFRACTION4chain 'A' and (resid 96 through 137 )
5X-RAY DIFFRACTION5chain 'A' and (resid 138 through 166 )
6X-RAY DIFFRACTION6chain 'A' and (resid 167 through 211 )
7X-RAY DIFFRACTION7chain 'A' and (resid 212 through 247 )
8X-RAY DIFFRACTION8chain 'A' and (resid 248 through 297 )
9X-RAY DIFFRACTION9chain 'A' and (resid 298 through 330 )
10X-RAY DIFFRACTION10chain 'A' and (resid 331 through 349 )
11X-RAY DIFFRACTION11chain 'D' and (resid 231 through 235 )
12X-RAY DIFFRACTION12chain 'D' and (resid 236 through 244 )

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