[English] 日本語
Yorodumi
- PDB-7ybc: Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR do... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ybc
TitleAspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with (S)-4-hydroxy-4-methyl-2-oxoglutarate and factor X-derived peptide (39mer-4Ser)
Components
  • Aspartyl/asparaginyl beta-hydroxylase
  • Coagulation factor XFactor X
KeywordsOXIDOREDUCTASE / Aspartyl/asparaginyl beta-hydroxylase / Dioxygenase
Function / homology
Function and homology information


peptide-aspartate beta-dioxygenase / regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / 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 / limb morphogenesis / cortical endoplasmic reticulum ...peptide-aspartate beta-dioxygenase / regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / 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 / limb morphogenesis / cortical endoplasmic reticulum / coagulation factor Xa / pattern specification process / positive regulation of intracellular protein transport / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / activation of cysteine-type endopeptidase activity / Extrinsic Pathway of Fibrin Clot Formation / face morphogenesis / positive regulation of leukocyte chemotaxis / structural constituent of muscle / positive regulation of calcium ion transport into cytosol / response to ATP / roof of mouth development / positive regulation of ryanodine-sensitive calcium-release channel activity / Protein hydroxylation / positive regulation of proteolysis / detection of calcium ion / positive regulation of TOR signaling / calcium ion homeostasis / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Ion homeostasis / regulation of ryanodine-sensitive calcium-release channel activity / sarcoplasmic reticulum membrane / calcium channel complex / cellular response to calcium ion / Intrinsic Pathway of Fibrin Clot Formation / muscle contraction / calcium ion transmembrane transport / regulation of protein stability / Stimuli-sensing channels / phospholipid binding / Golgi lumen / blood coagulation / cell population proliferation / transmembrane transporter binding / electron transfer activity / positive regulation of cell migration / negative regulation of cell population proliferation / external side of plasma membrane / endoplasmic reticulum lumen / serine-type endopeptidase activity / calcium ion binding / endoplasmic reticulum membrane / structural molecule activity / positive regulation of DNA-templated transcription / endoplasmic reticulum / proteolysis / extracellular space / 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 / Coagulation Factor Xa inhibitory site ...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-type aspartate/asparagine hydroxylation site / EGF-like domain / 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 2. / EGF-like domain signature 1. / EGF-like domain / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Tetratricopeptide-like helical domain superfamily / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Chem-IOW / : / Coagulation factor X / Aspartyl/asparaginyl beta-hydroxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsNakashima, Y. / Brewitz, L. / Schofield, C.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: To Be Published
Title: Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with (S)-4-hydroxy-4-methyl-2-oxoglutarate and factor X-derived peptide (39mer-4Ser)
Authors: Nakashima, Y. / Brewitz, L. / Schofield, C.J.
History
DepositionJun 29, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)53,9195
Polymers53,5962
Non-polymers3233
Water5,585310
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-15 kcal/mol
Surface area19740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.372, 87.049, 124.396
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

-
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 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q12797, peptide-aspartate beta-dioxygenase
#2: Protein/peptide Coagulation factor X / Factor X / Stuart factor / Stuart-Prower factor


Mass: 4190.384 Da / Num. of mol.: 1 / Mutation: C90S, C95S, C112S, C121S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Gene: F10 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00742, coagulation factor Xa

-
Non-polymers , 4 types, 313 molecules

#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-IOW / (2~{S})-2-methyl-2-oxidanyl-4-oxidanylidene-pentanedioic acid


Mass: 176.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O6 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Sodium acetate trihydrate, 20 % w/v Polyethylene glycol 3,350, 0.1 M Bis Tris propane

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.84→71.32 Å / Num. obs: 48417 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 27.61 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.279 / Rpim(I) all: 0.081 / Rrim(I) all: 0.29 / Net I/σ(I): 8.5
Reflection shellResolution: 1.84→1.87 Å / Redundancy: 13.2 % / Rmerge(I) obs: 4.176 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 2389 / CC1/2: 0.399 / Rpim(I) all: 1.195 / Rrim(I) all: 4.345 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JTC

5jtc


Resolution: 1.84→43.6 Å / SU ML: 0.2188 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.5508
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1987 2324 4.81 %
Rwork0.1776 46033 -
obs0.1786 48357 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.06 Å2
Refinement stepCycle: LAST / Resolution: 1.84→43.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3581 0 0 310 3891
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00493713
X-RAY DIFFRACTIONf_angle_d0.78595026
X-RAY DIFFRACTIONf_chiral_restr0.0445528
X-RAY DIFFRACTIONf_plane_restr0.0045659
X-RAY DIFFRACTIONf_dihedral_angle_d20.25691394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.880.33931530.32272626X-RAY DIFFRACTION98.69
1.88-1.920.30411480.29642630X-RAY DIFFRACTION99.46
1.92-1.960.29871640.2662635X-RAY DIFFRACTION99.96
1.96-2.010.29191190.24232703X-RAY DIFFRACTION100
2.01-2.060.27321270.22282662X-RAY DIFFRACTION99.96
2.06-2.130.22581350.21252691X-RAY DIFFRACTION100
2.13-2.190.19511260.18072715X-RAY DIFFRACTION99.96
2.19-2.270.24061230.18152676X-RAY DIFFRACTION100
2.27-2.360.20221110.17462704X-RAY DIFFRACTION100
2.36-2.470.24451430.17442691X-RAY DIFFRACTION100
2.47-2.60.19231350.16762697X-RAY DIFFRACTION100
2.6-2.760.23381480.17482704X-RAY DIFFRACTION100
2.76-2.980.20761460.17162718X-RAY DIFFRACTION99.97
2.98-3.280.20521400.17342718X-RAY DIFFRACTION100
3.28-3.750.14861230.15482757X-RAY DIFFRACTION100
3.75-4.730.13931460.13362779X-RAY DIFFRACTION99.97
4.73-43.60.19451370.18542927X-RAY DIFFRACTION99.77
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)
10.467860874496-0.152993387091-0.4791436950941.3125873603-1.172715755351.398088539230.189802593346-0.01650582884340.0922138591403-0.0788637883492-0.03403766763070.001692711252770.0654387307526-0.1630414524270.00220155361570.308893083668-0.0764576028283-0.02655816536780.280234886931-0.007204564508680.250694567887-16.4226408393-13.893830682312.1514564595
21.38219021430.3278223579330.859924265990.7544563209480.1601625789321.15795165887-0.03759055608340.253369726883-0.0179665436055-0.1061147521220.0887482114642-0.01608912604790.0377322816210.1697564966160.0004014129243730.19962764828-0.003452442121010.004418897912940.216818388617-0.001676348928720.215455282371-3.98926691954-25.608834248445.766678427
30.00715296941525-0.01192878734270.0062629234680.0335300394317-0.01376614678910.00467797769970.1728626371160.07659391415810.076908454693-0.0627272752959-0.09810958872030.0366964002098-0.0783827392527-0.0508102426838-0.0002070979413660.3653002163710.0221591109894-0.03831746671540.654604834444-0.01656495207120.346592778434-10.4741373048-18.789948538238.5762695587
40.005636282310970.004828351315645.23187295896E-50.0102635713302-0.01177238163230.01217957101960.07492708577020.03591934173060.130844161549-0.1123451113-0.01286397385460.0488501253247-0.0982559789967-0.190612239431.44664699763E-50.37565296104-0.0678535384357-0.03700085816380.4770396393410.006959386656090.313395224012-14.6273932573-21.766173210231.5899213895
50.02031437461020.012417334188-0.009885546387480.0239749976339-0.006094302369570.0134121402995-0.34223507580.0247404184255-0.0196447701182-0.168819694622-0.2623774705390.143342357251-0.08498475119040.0360372142118-0.0002284994685880.499389367402-0.128704880817-0.05557002571250.6273937102490.07582681453510.312311034217-8.64669770845-15.847854250628.1199394951
60.114470305323-0.0116087151215-0.2478803601170.002329604659880.043038745590.6953551742990.05250566895470.001740644920880.02527611145850.0738319855691-0.0204150184334-0.1215344997940.02310081115980.0465153678545-8.39309183132E-60.46542388653-0.187351937795-0.1311629773520.7729270844220.1868126174760.521274879363-1.62750604403-9.7975559176720.1105423758
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 330 through 538 )
2X-RAY DIFFRACTION2chain 'A' and (resid 539 through 758 )
3X-RAY DIFFRACTION3chain 'B' and (resid 99 through 103 )
4X-RAY DIFFRACTION4chain 'B' and (resid 104 through 108 )
5X-RAY DIFFRACTION5chain 'B' and (resid 109 through 113 )
6X-RAY DIFFRACTION6chain 'B' and (resid 114 through 116 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more