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- PDB-3d8c: Factor inhibiting HIF-1 alpha D201G mutant in complex with ZN(II)... -

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Basic information

Entry
Database: PDB / ID: 3d8c
TitleFactor inhibiting HIF-1 alpha D201G mutant in complex with ZN(II), alpha-ketoglutarate and HIF-1 alpha 19mer
Components
  • HYPOXIA-INDUCIBLE FACTOR 1 ALPHA
  • Hypoxia-inducible factor 1 alpha inhibitor
KeywordsTRANSCRIPTION REGULATOR / OXIDOREDUCTASE / FIH / HIF / DSBH / OXYGENASE / TRANSCRIPTION / HYPOXIA / INHIBITOR 2-OXOGLUTARATE / ASPARAGINYL HYDROXYLASE / Dioxygenase / Iron / Metal-binding / Nucleus / Transcription regulation
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 / positive regulation of vasculogenesis / carboxylic acid binding / 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 / positive regulation of vasculogenesis / carboxylic acid binding / ankyrin repeat binding / Notch binding / oxygen sensor activity / negative regulation of Notch signaling pathway / NF-kappaB binding / positive regulation of myoblast differentiation / ferrous iron binding / transcription corepressor activity / RNA polymerase II-specific DNA-binding transcription factor binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / zinc ion binding / nucleoplasm / cytoplasm / cytosol
Similarity search - Function
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 / RmlC-like jelly roll fold / Helix Hairpins ...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 / RmlC-like jelly roll fold / Helix Hairpins / Jelly Rolls / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / Hypoxia-inducible factor 1-alpha inhibitor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / ISOMORPHOUS WITH 1H2N / Resolution: 2.1 Å
AuthorsMcDonough, M.A. / Chowdhury, R. / Schofield, C.J.
Citation
Journal: J.Biol.Chem. / Year: 2008
Title: Evidence that two enzyme-derived histidine ligands are sufficient for iron binding and catalysis by factor inhibiting HIF (FIH).
Authors: Hewitson, K.S. / Holmes, S.L. / Ehrismann, D. / Hardy, A.P. / Chowdhury, R. / Schofield, C.J. / McDonough, M.A.
#1: Journal: J.Biol.Chem. / Year: 2003
Title: Structure of Factor-Inhibiting Hypoxia-Inducible Factor (Hif) Reveals Mechanism of Oxidative Modification of Hif-1 Alpha
Authors: Elkins, J.M. / Hewitson, K.S. / Mcneill, L.A. / Seibel, J.F. / Schlemminger, I. / Pugh, C.W. / Ratcliffe, P.J. / Schofield, C.J.
#2: Journal: J.Am.Chem.Soc. / Year: 2005
Title: Selective Inhibition of Factor Inhibiting Hypoxia Inducible Factor
Authors: Mcdonough, M.A. / Mcneill, L.A. / Tilliet, M. / Papamicael, C.A. / Chen, Q.Y. / Banerji, B. / Hewitson, K.S. / Schofield, C.J.
History
DepositionMay 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
B: HYPOXIA-INDUCIBLE FACTOR 1 ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8177
Polymers42,3212
Non-polymers4965
Water4,017223
1
A: Hypoxia-inducible factor 1 alpha inhibitor
B: HYPOXIA-INDUCIBLE FACTOR 1 ALPHA
hetero molecules

A: Hypoxia-inducible factor 1 alpha inhibitor
B: HYPOXIA-INDUCIBLE FACTOR 1 ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,63414
Polymers84,6434
Non-polymers99110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area6890 Å2
ΔGint-44 kcal/mol
Surface area30570 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-7 kcal/mol
Surface area16990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.427, 86.427, 148.065
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 AB

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


Mass: 40270.246 Da / Num. of mol.: 1 / Mutation: D201G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIF1AN, FIH1 / Plasmid: PET28A(+) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9NWT6, peptide-aspartate beta-dioxygenase
#2: Protein/peptide HYPOXIA-INDUCIBLE FACTOR 1 ALPHA / HIF-1 ALPHA / HIF1 ALPHA / ARNT- INTERACTING PROTEIN / MEMBER OF PAS PROTEIN 1 / MOP1


Mass: 2051.189 Da / Num. of mol.: 1 / Fragment: CTAD / Source method: obtained synthetically / Details: SYNTHETIC PEPTIDE FRAGMENT OF HIF-1 ALPHA

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Non-polymers , 5 types, 228 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 3.08 Å3/Da / Density % sol: 63 %
Description: REJECTION CRITERIA AS REJECTION PROBABILITY, REJECTION
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.6M AMMONIUM SULPHATE, 6% PEG400, 0.1M HEPES PH7.5, 24MG/ML PROTEIN WITH 1MM FE(II)SO4, 1MM ALPHA-KETOGLUTARATE, 1MM HIF-1ALPHA PEPTIDE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298.0K, PH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9696 / Wavelength: 0.9696 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 19, 2008 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.96961
20.96961
ReflectionResolution: 2.1→50 Å / Num. all: 33971 / Num. obs: 33850 / % possible obs: 99.7 % / Redundancy: 13.9 % / Biso Wilson estimate: 28.7 Å2 / Rmerge(I) obs: 0.101 / Rsym value: 0.0434 / Net I/σ(I): 23.18
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.743 / Mean I/σ(I) obs: 3.66 / Num. unique all: 3288 / Rsym value: 0.2569 / % possible all: 98.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
PXGENdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1phasing
RefinementMethod to determine structure: ISOMORPHOUS WITH 1H2N
Starting model: 1H2N

1h2n


Resolution: 2.1→38.65 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 139071.03 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.256 3216 10.1 %RANDOM
Rwork0.218 ---
obs0.218 31888 95.2 %-
all-31888 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 82.0785 Å2 / ksol: 0.355882 e/Å3
Displacement parametersBiso mean: 56.4 Å2
Baniso -1Baniso -2Baniso -3
1--6.12 Å20 Å20 Å2
2---6.12 Å20 Å2
3---12.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.1→38.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2822 0 27 223 3072
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.34 511 10.6 %
Rwork0.29 4331 -
obs--88.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2gol.pargol.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION52og.par2og.top

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