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- PDB-6hc8: Factor Inhibiting HIF (FIH) in complex with zinc, NOG and TRPA1 (... -

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Basic information

Entry
Database: PDB / ID: 6hc8
TitleFactor Inhibiting HIF (FIH) in complex with zinc, NOG and TRPA1 (313-339)
Components
  • Hypoxia-inducible factor 1-alpha inhibitor
  • Transient receptor potential cation channel subfamily A member 1
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 / TRPA CHANNEL / MEMBRANE PROTEIN
Function / homology
Function and homology information


temperature-gated cation channel activity / hypoxia-inducible factor-asparagine dioxygenase / : / [protein]-asparagine 3-dioxygenase activity / peptidyl-histidine dioxygenase activity / peptidyl-aspartic acid 3-dioxygenase activity / Cellular response to hypoxia / stereocilium bundle / carboxylic acid binding / positive regulation of vasculogenesis ...temperature-gated cation channel activity / hypoxia-inducible factor-asparagine dioxygenase / : / [protein]-asparagine 3-dioxygenase activity / peptidyl-histidine dioxygenase activity / peptidyl-aspartic acid 3-dioxygenase activity / Cellular response to hypoxia / stereocilium bundle / carboxylic acid binding / positive regulation of vasculogenesis / detection of chemical stimulus involved in sensory perception of pain / ankyrin repeat binding / thermoception / Notch binding / TRP channels / oxygen sensor activity / response to pain / negative regulation of Notch signaling pathway / intracellularly gated calcium channel activity / NF-kappaB binding / detection of mechanical stimulus involved in sensory perception of pain / positive regulation of myoblast differentiation / monoatomic ion transport / sensory perception of pain / response to cold / calcium ion transmembrane transport / ferrous iron binding / calcium channel activity / response to organic cyclic compound / cellular response to hydrogen peroxide / intracellular calcium ion homeostasis / transcription corepressor activity / channel activity / protein homotetramerization / cell surface receptor signaling pathway / response to xenobiotic stimulus / 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 / Jelly Rolls / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Ankyrin repeat ...: / Clavaminate synthase-like / Hypoxia-inducible factor 1-alpha inhibitor, domain II / Cupin-like domain 8 / Cupin-like domain / Jelly Rolls / A domain family that is part of the cupin metalloenzyme superfamily. / 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 A member 1 / 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. / 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 TRPA1 (313-339)
Authors: Leissing, T.M. / Clifton, I.J. / Saward, B.G. / Lu, X. / Hopkinson, R.J. / Schofield, C.J.
History
DepositionAug 14, 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
E: Transient receptor potential cation channel subfamily A member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0698
Polymers43,4842
Non-polymers5856
Water2,648147
1
A: Hypoxia-inducible factor 1-alpha inhibitor
E: Transient receptor potential cation channel subfamily A member 1
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)88,13716
Polymers86,9684
Non-polymers1,17012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area9630 Å2
ΔGint-160 kcal/mol
Surface area30870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.860, 86.860, 148.120
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 AE

#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
Details: Unmodelled gap between residues 3 and 9 exclusive. / 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 A member 1 / Ankyrin-like with transmembrane domains protein 1 / Transformation-sensitive protein p120


Mass: 3068.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O75762

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Non-polymers , 5 types, 153 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-OGA / N-OXALYLGLYCINE


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


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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 61.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Hepes pH = 7.5, 1.6 M ammonium sulfate, 6% 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: 1.9→86.86 Å / Num. obs: 45517 / % possible obs: 100 % / Redundancy: 17.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.024 / Rrim(I) all: 0.103 / Net I/σ(I): 13.3
Reflection shellResolution: 1.9→2 Å / Redundancy: 17.7 % / Rmerge(I) obs: 2.027 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 6544 / CC1/2: 0.59 / Rpim(I) all: 0.493 / Rrim(I) all: 2.086 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
MOSFLMdata reduction
SCALA3.3.22data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H2K

1h2k


Resolution: 1.9→74.927 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.02
RfactorNum. reflection% reflection
Rfree0.189 2210 4.87 %
Rwork0.17 --
obs0.1709 45389 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→74.927 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2841 0 34 147 3022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073014
X-RAY DIFFRACTIONf_angle_d0.7664104
X-RAY DIFFRACTIONf_dihedral_angle_d11.0791764
X-RAY DIFFRACTIONf_chiral_restr0.054419
X-RAY DIFFRACTIONf_plane_restr0.005543
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94130.35581340.32162644X-RAY DIFFRACTION100
1.9413-1.98650.2991500.28472654X-RAY DIFFRACTION100
1.9865-2.03620.27491310.24152630X-RAY DIFFRACTION100
2.0362-2.09120.24831320.22472660X-RAY DIFFRACTION100
2.0912-2.15280.21681430.21252636X-RAY DIFFRACTION100
2.1528-2.22230.20511460.19012664X-RAY DIFFRACTION100
2.2223-2.30170.18111320.18022661X-RAY DIFFRACTION100
2.3017-2.39380.21481360.17472681X-RAY DIFFRACTION100
2.3938-2.50280.20981430.16772665X-RAY DIFFRACTION100
2.5028-2.63480.20741270.17152706X-RAY DIFFRACTION100
2.6348-2.79980.21881530.17482672X-RAY DIFFRACTION100
2.7998-3.0160.18761290.18182714X-RAY DIFFRACTION100
3.016-3.31950.20411270.17942727X-RAY DIFFRACTION100
3.3195-3.79990.17651440.16052731X-RAY DIFFRACTION100
3.7999-4.78730.13121340.1272798X-RAY DIFFRACTION100
4.7873-74.98530.19591490.17622936X-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)
12.24330.2021-0.95230.4893-0.02120.3816-0.14491.0769-0.8523-0.3359-0.48110.17520.2268-0.47670.54130.56910.03220.06740.7807-0.28720.7602-33.02487.647-22.0042
23.3978-0.3755-1.92572.86220.17372.5253-0.04620.0836-0.31090.07160.0504-0.4018-0.00210.29220.0110.30230.0672-0.06510.5318-0.17340.4553-19.141719.8267-17.2689
33.7375-2.171-1.29879.26212.50035.4014-0.5241-0.9094-0.14611.84950.4510.1020.42170.57430.13160.67770.10260.0360.7780.00440.4915-32.16620.31276.2716
43.5723-0.2722-0.50971.25340.06253.7608-0.1774-1.1474-0.78360.6710.0494-0.43440.37310.98870.14910.60790.2641-0.1420.9620.02760.658-14.245912.6786-1.5466
53.4296-0.8074-2.24294.67870.38372.03650.4366-0.3320.39910.1160.1969-0.4573-0.37850.3633-0.59080.3379-0.0222-0.01180.599-0.19490.5631-17.02929.7822-15.668
63.4182-0.589-2.21831.72571.27833.8494-0.04010.0271-0.40220.1790.05850.00980.13360.0743-0.02150.26550.0258-0.02640.4259-0.07950.3549-33.817321.3021-7.9974
74.7344-0.1155-1.69561.37140.31641.99620.00960.2471-0.41850.1102-0.0221-0.09260.20330.04910.0190.30170.0116-0.03410.4973-0.14750.4029-32.273319.193-12.7026
84.7732-0.3529-0.57494.23361.50972.47870.25940.16660.6938-0.53930.1683-0.4628-0.5859-0.0349-0.42570.53740.01680.13460.4497-0.07010.5091-36.911140.839-7.2954
99.7166-2.79792.60743.8951-2.15524.5403-0.0428-0.2173-0.15660.50330.090.06610.21590.6135-0.06290.53830.04520.08240.4679-0.04820.335-50.514637.88874.9302
103.45252.6017-1.36692.6244-0.29691.4623-0.8330.01671.1040.4606-0.5951-0.2879-1.41370.54951.32061.02710.0736-0.10971.0616-0.19190.7332-36.041247.1705-5.4116
115.48-3.4012-1.55793.0853-0.42072.4131-0.0547-0.38531.08580.46690.3041-1.4547-0.34090.3364-0.33850.6422-0.0131-0.1370.9583-0.21750.9296-26.934732.5578-3.2283
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 38 )
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 95 )
3X-RAY DIFFRACTION3chain 'A' and (resid 96 through 118 )
4X-RAY DIFFRACTION4chain 'A' and (resid 119 through 166 )
5X-RAY DIFFRACTION5chain 'A' and (resid 167 through 190 )
6X-RAY DIFFRACTION6chain 'A' and (resid 191 through 247 )
7X-RAY DIFFRACTION7chain 'A' and (resid 248 through 297 )
8X-RAY DIFFRACTION8chain 'A' and (resid 298 through 330 )
9X-RAY DIFFRACTION9chain 'A' and (resid 331 through 349 )
10X-RAY DIFFRACTION10chain 'E' and (resid 324 through 328 )
11X-RAY DIFFRACTION11chain 'E' and (resid 329 through 339 )

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