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- PDB-5l0s: human POGLUT1 in complex with Factor VII EGF1 and UDP -

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Basic information

Entry
Database: PDB / ID: 5l0s
Titlehuman POGLUT1 in complex with Factor VII EGF1 and UDP
Components
  • Coagulation factor VII
  • Protein O-glucosyltransferase 1
KeywordsTRANSFERASE / transferase glycosyltransferase GT-B glucosyltransferase
Function / homology
Function and homology information


EGF-domain serine glucosyltransferase / EGF-domain serine xylosyltransferase / EGF-domain serine glucosyltransferase activity / EGF-domain serine xylosyltransferase activity / muscle tissue development / regulation of gastrulation / protein O-linked glycosylation via serine / UDP-xylosyltransferase activity / Pre-NOTCH Processing in the Endoplasmic Reticulum / UDP-glucosyltransferase activity ...EGF-domain serine glucosyltransferase / EGF-domain serine xylosyltransferase / EGF-domain serine glucosyltransferase activity / EGF-domain serine xylosyltransferase activity / muscle tissue development / regulation of gastrulation / protein O-linked glycosylation via serine / UDP-xylosyltransferase activity / Pre-NOTCH Processing in the Endoplasmic Reticulum / UDP-glucosyltransferase activity / circulatory system development / coagulation factor VIIa / response to Thyroid stimulating hormone / response to 2,3,7,8-tetrachlorodibenzodioxine / response to astaxanthin / response to thyrotropin-releasing hormone / response to genistein / serine-type peptidase complex / positive regulation of platelet-derived growth factor receptor signaling pathway / glucosyltransferase activity / response to vitamin K / response to carbon dioxide / paraxial mesoderm development / response to thyroxine / positive regulation of leukocyte chemotaxis / axial mesoderm development / protein O-linked glycosylation / response to cholesterol / response to growth hormone / positive regulation of positive chemotaxis / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of Notch signaling pathway / gastrulation / positive regulation of TOR signaling / endomembrane system / positive regulation of blood coagulation / animal organ regeneration / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / somitogenesis / Removal of aminoterminal propeptides from gamma-carboxylated proteins / serine-type peptidase activity / BMAL1:CLOCK,NPAS2 activates circadian gene expression / protein processing / Golgi lumen / circadian rhythm / response to estrogen / blood coagulation / response to estradiol / collagen-containing extracellular matrix / vesicle / response to hypoxia / positive regulation of cell migration / endoplasmic reticulum lumen / signaling receptor binding / serine-type endopeptidase activity / calcium ion binding / endoplasmic reticulum / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Glycosyl transferase CAP10 domain / Glycosyl transferase family 90 / Putative lipopolysaccharide-modifying enzyme. / 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. ...Glycosyl transferase CAP10 domain / Glycosyl transferase family 90 / Putative lipopolysaccharide-modifying enzyme. / 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
URIDINE-5'-DIPHOSPHATE / Coagulation factor VII / Protein O-glucosyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsLi, Z. / Rini, J.M.
CitationJournal: Nat Commun / Year: 2017
Title: Structural basis of Notch O-glucosylation and O-xylosylation by mammalian protein-O-glucosyltransferase 1 (POGLUT1).
Authors: Li, Z. / Fischer, M. / Satkunarajah, M. / Zhou, D. / Withers, S.G. / Rini, J.M.
History
DepositionJul 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Database references / Category: citation
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
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
Revision 1.3Mar 24, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line ..._chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein O-glucosyltransferase 1
B: Coagulation factor VII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,89510
Polymers46,5672
Non-polymers1,3288
Water6,792377
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-33 kcal/mol
Surface area17800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.580, 76.920, 82.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide / Sugars , 3 types, 5 molecules AB

#1: Protein Protein O-glucosyltransferase 1 / CAP10-like 46 kDa protein / hCLP46 / KTEL motif-containing protein 1 / Myelodysplastic syndromes ...CAP10-like 46 kDa protein / hCLP46 / KTEL motif-containing protein 1 / Myelodysplastic syndromes relative protein / O-glucosyltransferase Rumi homolog / hRumi / Protein O-xylosyltransferase


Mass: 42077.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: POGLUT1, C3orf9, CLP46, KTELC1, MDSRP, MDS010, UNQ490/PRO1006
Plasmid: PB-T-PAF / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human)
References: UniProt: Q8NBL1, Transferases; Glycosyltransferases; Hexosyltransferases, protein xylosyltransferase
#2: Protein/peptide Coagulation factor VII / / Proconvertin / Serum prothrombin conversion accelerator / SPCA


Mass: 4489.917 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F7 / Plasmid: pMal / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P08709, coagulation factor VIIa
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 382 molecules

#4: 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
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 2.41 Å3/Da / Density % sol: 49.04 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG5000 MME, 50 mM MES pH 6.5, 2mM CaCl2, 250mM NaCl, 5% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 79619 / % possible obs: 99 % / Redundancy: 6.4 % / Biso Wilson estimate: 17.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Net I/σ(I): 17.61
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.898 / Mean I/σ(I) obs: 1.68 / CC1/2: 0.653 / % possible all: 95

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→44.001 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 13.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1588 3981 5 %0
Rwork0.1394 75631 --
obs0.1404 79612 99.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.35 Å2 / Biso mean: 29.8733 Å2 / Biso min: 11.02 Å2
Refinement stepCycle: final / Resolution: 1.45→44.001 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3240 0 136 377 3753
Biso mean--29.26 37.73 -
Num. residues----395
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083484
X-RAY DIFFRACTIONf_angle_d1.0374741
X-RAY DIFFRACTIONf_chiral_restr0.077487
X-RAY DIFFRACTIONf_plane_restr0.007606
X-RAY DIFFRACTIONf_dihedral_angle_d16.2381322
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.45-1.46770.27431290.28092455258492
1.4677-1.48630.27431350.26042569270496
1.4863-1.50580.23331410.2472679282099
1.5058-1.52650.22661410.212226722813100
1.5265-1.54830.24481400.19892664280499
1.5483-1.57140.19571420.184627002842100
1.5714-1.59590.18481400.179926592799100
1.5959-1.62210.18331420.158626942836100
1.6221-1.65010.17191410.149826742815100
1.6501-1.68010.17211430.151927192862100
1.6801-1.71240.14771420.143726962838100
1.7124-1.74730.1751410.142726902831100
1.7473-1.78530.16021410.139326812822100
1.7853-1.82690.14651430.132727162859100
1.8269-1.87260.15041430.126427112854100
1.8726-1.92320.1571420.12227012843100
1.9232-1.97980.13941430.119927142857100
1.9798-2.04370.13851420.117226952837100
2.0437-2.11670.14321440.118327322876100
2.1167-2.20150.12631420.118127072849100
2.2015-2.30170.17131440.121327272871100
2.3017-2.4230.15731440.121127382882100
2.423-2.57480.14631430.12627252868100
2.5748-2.77360.14481450.127327512896100
2.7736-3.05260.13871440.130627442888100
3.0526-3.49420.14441470.13227752922100
3.4942-4.40160.1471450.12822764290999
4.4016-44.02150.18581520.16572879303198
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)
13.0889-0.7220.87071.014-0.52161.811-0.0797-0.3268-0.00960.08190.17820.1347-0.0321-0.4829-0.11850.1886-0.01440.020.29030.04140.13624.249230.678834.7269
22.1986-0.74930.27862.066-0.60383.98190.0087-0.0854-0.35890.0604-0.0368-0.14490.42930.3246-0.04740.20620.0813-0.06380.22010.030.306932.147814.142530.9797
32.49560.1531.0862.1973-0.00512.8180.0425-0.0756-0.13050.0528-0.0018-0.18160.03260.2421-0.0190.11420.0249-0.02450.15650.00250.158827.882222.032727.9822
41.3764-0.43380.41651.6933-0.57111.55760.05180.0356-0.0403-0.00470.0066-0.0565-0.01310.1154-0.02930.1102-0.0046-0.00880.1116-0.00370.124319.715227.477521.3237
52.3868-0.41980.4932.340.30662.38280.11950.1968-0.0611-0.1537-0.02570.1844-0.0187-0.176-0.0950.14250.0004-0.00940.18390.03160.13153.209331.83788.6209
62.6061.4862-0.24651.0390.61173.01430.19690.7825-0.4751-0.3282-0.13590.08470.21860.0461-0.06740.22930.0141-0.04990.2333-0.03450.16258.61424.49932.0898
71.6142-0.0610.16871.6156-0.01051.81650.05580.1746-0.0325-0.1750.04590.0922-0.0376-0.0273-0.090.1357-0.0003-0.01220.14510.00450.10589.39131.51699.9377
82.1683-0.35010.34271.0583-0.57971.57620.0144-0.045-0.10530.02890.11580.1417-0.0189-0.2589-0.12210.12080.0011-0.00060.15940.0340.14051.912730.571221.1033
99.2715-0.68883.73661.1922-0.53933.7791-0.2391-0.23560.57610.23260.13670.1234-0.5022-0.29430.13130.26380.0550.02370.15790.00810.19664.814942.044525.7739
102.4021-0.54070.21081.9414-0.24141.8238-0.0393-0.235-0.07650.26430.0323-0.40910.07360.3734-0.0190.16760.0132-0.06190.22480.00650.209230.09623.907834.6518
114.6822-2.3767-1.084.2242-0.19515.9624-0.04910.178-0.665-0.1245-0.1435-0.09150.77270.19320.13760.32130.04740.01260.2602-0.060.295526.163218.15027.2699
124.64942.44880.50592.50720.91386.45860.20560.32220.2486-0.5250.2964-1.2609-0.12281.2457-0.19390.34770.01520.14140.452-0.0710.548635.735126.62314.5462
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 68 )A30 - 68
2X-RAY DIFFRACTION2chain 'A' and (resid 69 through 104 )A69 - 104
3X-RAY DIFFRACTION3chain 'A' and (resid 105 through 139 )A105 - 139
4X-RAY DIFFRACTION4chain 'A' and (resid 140 through 197 )A140 - 197
5X-RAY DIFFRACTION5chain 'A' and (resid 198 through 227 )A198 - 227
6X-RAY DIFFRACTION6chain 'A' and (resid 228 through 248 )A228 - 248
7X-RAY DIFFRACTION7chain 'A' and (resid 249 through 279 )A249 - 279
8X-RAY DIFFRACTION8chain 'A' and (resid 280 through 331 )A280 - 331
9X-RAY DIFFRACTION9chain 'A' and (resid 332 through 349 )A332 - 349
10X-RAY DIFFRACTION10chain 'A' and (resid 350 through 385 )A350 - 385
11X-RAY DIFFRACTION11chain 'B' and (resid 47 through 71 )B47 - 71
12X-RAY DIFFRACTION12chain 'B' and (resid 72 through 85 )B72 - 85

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