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- PDB-9xs7: Factor inhibiting HIF-1 alpha in complex with Mn(II) and rhein -

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Basic information

Entry
Database: PDB / ID: 9xs7
TitleFactor inhibiting HIF-1 alpha in complex with Mn(II) and rhein
ComponentsHypoxia-inducible factor 1-alpha inhibitor
KeywordsOXIDOREDUCTASE / Factor inhibiting HIF-1 alpha / Dioxygenase
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 / positive regulation of myoblast differentiation / NF-kappaB binding / 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 / DNA-templated transcription / nucleoplasm / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
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. / RmlC-like jelly roll fold
Similarity search - Domain/homology
: / Chem-RHN / Hypoxia-inducible factor 1-alpha inhibitor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsNakashima, Y. / Akhsanitaqwim, Y. / Morita, H.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24K18295 Japan
Japan Society for the Promotion of Science (JSPS)25K02418 Japan
CitationJournal: J.Nat.Prod. / Year: 2026
Title: Structural Insights into Metal-Chelating Natural Inhibitors of Factor Inhibiting HIF-1 alpha.
Authors: Akhsanitaqwim, Y. / Nakashima, Y. / Ikumi, N. / Morita, H.
History
DepositionNov 20, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6673
Polymers40,3281
Non-polymers3392
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.670, 86.670, 146.345
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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


Mass: 40328.281 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 BL21(DE3) (bacteria)
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: Chemical ChemComp-RHN / 4,5-dihydroxy-9,10-dioxo-9,10-dihydroanthracene-2-carboxylic acid / Rhein / Rhubarb Yellow


Mass: 284.220 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H8O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.41 Å3/Da / Density % sol: 63.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% (w/v) PEG 3,350, 0.2 M sodium malonate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.005 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 2, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.005 Å / Relative weight: 1
ReflectionResolution: 2.51→48.78 Å / Num. obs: 18719 / % possible obs: 95 % / Redundancy: 7.1 % / Biso Wilson estimate: 54.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.2
Reflection shellResolution: 2.51→2.61 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.918 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2127 / CC1/2: 0.686 / % possible all: 96.7

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→42.51 Å / SU ML: 0.2941 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.1891
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2313 1865 10 %
Rwork0.1889 16793 -
obs0.1932 18658 94.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.08 Å2
Refinement stepCycle: LAST / Resolution: 2.51→42.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2761 0 21 64 2846
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00322865
X-RAY DIFFRACTIONf_angle_d0.59733900
X-RAY DIFFRACTIONf_chiral_restr0.0455393
X-RAY DIFFRACTIONf_plane_restr0.0044516
X-RAY DIFFRACTIONf_dihedral_angle_d18.69511049
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.580.29271450.24891301X-RAY DIFFRACTION96.79
2.58-2.650.30781420.24441282X-RAY DIFFRACTION96.15
2.65-2.740.28121420.24011284X-RAY DIFFRACTION96.42
2.74-2.840.28181440.24181286X-RAY DIFFRACTION95.91
2.84-2.950.30671430.23011286X-RAY DIFFRACTION95.97
2.95-3.090.26711430.22151296X-RAY DIFFRACTION95.68
3.09-3.250.27111430.22231281X-RAY DIFFRACTION95.12
3.25-3.450.24481420.20321280X-RAY DIFFRACTION94.74
3.45-3.720.24781420.19681283X-RAY DIFFRACTION93.87
3.72-4.090.24921430.17511282X-RAY DIFFRACTION93.38
4.09-4.680.16331410.13721279X-RAY DIFFRACTION92.87
4.68-5.90.20041450.1661303X-RAY DIFFRACTION92.17
5.9-42.510.21291500.18461350X-RAY DIFFRACTION89.5
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)
11.31174021358-0.0650327369047-0.01997507088891.084796304191.198712844851.19935340086-0.182492534582-0.256676751431-0.2314284265860.575261950580.01478722248880.5788956307110.150721244926-0.1956472730260.0002965764891730.5143068636820.04475369631210.1377754876060.312906563392-0.004762049191260.42701178938715.6746753388-24.402502233821.5949085178
21.99866496493-0.624834376758-0.279914046280.5583028107070.2700136310050.2324082480030.1130363337290.870808548778-0.512003870839-0.439378184953-0.44281063220.248482975115-0.557959238958-0.330254005291-0.07157476200620.7640173112480.126178571812-0.07885360740140.6550147019140.02593754167560.41112455690813.8547152594-21.5704655832-3.63221589763
33.543671591090.0205113937632-0.574426652010.004556772637840.06467641333971.62097679541-0.3786457448090.2206937714040.987950546402-0.4082382295650.0397157088369-0.0853468903808-0.7407013679740.434933324524-0.3704338401061.03840608862-0.02714875041170.1479442645850.4203453818280.1969859656020.55827999449122.4263115227-5.3281079713910.498078373
40.838587935267-0.759026596315-0.6798605925521.556467206550.8734728416411.00262053407-0.04393267149490.05402381595190.04332126897380.02949297190630.1301181932530.0371795756877-0.03197033811990.07778873757270.001046523635640.357230857817-0.00149606528380.070477142180.231604640489-0.009750569151080.28910384324726.8658425741-33.04347342338.85092336531
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 82 )
2X-RAY DIFFRACTION2chain 'A' and (resid 83 through 149 )
3X-RAY DIFFRACTION3chain 'A' and (resid 150 through 166 )
4X-RAY DIFFRACTION4chain 'A' and (resid 167 through 349 )

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