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- PDB-6hl5: Factor Inhibiting HIF (FIH) in complex with zinc, NOG and ASPP1(9... -

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Basic information

Entry
Database: PDB / ID: 6hl5
TitleFactor Inhibiting HIF (FIH) in complex with zinc, NOG and ASPP1(932-954)
Components
  • Apoptosis-stimulating of p53 protein 1
  • 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 / Cellular response to hypoxia / carboxylic acid binding / positive regulation of vasculogenesis ...: / : / hypoxia-inducible factor-asparagine dioxygenase / : / [protein]-asparagine 3-dioxygenase activity / peptidyl-histidine dioxygenase activity / 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 / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / Regulation of TP53 Activity through Association with Co-factors / negative regulation of Notch signaling pathway / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / transcription factor binding / intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of cell cycle / NF-kappaB binding / positive regulation of myoblast differentiation / regulation of signal transduction by p53 class mediator / ferrous iron binding / transcription corepressor activity / p53 binding / regulation of apoptotic process / perinuclear region of cytoplasm / protein homodimerization activity / mitochondrion / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Apoptosis-stimulating of p53 protein 1 / Clavaminate synthase-like / Hypoxia-inducible factor 1-alpha inhibitor, domain II / Domain of unknown function DUF3447 / Cupin-like domain 8 / Cupin-like domain / A domain family that is part of the cupin metalloenzyme superfamily. / Jelly Rolls / JmjC domain / JmjC domain profile. ...Apoptosis-stimulating of p53 protein 1 / Clavaminate synthase-like / Hypoxia-inducible factor 1-alpha inhibitor, domain II / Domain of unknown function DUF3447 / Cupin-like domain 8 / Cupin-like domain / A domain family that is part of the cupin metalloenzyme superfamily. / Jelly Rolls / JmjC domain / JmjC domain profile. / RmlC-like jelly roll fold / SH3 domain / 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 1 / 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. / Chowdhury, R. / 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 ASPP1(932-954)
Authors: Leissing, T.M. / Chowdhury, R. / Clifton, I.J. / Lu, X. / Schofield, C.J.
History
DepositionSep 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,84712
Polymers42,8822
Non-polymers96510
Water2,504139
1
A: Hypoxia-inducible factor 1-alpha inhibitor
S: Apoptosis-stimulating of p53 protein 1
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)87,69424
Polymers85,7644
Non-polymers1,93020
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area10750 Å2
ΔGint-213 kcal/mol
Surface area29320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.198, 86.198, 147.109
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 1 / Protein phosphatase 1 regulatory subunit 13B


Mass: 2466.707 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q96KQ4

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Non-polymers , 5 types, 149 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-ZN / ZINC ION


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


Mass: 147.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#7: Water ChemComp-HOH / water / 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: 3.19 Å3/Da / Density % sol: 61.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Hepes pH = 7.5, 1.2 M ammonium sulfate, 4.5% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.98→56.31 Å / Num. obs: 39456 / % possible obs: 100 % / Redundancy: 18.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17
Reflection shellResolution: 1.98→2.03 Å / Redundancy: 17.9 % / Rmerge(I) obs: 2.35 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2880 / % 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→56.31 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.58
RfactorNum. reflection% reflection
Rfree0.2013 2001 5.11 %
Rwork0.1818 --
obs0.1829 39176 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.98→56.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2779 0 55 139 2973
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142919
X-RAY DIFFRACTIONf_angle_d1.153971
X-RAY DIFFRACTIONf_dihedral_angle_d12.0851699
X-RAY DIFFRACTIONf_chiral_restr0.07407
X-RAY DIFFRACTIONf_plane_restr0.008521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.02950.37361170.36082592X-RAY DIFFRACTION98
2.0295-2.08440.36711140.3242592X-RAY DIFFRACTION98
2.0844-2.14570.33851220.29152620X-RAY DIFFRACTION99
2.1457-2.2150.28881510.26622597X-RAY DIFFRACTION99
2.215-2.29420.27891500.22822594X-RAY DIFFRACTION99
2.2942-2.3860.2651420.21622626X-RAY DIFFRACTION100
2.386-2.49460.21761540.19752618X-RAY DIFFRACTION100
2.4946-2.62610.20241290.18592646X-RAY DIFFRACTION100
2.6261-2.79070.23051620.18712647X-RAY DIFFRACTION100
2.7907-3.00610.22231330.18382658X-RAY DIFFRACTION100
3.0061-3.30860.22711460.182682X-RAY DIFFRACTION100
3.3086-3.78730.18241580.16132694X-RAY DIFFRACTION100
3.7873-4.77120.14741510.13212726X-RAY DIFFRACTION100
4.7712-56.33230.18291720.17972883X-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)
10.8888-0.96370.61342.2154-1.56791.1826-0.2638-0.24130.00820.8283-0.222-0.9928-0.25520.44690.29070.7380.0244-0.2510.43340.00130.6617-10.546329.719822.4751
22.0301-0.63640.38333.8035-1.38822.16920.07610.1899-0.4907-0.0996-0.0592-0.11190.50930.0675-0.0640.56170.0837-0.14720.2889-0.05640.4398-19.271616.408614.4039
31.5614-0.73690.45983.4756-1.19561.53710.25720.6236-0.1065-1.0713-0.2828-0.34190.72470.32460.03070.89950.1737-0.00430.5385-0.10840.464-15.793719.5445-1.0986
41.2148-0.99350.79643.6402-1.82792.39410.0240.062-0.13030.04280.1273-0.00030.1009-0.0569-0.13390.43290.022-0.08250.2406-0.020.3353-25.208330.945110.3276
53.3385-2.8005-0.70939.48621.08914.63740.05790.28620.1477-0.49130.0370.05950.2805-0.0262-0.33130.34720.0075-0.03840.43580.09950.3341-37.901550.2174-4.8662
60.4401-0.13310.67931.4587-1.27561.89510.21430.1605-0.7623-0.22030.21370.78360.2864-0.4399-0.37240.9383-0.2018-0.08250.8942-0.00881.1132-36.275328.6694.5175
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 49 )
2X-RAY DIFFRACTION2chain 'A' and (resid 50 through 95 )
3X-RAY DIFFRACTION3chain 'A' and (resid 96 through 166 )
4X-RAY DIFFRACTION4chain 'A' and (resid 167 through 330 )
5X-RAY DIFFRACTION5chain 'A' and (resid 331 through 349 )
6X-RAY DIFFRACTION6chain 'S' and (resid 938 through 951 )

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