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- PDB-2cgo: FACTOR INHIBITING HIF-1 ALPHA with fumarate -

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Basic information

Entry
Database: PDB / ID: 2cgo
TitleFACTOR INHIBITING HIF-1 ALPHA with fumarate
ComponentsHYPOXIA-INDUCIBLE FACTOR 1 ALPHA INHIBITOR
KeywordsOXIDOREDUCTASE / 2-OXOGLUTARATE / ACETYLATION / ACTIVATOR / ALTERNATIVE SPLICING / ASPARAGINYL HYDROXYLASE / DNA-BINDING / DSBH / FI / HIF / HYDROXYLATION / HYPOXIA / NUCLEAR PROTEIN / OXYGENASE / PHOSPHORYLATION / POLYMORPHISM / S-NITROSYLATION / TRANSCRIPTION / TRANSCRIPTION ACTIVATOR/INHIBITOR / TRANSCRIPTION REGULATION / DIOXYGENASE / IRON / METAL-BINDING
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
: / FUMARIC ACID / Hypoxia-inducible factor 1-alpha inhibitor
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMcDonough, M.A. / Clifton, I.J. / Schofield, C.J.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structural and Mechanistic Studies on the Inhibition of the Hypoxia-Inducible Transcription Factor Hydroxylases by Tricarboxylic Acid Cycle Intermediates.
Authors: Hewitson, K. / Lienard, B. / McDonough, M.A. / Clifton, I.J. / Butler, D. / Soares, A.S. / Oldham, N.J. / McNeill, L.A. / Schofield, C.J.
History
DepositionMar 9, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2012Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Feb 21, 2018Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.page_last / _citation_author.name
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr1_label_seq_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Dec 13, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYPOXIA-INDUCIBLE FACTOR 1 ALPHA INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8847
Polymers40,3281
Non-polymers5566
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)86.660, 86.660, 147.349
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein HYPOXIA-INDUCIBLE FACTOR 1 ALPHA INHIBITOR / FACTOR INHIBITING HIF1 / HYPOXIA-INDUCIBLE FACTOR ASPARAGINE HYDROXYLASE / FIH-1


Mass: 40328.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9NWT6, peptide-aspartate beta-dioxygenase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-FUM / FUMARIC ACID


Mass: 116.072 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4O4
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 3.52 Å3/Da / Density % sol: 65 %
Crystal growpH: 7.5
Details: 1.25M AMMONIUM SULFATE, 100MM HEPES PH7.5, 6% PEG400, 1MM IRON (II) SULFATE, 20MM FUMARIC ACID, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 28, 2005
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.3→37.5 Å / Num. obs: 888919 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 13.9 % / Biso Wilson estimate: 54.6 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 28.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 13.9 % / Mean I/σ(I) obs: 2.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H2K

1h2k


Resolution: 2.3→74.74 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / SU B: 11.323 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.227 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.237 2532 9.9 %RANDOM
Rwork0.187 ---
obs0.192 23064 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 43.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å20 Å2
2--0.56 Å20 Å2
3----1.13 Å2
Refinement stepCycle: LAST / Resolution: 2.3→74.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2777 0 29 121 2927
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0222884
X-RAY DIFFRACTIONr_bond_other_d0.0030.021969
X-RAY DIFFRACTIONr_angle_refined_deg2.0121.9563915
X-RAY DIFFRACTIONr_angle_other_deg1.06734776
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2195337
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.68624.645155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.86215471
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0751516
X-RAY DIFFRACTIONr_chiral_restr0.1290.2391
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023217
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02595
X-RAY DIFFRACTIONr_nbd_refined0.2230.2675
X-RAY DIFFRACTIONr_nbd_other0.2090.22105
X-RAY DIFFRACTIONr_nbtor_refined0.190.21377
X-RAY DIFFRACTIONr_nbtor_other0.0950.21473
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2180.2129
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0790.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0490.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1590.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2350.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2250.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5581.52142
X-RAY DIFFRACTIONr_mcbond_other0.311.5680
X-RAY DIFFRACTIONr_mcangle_it1.8522730
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.08131424
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.214.51185
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 171 -
Rwork0.291 1619 -
obs--96.86 %

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