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- PDB-9ho3: Aspartyl/Asparaginyl beta-hydroxylase (AspH) in complex with Fe, ... -

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Basic information

Entry
Database: PDB / ID: 9ho3
TitleAspartyl/Asparaginyl beta-hydroxylase (AspH) in complex with Fe, 2OG, nitric oxide, and Factor X peptide fragment
Components
  • Aspartyl/asparaginyl beta-hydroxylase
  • Coagulation factor X
KeywordsOXIDOREDUCTASE / Aspartyl/Asparaginyl beta-hydroxylase / AspH / 2-oxoglutarate / nitric oxide / oxygen mimick
Function / homology
Function and homology information


peptide-aspartate beta-dioxygenase / : / regulation of protein depolymerization / activation of store-operated calcium channel activity / regulation of cell communication by electrical coupling / junctional sarcoplasmic reticulum membrane / peptidyl-aspartic acid 3-dioxygenase activity / sarcoplasmic reticulum lumen / cortical endoplasmic reticulum / limb morphogenesis ...peptide-aspartate beta-dioxygenase / : / regulation of protein depolymerization / activation of store-operated calcium channel activity / regulation of cell communication by electrical coupling / junctional sarcoplasmic reticulum membrane / peptidyl-aspartic acid 3-dioxygenase activity / sarcoplasmic reticulum lumen / cortical endoplasmic reticulum / limb morphogenesis / positive regulation of intracellular protein transport / coagulation factor Xa / pattern specification process / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / : / face morphogenesis / structural constituent of muscle / response to ATP / positive regulation of proteolysis / roof of mouth development / Protein hydroxylation / positive regulation of calcium ion transport into cytosol / positive regulation of TOR signaling / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / : / Gamma-carboxylation of protein precursors / detection of calcium ion / Removal of aminoterminal propeptides from gamma-carboxylated proteins / regulation of cytosolic calcium ion concentration / calcium ion homeostasis / : / Ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / sarcoplasmic reticulum membrane / calcium channel complex / cellular response to calcium ion / muscle contraction / regulation of protein stability / phospholipid binding / Golgi lumen / Stimuli-sensing channels / calcium ion transmembrane transport / blood coagulation / transmembrane transporter binding / electron transfer activity / cell population proliferation / positive regulation of cell migration / endoplasmic reticulum lumen / negative regulation of cell population proliferation / serine-type endopeptidase activity / external side of plasma membrane / calcium ion binding / endoplasmic reticulum membrane / positive regulation of DNA-templated transcription / structural molecule activity / endoplasmic reticulum / proteolysis / : / extracellular region / plasma membrane
Similarity search - Function
Aspartyl beta-hydroxylase/Triadin domain / Aspartyl/asparaginyl beta-hydroxylase family / Aspartyl beta-hydroxylase N-terminal region / Aspartyl/asparaginy/proline hydroxylase / Aspartyl/Asparaginyl beta-hydroxylase / Isopenicillin N synthase-like superfamily / Tetratricopeptide repeat / Peptidase S1A, coagulation factor VII/IX/X/C/Z / : / Coagulation factor-like, Gla domain superfamily ...Aspartyl beta-hydroxylase/Triadin domain / Aspartyl/asparaginyl beta-hydroxylase family / Aspartyl beta-hydroxylase N-terminal region / Aspartyl/asparaginy/proline hydroxylase / Aspartyl/Asparaginyl beta-hydroxylase / Isopenicillin N synthase-like superfamily / Tetratricopeptide repeat / Peptidase S1A, coagulation factor VII/IX/X/C/Z / : / Coagulation factor-like, Gla domain superfamily / Coagulation Factor Xa inhibitory site / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / TPR repeat region circular profile. / Epidermal growth factor-like domain. / TPR repeat profile. / Tetratricopeptide repeats / EGF-like domain profile. / Tetratricopeptide repeat / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Tetratricopeptide-like helical domain superfamily / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / : / NITRIC OXIDE / Coagulation factor X / Aspartyl/asparaginyl beta-hydroxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
Authorsde Munnik, M. / Rabe, P. / Brasnett, A. / Brewitz, L. / Schofield, C.J.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V001892/1 United Kingdom
Wellcome Trust227298/Z/23/Z United Kingdom
CitationJournal: Nat Commun / Year: 2026
Title: Structural basis of the promiscuity of the unusual Fe(II) and 2-oxoglutarate dependent human aspartate/asparagine-beta-hydroxylase.
Authors: de Munnik, M. / Brasnett, A. / Zhou, T. / Myers, W. / Wang, Y. / Chatterjee, K. / Tumber, A. / Marshall, S.A. / Simon, P.S. / Aller, P. / Shilova, A. / Axford, D. / Makita, H. / Paley, D.W. ...Authors: de Munnik, M. / Brasnett, A. / Zhou, T. / Myers, W. / Wang, Y. / Chatterjee, K. / Tumber, A. / Marshall, S.A. / Simon, P.S. / Aller, P. / Shilova, A. / Axford, D. / Makita, H. / Paley, D.W. / Tiwari, V. / Stead, A.T. / Dehe, S. / Sanchez, H. / Rosenberg, D.J. / Alonso-Mori, R. / Bhowmick, A. / Yano, J. / Yachandra, V.K. / Park, J. / Park, S. / Orville, A.M. / Brewitz, L. / Kern, J.F. / Schofield, C.J. / Rabe, P.
History
DepositionDec 11, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aspartyl/asparaginyl beta-hydroxylase
B: Coagulation factor X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8907
Polymers53,5962
Non-polymers2945
Water2,702150
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-33 kcal/mol
Surface area19160 Å2
Unit cell
Length a, b, c (Å)49.830, 86.490, 123.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Aspartyl/asparaginyl beta-hydroxylase / Aspartate beta-hydroxylase / ASP beta-hydroxylase / Peptide-aspartate beta-dioxygenase


Mass: 49405.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASPH, BAH / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q12797, peptide-aspartate beta-dioxygenase
#2: Protein/peptide Coagulation factor X


Mass: 4190.384 Da / Num. of mol.: 1 / Mutation: C90S, C95S, C112S, C121S / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P00742

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Non-polymers , 6 types, 155 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Fe
#6: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#7: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.75 Å3/Da / Density % sol: 55.3 % / Description: needle morphology, 4 um x 4 um x 300 um
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M bis tris propane pH 7.5, 16% PEG3350, 0.1 M KSCN

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryogenic / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97628 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 19, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 2.39→49.83 Å / Num. obs: 21828 / % possible obs: 100 % / Redundancy: 12.8 % / CC1/2: 0.994 / Rmerge(I) obs: 0.368 / Rpim(I) all: 0.107 / Rrim(I) all: 0.383 / Χ2: 0.99 / Net I/σ(I): 8.4 / Num. measured all: 279350
Reflection shellResolution: 2.39→2.45 Å / % possible obs: 100 % / Redundancy: 10.3 % / Rmerge(I) obs: 2.305 / Num. measured all: 16227 / Num. unique obs: 1573 / CC1/2: 0.388 / Rpim(I) all: 0.746 / Rrim(I) all: 2.426 / Χ2: 0.86 / Net I/σ(I) obs: 1.1

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Processing

Software
NameVersionClassification
PHENIX1.21.1-5286refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.39→46.2 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2422 1046 4.81 %
Rwork0.1988 --
obs0.2009 21768 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.39→46.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3507 0 15 150 3672
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033609
X-RAY DIFFRACTIONf_angle_d0.5344886
X-RAY DIFFRACTIONf_dihedral_angle_d12.5611325
X-RAY DIFFRACTIONf_chiral_restr0.04517
X-RAY DIFFRACTIONf_plane_restr0.004642
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.520.38891560.32592895X-RAY DIFFRACTION100
2.52-2.670.281360.28122898X-RAY DIFFRACTION100
2.67-2.880.30291470.26782932X-RAY DIFFRACTION100
2.88-3.170.30581500.23922945X-RAY DIFFRACTION100
3.17-3.630.26431540.21112927X-RAY DIFFRACTION100
3.63-4.570.20611360.15733014X-RAY DIFFRACTION100
4.57-46.20.18491670.15813111X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 9.5918 Å / Origin y: -19.9547 Å / Origin z: -29.6558 Å
111213212223313233
T0.3228 Å20.0166 Å20.0181 Å2-0.392 Å20.0128 Å2--0.3626 Å2
L0.067 °20.1023 °20.0777 °2-0.1727 °20.2719 °2--1.3353 °2
S-0.0001 Å °-0.0253 Å °-0.0067 Å °0.056 Å °0.0062 Å °0.0493 Å °0.0444 Å °-0.0304 Å °-0.0043 Å °
Refinement TLS groupSelection details: all

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