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- PDB-1h2m: Factor Inhibiting HIF-1 alpha in complex with HIF-1 alpha fragmen... -

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Basic information

Entry
Database: PDB / ID: 1h2m
TitleFactor Inhibiting HIF-1 alpha in complex with HIF-1 alpha fragment peptide
Components
  • FACTOR INHIBITING HIF1
  • HYPOXIA-INDUCIBLE FACTOR 1 ALPHA
KeywordsTRANSCRIPTION ACTIVATOR/INHIBITOR / TRANSCRIPTION ACTIVATOR-INHIBITOR COMPLEX / FIH / HIF / DSBH / OXYGENASE / TRANSCRIPTION / HYPOXIA / 2- OXOGLUTARATE / ASPARAGINYL HYDROXYLASE / HYDROXYLASE
Function / homology
Function and homology information


epithelial cell differentiation involved in mammary gland alveolus development / neural fold elevation formation / iris morphogenesis / positive regulation of chemokine-mediated signaling pathway / hypoxia-inducible factor-1alpha signaling pathway / elastin metabolic process / glandular epithelial cell maturation / hypoxia-inducible factor-asparagine dioxygenase / : / regulation of transforming growth factor beta2 production ...epithelial cell differentiation involved in mammary gland alveolus development / neural fold elevation formation / iris morphogenesis / positive regulation of chemokine-mediated signaling pathway / hypoxia-inducible factor-1alpha signaling pathway / elastin metabolic process / glandular epithelial cell maturation / hypoxia-inducible factor-asparagine dioxygenase / : / regulation of transforming growth factor beta2 production / [protein]-asparagine 3-dioxygenase activity / connective tissue replacement involved in inflammatory response wound healing / peptidyl-histidine dioxygenase activity / cardiac ventricle morphogenesis / negative regulation of mesenchymal cell apoptotic process / hemoglobin biosynthetic process / peptidyl-aspartic acid 3-dioxygenase activity / positive regulation of hormone biosynthetic process / mesenchymal cell apoptotic process / positive regulation of mitophagy / Cellular response to hypoxia / retina vasculature development in camera-type eye / intestinal epithelial cell maturation / negative regulation of growth / regulation of protein neddylation / collagen metabolic process / PTK6 Expression / intracellular oxygen homeostasis / negative regulation of bone mineralization / carboxylic acid binding / B-1 B cell homeostasis / positive regulation of vasculogenesis / vascular endothelial growth factor production / lactate metabolic process / ankyrin repeat binding / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / transcription regulator activator activity / dopaminergic neuron differentiation / STAT3 nuclear events downstream of ALK signaling / positive regulation of cytokine production involved in inflammatory response / negative regulation of thymocyte apoptotic process / motile cilium / positive regulation of vascular endothelial growth factor receptor signaling pathway / oxygen sensor activity / positive regulation of signaling receptor activity / insulin secretion involved in cellular response to glucose stimulus / response to iron ion / negative regulation of TOR signaling / response to muscle activity / Notch binding / neural crest cell migration / Regulation of gene expression by Hypoxia-inducible Factor / regulation of glycolytic process / embryonic hemopoiesis / DNA-binding transcription repressor activity / regulation of aerobic respiration / DNA-binding transcription activator activity / PTK6 promotes HIF1A stabilization / digestive tract morphogenesis / muscle cell cellular homeostasis / positive regulation of neuroblast proliferation / axonal transport of mitochondrion / positive regulation of epithelial cell migration / negative regulation of Notch signaling pathway / heart looping / bone mineralization / outflow tract morphogenesis / E-box binding / intracellular glucose homeostasis / positive regulation of insulin secretion involved in cellular response to glucose stimulus / TOR signaling / NF-kappaB binding / neuroblast proliferation / positive regulation of vascular endothelial growth factor production / negative regulation of reactive oxygen species metabolic process / embryonic placenta development / epithelial to mesenchymal transition / positive regulation of blood vessel endothelial cell migration / positive regulation of myoblast differentiation / cellular response to interleukin-1 / cis-regulatory region sequence-specific DNA binding / chondrocyte differentiation / positive regulation of chemokine production / axon cytoplasm / positive regulation of endothelial cell proliferation / lactation / positive regulation of glycolytic process / positive regulation of erythrocyte differentiation / negative regulation of miRNA transcription / response to reactive oxygen species / nuclear receptor binding / positive regulation of nitric-oxide synthase activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / ferrous iron binding / Hsp90 protein binding / euchromatin / visual learning / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / NOTCH1 Intracellular Domain Regulates Transcription / cerebral cortex development
Similarity search - Function
Hypoxia-inducible factor-1 alpha / Clavaminate synthase-like / Hypoxia-inducible factor 1-alpha inhibitor, domain II / HIF-1 alpha, transactivation domain, C-terminal / HIF-1 alpha C terminal transactivation domain / Hypoxia-inducible factor, alpha subunit-like / Hypoxia-inducible factor-1 / Cupin-like domain 8 / Cupin-like domain / PAS fold-3 ...Hypoxia-inducible factor-1 alpha / Clavaminate synthase-like / Hypoxia-inducible factor 1-alpha inhibitor, domain II / HIF-1 alpha, transactivation domain, C-terminal / HIF-1 alpha C terminal transactivation domain / Hypoxia-inducible factor, alpha subunit-like / Hypoxia-inducible factor-1 / Cupin-like domain 8 / Cupin-like domain / PAS fold-3 / PAS fold / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / A domain family that is part of the cupin metalloenzyme superfamily. / Jelly Rolls / JmjC domain / JmjC domain profile. / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / RmlC-like jelly roll fold / PAS domain superfamily / Helix Hairpins / Jelly Rolls / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
N-OXALYLGLYCINE / Hypoxia-inducible factor 1-alpha / Hypoxia-inducible factor 1-alpha inhibitor / Hypoxia-inducible factor 1-alpha inhibitor
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsElkins, J.M. / Hewitson, K.S. / McNeill, L.A. / Schlemminger, I. / Seibel, J.F. / Schofield, C.J.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Structure of Factor-Inhibiting Hypoxia-Inducible Factor (Hif) Reveals Mechanism of Oxidative Modification of Hif-1Alpha
Authors: Elkins, J.M. / Hewitson, K.S. / McNeill, L.A. / Seibel, J.F. / Schlemminger, I. / Pugh, C. / Ratcliffe, P. / Schofield, C.J.
History
DepositionAug 12, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2002Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2018Group: Database references / Category: citation / citation_author / Item: _citation.page_last / _citation_author.name
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FACTOR INHIBITING HIF1
S: HYPOXIA-INDUCIBLE FACTOR 1 ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3956
Polymers45,9912
Non-polymers4054
Water1,78399
1
A: FACTOR INHIBITING HIF1
S: HYPOXIA-INDUCIBLE FACTOR 1 ALPHA
hetero molecules

A: FACTOR INHIBITING HIF1
S: HYPOXIA-INDUCIBLE FACTOR 1 ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,79012
Polymers91,9814
Non-polymers8098
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
MethodPQS
Unit cell
Length a, b, c (Å)86.249, 86.249, 148.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsTHE PROTEIN IS A DIMERIC FORMED BY CHAIN A.A HETERODIMERIC ASSOCIATION OF CHAIN A WITH CHAIN SPRODUCES A TETRAMER.THE BURIED SURFACE AREA SHOWN BELOW IS AN AVERAGECALCULATED FOR THE HETEROTETRAMER AND DOES NOTCORRESPOND TO THE BURIED SURFACE AREA FOR THEHOMODIMER OF CHAIN A

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Components

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Protein , 2 types, 2 molecules AS

#1: Protein FACTOR INHIBITING HIF1 / FIH1


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: Q969Q7, UniProt: Q9NWT6*PLUS
#2: Protein HYPOXIA-INDUCIBLE FACTOR 1 ALPHA / HIF-1 ALPHA / ARNT INTERACTING PROTEIN / MEMBER OF PAS PROTEIN 1 / MOP1 / HIF1 ALPHA / HIF1A.


Mass: 5662.284 Da / Num. of mol.: 1
Fragment: C-TERMINAL TRANSACTIVATION DOMAIN FRAGMENT, RESIDUES 775-826
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-GP-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q16665

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Non-polymers , 4 types, 103 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 / 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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 3.4 Å3/Da / Density % sol: 63 %
Crystal growpH: 7.5
Details: 1.2M AMMONIUM SULPHATE, 4% PEG400, 0.1M HEPES PH7.5, 11MG/ML PROTEIN WITH 1MM ZN(II), 2.5MM NOG AND 2.5MM PEPTIDE, pH 7.50
Crystal grow
*PLUS
Temperature: 17 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.2 Mammonium sulfate1reservoir
24 %PEG4001reservoir
30.1 MHEPES1reservoirpH7.5
411 mg/mlFIH1drop
51 mMFe2+1drop
62 mM2OG/NOG1drop
71 mMCAD fragment1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: May 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.5→87.71 Å / Num. obs: 20058 / % possible obs: 99.7 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 10.7
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 2.6 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→18 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.935 / SU B: 9.825 / SU ML: 0.224 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.334 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1516 7.6 %RANDOM
Rwork0.192 ---
obs0.194 18404 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å20 Å20 Å2
2---0.68 Å20 Å2
3---1.35 Å2
Refinement stepCycle: LAST / Resolution: 2.5→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2859 0 21 99 2979
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0212957
X-RAY DIFFRACTIONr_bond_other_d0.0010.022546
X-RAY DIFFRACTIONr_angle_refined_deg1.6121.9484022
X-RAY DIFFRACTIONr_angle_other_deg0.83235944
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0243350
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.01515512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0970.2413
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023315
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02602
X-RAY DIFFRACTIONr_nbd_refined0.2320.3731
X-RAY DIFFRACTIONr_nbd_other0.2140.32492
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.5193
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1260.56
X-RAY DIFFRACTIONr_metal_ion_refined0.0540.52
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.315
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2550.354
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2440.57
X-RAY DIFFRACTIONr_symmetry_hbond_other0.0530.51
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7611.51767
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.42122846
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2231190
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6784.51176
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: 2.5→2.56 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.297 106
Rwork0.227 1267
Refinement TLS params.Method: refined / Origin x: 22.599 Å / Origin y: 26.92 Å / Origin z: 28.634 Å
111213212223313233
T0.1903 Å2-0.0025 Å2-0.0536 Å2-0.0302 Å20.0309 Å2--0.0452 Å2
L0.7638 °20.7977 °20.42 °2-2.2674 °21.0769 °2--1.0629 °2
S0.0306 Å °-0.1225 Å °-0.049 Å °0.1656 Å °0.0303 Å °0.0478 Å °0.2046 Å °0.0231 Å °-0.0609 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 349
2X-RAY DIFFRACTION1S795 - 822
Refinement
*PLUS
Rfactor Rfree: 0.225 / Rfactor Rwork: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS

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