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- PDB-5f84: Crystal structure of Drosophila Poglut1 (Rumi) complexed with its... -

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Basic information

Entry
Database: PDB / ID: 5f84
TitleCrystal structure of Drosophila Poglut1 (Rumi) complexed with its glycoprotein product (glucosylated EGF repeat) and UDP
Components
  • Coagulation factor IXFactor IX
  • O-glucosyltransferase rumi
KeywordsTransferase/Hydrolase / glycosyltransferase / protein O-glucosyltransferase / Notch regulation / EGF repeat / Transferase-Hydrolase complex
Function / homology
Function and homology information


EGF-domain serine glucosyltransferase activity / EGF-domain serine xylosyltransferase activity / muscle tissue development / rhabdomere development / protein O-linked glycosylation via serine / UDP-xylosyltransferase activity / Defective F9 secretion / Defective gamma-carboxylation of F9 / coagulation factor IXa / UDP-glucosyltransferase activity ...EGF-domain serine glucosyltransferase activity / EGF-domain serine xylosyltransferase activity / muscle tissue development / rhabdomere development / protein O-linked glycosylation via serine / UDP-xylosyltransferase activity / Defective F9 secretion / Defective gamma-carboxylation of F9 / coagulation factor IXa / UDP-glucosyltransferase activity / glucosyltransferase activity / Defective F9 activation / protein O-linked glycosylation / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / zymogen activation / Extrinsic Pathway of Fibrin Clot Formation / Transferases; Glycosyltransferases; Hexosyltransferases / positive regulation of Notch signaling pathway / negative regulation of Notch signaling pathway / Protein hydroxylation / endomembrane system / cell fate commitment / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Removal of aminoterminal propeptides from gamma-carboxylated proteins / Notch signaling pathway / Intrinsic Pathway of Fibrin Clot Formation / Golgi lumen / blood coagulation / collagen-containing extracellular matrix / endopeptidase activity / endoplasmic reticulum lumen / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular exosome / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
Glycosyl transferase CAP10 domain / Glycosyl transferase family 90 / Putative lipopolysaccharide-modifying enzyme. / Endoplasmic reticulum targeting sequence. / 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 ...Glycosyl transferase CAP10 domain / Glycosyl transferase family 90 / Putative lipopolysaccharide-modifying enzyme. / Endoplasmic reticulum targeting sequence. / 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. / Epidermal growth factor-like domain. / EGF-like domain profile. / 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 / 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
beta-D-glucopyranose / URIDINE-5'-DIPHOSPHATE / Coagulation factor IX / O-glucosyltransferase rumi
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsYu, H.J. / Li, H.L.
CitationJournal: Nat. Chem. Biol. / Year: 2016
Title: Structural analysis of Notch-regulating Rumi reveals basis for pathogenic mutations.
Authors: Yu, H. / Takeuchi, H. / Takeuchi, M. / Liu, Q. / Kantharia, J. / Haltiwanger, R.S. / Li, H.
History
DepositionDec 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: O-glucosyltransferase rumi
B: Coagulation factor IX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5959
Polymers52,5302
Non-polymers1,0657
Water1,71195
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-64 kcal/mol
Surface area17950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)271.016, 271.016, 47.427
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-505-

SO4

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Components

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Protein / Protein/peptide / Sugars , 3 types, 3 molecules AB

#1: Protein O-glucosyltransferase rumi


Mass: 46820.172 Da / Num. of mol.: 1 / Fragment: UNP residues 21-407
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: rumi, CG31152 / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
References: UniProt: Q8T045, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Protein/peptide Coagulation factor IX / Factor IX / Christmas factor / Plasma thromboplastin component / PTC


Mass: 5710.229 Da / Num. of mol.: 1 / Fragment: UNP residues 92-130
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F9 / Production host: Escherichia coli (E. coli) / References: UniProt: P00740, coagulation factor IXa
#5: Sugar ChemComp-BGC / beta-D-glucopyranose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 101 molecules

#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.19 Å3/Da / Density % sol: 61.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.62M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 22870 / % possible obs: 99.6 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 15
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.546 / Mean I/σ(I) obs: 1.8 / % possible all: 96.1

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.908 / Cross valid method: THROUGHOUT / ESU R: 0.33 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23932 1167 5.1 %RANDOM
Rwork0.19209 ---
obs0.19446 21603 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.046 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å20.42 Å20 Å2
2--0.83 Å20 Å2
3----1.25 Å2
Refinement stepCycle: 1 / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3323 0 61 95 3479
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.023483
X-RAY DIFFRACTIONr_bond_other_d00.022465
X-RAY DIFFRACTIONr_angle_refined_deg1.2841.9644717
X-RAY DIFFRACTIONr_angle_other_deg4.1963.0055922
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0575402
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.623.39177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.94215585
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9111526
X-RAY DIFFRACTIONr_chiral_restr0.0710.2471
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213819
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02771
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
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: 2.503→2.568 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 86 -
Rwork0.326 1499 -
obs--95.2 %

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