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- PDB-1h2k: Factor Inhibiting HIF-1 alpha in complex with HIF-1 alpha fragmen... -

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Basic information

Entry
Database: PDB / ID: 1h2k
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 / PHOSPHORYLATION
Function / homology
Function and homology information


epithelial cell differentiation involved in mammary gland alveolus development / neural fold elevation formation / iris morphogenesis / intestinal epithelial cell maturation / positive regulation of nitric oxide metabolic process / hypoxia-inducible factor-1alpha signaling pathway / positive regulation of chemokine-mediated signaling pathway / elastin metabolic process / regulation of transforming growth factor beta2 production / glandular epithelial cell maturation ...epithelial cell differentiation involved in mammary gland alveolus development / neural fold elevation formation / iris morphogenesis / intestinal epithelial cell maturation / positive regulation of nitric oxide metabolic process / hypoxia-inducible factor-1alpha signaling pathway / positive regulation of chemokine-mediated signaling pathway / elastin metabolic process / regulation of transforming growth factor beta2 production / glandular epithelial cell maturation / hypoxia-inducible factor-asparagine dioxygenase / : / [protein]-asparagine 3-dioxygenase activity / peptidyl-histidine dioxygenase activity / hemoglobin biosynthetic process / cardiac ventricle morphogenesis / connective tissue replacement involved in inflammatory response wound healing / negative regulation of mesenchymal cell apoptotic process / peptidyl-aspartic acid 3-dioxygenase activity / negative regulation of growth / positive regulation of hormone biosynthetic process / regulation of vascular endothelial growth factor receptor signaling pathway / Cellular response to hypoxia / retina vasculature development in camera-type eye / mesenchymal cell apoptotic process / regulation of protein neddylation / negative regulation of bone mineralization / PTK6 Expression / intracellular oxygen homeostasis / collagen metabolic process / B-1 B cell homeostasis / carboxylic acid binding / positive regulation of vasculogenesis / vascular endothelial growth factor production / ankyrin repeat binding / dopaminergic neuron differentiation / transcription regulator activator activity / STAT3 nuclear events downstream of ALK signaling / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / negative regulation of thymocyte apoptotic process / lactate metabolic process / positive regulation of cytokine production involved in inflammatory response / negative regulation of TOR signaling / insulin secretion involved in cellular response to glucose stimulus / positive regulation of vascular endothelial growth factor receptor signaling pathway / Notch binding / response to iron ion / neural crest cell migration / Regulation of gene expression by Hypoxia-inducible Factor / oxygen sensor activity / embryonic hemopoiesis / regulation of glycolytic process / motile cilium / DNA-binding transcription repressor activity / PTK6 promotes HIF1A stabilization / DNA-binding transcription activator activity / digestive tract morphogenesis / muscle cell cellular homeostasis / positive regulation of neuroblast proliferation / axonal transport of mitochondrion / bone mineralization / heart looping / response to muscle activity / E-box binding / intracellular glucose homeostasis / TOR signaling / outflow tract morphogenesis / positive regulation of vascular endothelial growth factor production / positive regulation of macroautophagy / positive regulation of epithelial cell migration / cellular response to interleukin-1 / epithelial to mesenchymal transition / negative regulation of Notch signaling pathway / neuroblast proliferation / positive regulation of blood vessel endothelial cell migration / chondrocyte differentiation / NF-kappaB binding / positive regulation of myoblast differentiation / positive regulation of insulin secretion involved in cellular response to glucose stimulus / embryonic placenta development / cis-regulatory region sequence-specific DNA binding / positive regulation of chemokine production / lactation / positive regulation of endothelial cell proliferation / axon cytoplasm / negative regulation of miRNA transcription / positive regulation of erythrocyte differentiation / positive regulation of glycolytic process / response to reactive oxygen species / transcription corepressor binding / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Hsp90 protein binding / ferrous iron binding / euchromatin / transcription coactivator binding / cerebral cortex development / visual learning / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / cellular response to virus
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 1-alpha bHLH domain / Hypoxia-inducible factor, alpha subunit-like / Hypoxia-inducible factor-1 / Cupin-like domain 8 / Cupin-like domain ...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 1-alpha bHLH 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. / JmjC domain / JmjC domain profile. / Jelly Rolls / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / 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 / MAD / Resolution: 2.15 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)45,2306
Polymers44,8352
Non-polymers3954
Water3,495194
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)90,46112
Polymers89,6704
Non-polymers7908
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)86.161, 86.161, 146.656
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 / Protein/peptide , 2 types, 2 molecules AS

#1: Protein FACTOR INHIBITING HIF1


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/peptide HYPOXIA-INDUCIBLE FACTOR 1 ALPHA / HIF-1 ALPHA / ARNT INTERACTING PROTEIN / MEMBER OF PAS PROTEIN 1


Mass: 4506.937 Da / Num. of mol.: 1
Fragment: C-TERMINAL TRANSACTIVATION DOMAIN FRAGMENT, RESIDUES 786-826
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, 198 molecules

#3: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#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.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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, ARGON ATMOSPHERE, 11MG/ML PROTEIN WITH 1MM FE(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: 2.15→18.17 Å / Num. obs: 30574 / % possible obs: 99.2 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 9.9
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 1.5 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.15→18.5 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.588 / SU ML: 0.147 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.213 2340 7.7 %RANDOM
Rwork0.178 ---
obs0.18 28171 99.3 %-
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: 25.73 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20 Å2
2---0.27 Å20 Å2
3---0.55 Å2
Refinement stepCycle: LAST / Resolution: 2.15→18.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2875 0 21 194 3090
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212973
X-RAY DIFFRACTIONr_bond_other_d0.0010.022561
X-RAY DIFFRACTIONr_angle_refined_deg1.3741.9494044
X-RAY DIFFRACTIONr_angle_other_deg0.72235979
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0183352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.69815515
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0860.2416
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023333
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02604
X-RAY DIFFRACTIONr_nbd_refined0.2180.3714
X-RAY DIFFRACTIONr_nbd_other0.2040.32499
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.5259
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0870.54
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2450.318
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2480.372
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2550.513
X-RAY DIFFRACTIONr_symmetry_hbond_other0.0520.51
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.15→2.21 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.257 152
Rwork0.222 1906
Refinement TLS params.Method: refined / Origin x: 21.662 Å / Origin y: 27.462 Å / Origin z: 28.237 Å
111213212223313233
T0.1474 Å2-0.0099 Å2-0.0455 Å2-0.0149 Å20.0363 Å2--0.0919 Å2
L1.0098 °20.6963 °20.484 °2-2.2577 °21.042 °2--1.2037 °2
S0.0288 Å °-0.1525 Å °-0.04 Å °0.1459 Å °0.0002 Å °0.1021 Å °0.1876 Å °-0.0468 Å °-0.029 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 349
2X-RAY DIFFRACTION1S795 - 823
Refinement
*PLUS
Rfactor Rfree: 0.213 / Rfactor Rwork: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS

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