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- PDB-3od4: Crystal Structure of Factor Inhibiting HIF-1 Alpha Complexed with... -

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Basic information

Entry
Database: PDB / ID: 3od4
TitleCrystal Structure of Factor Inhibiting HIF-1 Alpha Complexed with Inhibitor
ComponentsHypoxia-inducible factor 1-alpha inhibitor
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / OXIDOREDUCTASE / ASPARAGINYL HYDROXYLASE / DIOXYGENASE / TRANSCRIPTION / METAL-BINDING / HIF / IRON / HYDROXYLATION / OXYGENASE / NUCLEUS / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
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 / Cellular response to hypoxia / carboxylic acid binding / positive regulation of vasculogenesis / ankyrin repeat binding / oxygen sensor activity ...hypoxia-inducible factor-asparagine dioxygenase / : / [protein]-asparagine 3-dioxygenase activity / peptidyl-histidine dioxygenase activity / peptidyl-aspartic acid 3-dioxygenase activity / Cellular response to hypoxia / carboxylic acid binding / positive regulation of vasculogenesis / ankyrin repeat binding / oxygen sensor activity / Notch binding / negative regulation of Notch signaling pathway / NF-kappaB binding / positive regulation of myoblast differentiation / ferrous iron binding / transcription corepressor activity / perinuclear region of cytoplasm / 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. / Jelly Rolls / JmjC domain / JmjC domain profile. / 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. / Jelly Rolls / JmjC domain / JmjC domain profile. / RmlC-like jelly roll fold / Helix Hairpins / Jelly Rolls / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
8-hydroxyquinoline-5-carboxylic acid / Hypoxia-inducible factor 1-alpha inhibitor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsKing, O.N.F. / Bashford-Rogers, R. / Maloney, D.J. / Jadhav, A. / Heightman, T.D. / Simeonov, A. / Clifton, I.J. / McDonough, M.A. / Schofield, C.J.
CitationJournal: To be Published
Title: Crystal Structure of Factor Inhibiting HIF-1 Alpha Complexed with Inhibitor
Authors: King, O.N.F. / Bashford-Rogers, R. / Maloney, D.J. / Jadhav, A. / Heightman, T.D. / Simeonov, A. / Clifton, I.J. / McDonough, M.A. / Schofield, C.J.
History
DepositionAug 10, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)41,23910
Polymers40,3281
Non-polymers9119
Water2,630146
1
A: Hypoxia-inducible factor 1-alpha inhibitor
hetero molecules

A: Hypoxia-inducible factor 1-alpha inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,47920
Polymers80,6572
Non-polymers1,82218
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area3130 Å2
ΔGint-26 kcal/mol
Surface area32440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.400, 86.400, 147.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-397-

HOH

21A-421-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 40328.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FIH1, HIF1AN / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q9NWT6, peptide-aspartate beta-dioxygenase

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Non-polymers , 5 types, 155 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-8XQ / 8-hydroxyquinoline-5-carboxylic acid


Mass: 189.167 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H7NO3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 3.41 Å3/Da / Density % sol: 63.89 % / Mosaicity: 0.61 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.75M AMMONIUM SULFATE, 0.1M HEPES PH 7.5, 2% PEG 400, 2MM ZNCL2, 0.1MM LIGAND , VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 14, 2009 / Details: Mirrors
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.2→74.513 Å / Num. all: 29076 / Num. obs: 29076 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.9 % / Biso Wilson estimate: 44.5 Å2 / Rsym value: 0.086 / Net I/σ(I): 13.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.2-2.329.20.7310.691.13828741470.2380.7310.693.1100
2.32-2.469.20.4690.4431.83632239560.1530.4690.4434.5100
2.46-2.639.20.3290.3112.53408837160.1070.3290.3116100
2.63-2.849.10.2160.2043.73169334730.0710.2160.2048.7100
2.84-3.119.10.1320.1245.92917432200.0440.1320.12413.3100
3.11-3.488.90.0870.0828.22611429230.0290.0870.08218.7100
3.48-4.028.80.0770.0728.72287825980.0260.0770.07224.9100
4.02-4.928.30.0780.0737.81857822310.0270.0780.07328.399.9
4.92-6.968.20.060.05710.21443217700.0210.060.05727.8100
6.96-42.66780.0410.03915836510420.0140.0410.03930.298

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
PHASERphasing
PHENIX1.6_289refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→38.639 Å / Occupancy max: 1 / Occupancy min: 0.37 / SU ML: 0.27 / σ(F): 0.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2117 1444 5.14 %Random
Rwork0.1758 ---
all0.1776 28069 --
obs0.1776 28069 96.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.062 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso max: 175.97 Å2 / Biso mean: 62.83 Å2 / Biso min: 29.28 Å2
Baniso -1Baniso -2Baniso -3
1--2.8993 Å2-0 Å20 Å2
2---2.8993 Å2-0 Å2
3---5.7986 Å2
Refinement stepCycle: LAST / Resolution: 2.2→38.639 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2797 0 54 146 2997
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012985
X-RAY DIFFRACTIONf_angle_d1.1674059
X-RAY DIFFRACTIONf_chiral_restr0.081401
X-RAY DIFFRACTIONf_plane_restr0.006537
X-RAY DIFFRACTIONf_dihedral_angle_d17.0851104
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2001-2.27870.26691300.222473260391
2.2787-2.36990.2751340.19912480261492
2.3699-2.47780.21371470.17922587273495
2.4778-2.60840.20711460.1792589273596
2.6084-2.77170.23511350.18182630276597
2.7717-2.98570.24841590.1832661282098
2.9857-3.2860.24611570.19822698285599
3.286-3.76110.2221390.15932754289399
3.7611-4.73730.15161440.139128062950100
4.7373-38.64520.20181530.17762947310099
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)
10.0923-0.05420.07480.0297-0.05180.107-0.52160.19360.47710.3667-0.57140.2717-1.15290.26730.00181.211-0.3259-0.25811.0493-0.04841.26097.386727.211910.1394
21.96570.3107-0.10244.62821.0253.2147-0.1297-0.1366-0.0224-0.1021-0.00420.3780.2494-0.1319-0.00030.4447-0.0696-0.20240.22170.02190.334916.56222.257521.0049
30.19090.1144-0.08160.0783-0.01750.1292-0.4202-2.40230.04770.9067-0.30621.3283-0.1076-0.9785-0.00211.0350.0493-0.08140.9823-0.11850.899223.198831.672245.5275
41.04080.88131.21131.8045-0.05382.6731-0.1291-0.5014-0.17671.00880.00380.53971.1622-0.5137-0.00051.057-0.21290.08510.50860.1180.528811.98413.72236.9301
50.33650.89940.293.45641.75242.8939-0.0094-0.0958-0.03170.22960.1686-0.07080.18530.2548-0.00060.515-0.0065-0.15550.2070.01310.362724.120722.215923.2494
61.53061.13260.27831.76180.0942.16970.0722-0.14960.0644-0.04960.0430.444-0.2597-0.1410.00020.59320.0028-0.10790.2549-0.01010.407721.957942.416232.0792
70.4967-0.5312-0.01364.63230.79464.542-0.0627-0.2225-0.0845-0.11850.1682-0.19090.14280.2699-0.00020.4936-0.0159-0.12330.1997-0.00260.331823.828726.023622.8255
83.74221.18461.72563.21540.16491.36910.0376-0.0099-0.29590.05540.1898-0.36020.46480.404-0.00030.4197-0.0035-0.02220.42-0.08630.379139.197943.294435.7837
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 8:24)A8 - 24
2X-RAY DIFFRACTION2(chain A and resid 25:100)A25 - 100
3X-RAY DIFFRACTION3(chain A and resid 101:118)A101 - 118
4X-RAY DIFFRACTION4(chain A and resid 119:161)A119 - 161
5X-RAY DIFFRACTION5(chain A and resid 162:224)A162 - 224
6X-RAY DIFFRACTION6(chain A and resid 225:261)A225 - 261
7X-RAY DIFFRACTION7(chain A and resid 262:306)A262 - 306
8X-RAY DIFFRACTION8(chain A and resid 307:349)A307 - 349

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