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- PDB-5kxh: mouse POFUT1 in complex with mouse Factor VII EGF1 and GDP -

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Basic information

Entry
Database: PDB / ID: 5kxh
Titlemouse POFUT1 in complex with mouse Factor VII EGF1 and GDP
Components
  • Coagulation factor VII
  • GDP-fucose protein O-fucosyltransferase 1
KeywordsTRANSFERASE / glycosyltransferase O-fucosylation GT-B inverting
Function / homology
Function and homology information


Extrinsic Pathway of Fibrin Clot Formation / 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 / peptide-O-fucosyltransferase / protein O-linked fucosylation / peptide-O-fucosyltransferase activity / fucosyltransferase activity / regulation of Notch signaling pathway / fucose metabolic process ...Extrinsic Pathway of Fibrin Clot Formation / 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 / peptide-O-fucosyltransferase / protein O-linked fucosylation / peptide-O-fucosyltransferase activity / fucosyltransferase activity / regulation of Notch signaling pathway / fucose metabolic process / 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 / response to vitamin K / response to carbon dioxide / response to thyroxine / protein O-linked glycosylation / response to cholesterol / response to growth hormone / positive regulation of positive chemotaxis / positive regulation of leukocyte chemotaxis / positive regulation of TOR signaling / positive regulation of blood coagulation / animal organ regeneration / somitogenesis / Notch signaling pathway / response to nutrient levels / protein processing / circadian rhythm / response to estrogen / blood coagulation / response to estradiol / nervous system development / heart development / angiogenesis / endopeptidase activity / vesicle / response to hypoxia / serine-type endopeptidase activity / signaling receptor binding / calcium ion binding / endoplasmic reticulum / extracellular space / extracellular region / membrane
Similarity search - Function
GDP-fucose protein O-fucosyltransferase 1 / GDP-fucose protein O-fucosyltransferase / GDP-fucose protein O-fucosyltransferase / Rossmann fold - #11340 / Rossmann fold - #11350 / 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 ...GDP-fucose protein O-fucosyltransferase 1 / GDP-fucose protein O-fucosyltransferase / GDP-fucose protein O-fucosyltransferase / Rossmann fold - #11340 / Rossmann fold - #11350 / 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. / Epidermal growth factor-like domain. / EGF-like domain profile. / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Coagulation factor VII / GDP-fucose protein O-fucosyltransferase 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsLi, Z. / Rini, J.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: Recognition of EGF-like domains by the Notch-modifying O-fucosyltransferase POFUT1.
Authors: Li, Z. / Han, K. / Pak, J.E. / Satkunarajah, M. / Zhou, D. / Rini, J.M.
History
DepositionJul 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Database references
Revision 1.2Jun 28, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.5Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Jul 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 1.7Mar 24, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_strain

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GDP-fucose protein O-fucosyltransferase 1
B: Coagulation factor VII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8556
Polymers44,8772
Non-polymers9784
Water9,062503
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-14 kcal/mol
Surface area17100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.970, 66.540, 110.640
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, 4 molecules AB

#1: Protein GDP-fucose protein O-fucosyltransferase 1 / Peptide-O-fucosyltransferase 1 / O-FucT-1


Mass: 40457.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pofut1 / Plasmid: PB-T-PAF
Details (production host): PiggyBac mammlian stable expression vector
Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: Q91ZW2, peptide-O-fucosyltransferase
#2: Protein/peptide Coagulation factor VII / Serum prothrombin conversion accelerator


Mass: 4419.888 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: F7, Cf7 / Production host: Escherichia coli / References: UniProt: P70375, 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / References: peptide-O-fucosyltransferase
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 , 3 types, 505 molecules

#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C10H15N5O11P2 / References: peptide-O-fucosyltransferase / Comment: GDP, energy-carrying molecule*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 503 / 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: 2.13 Å3/Da / Density % sol: 42.36 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 20% PEG 2000 MME 50mM Tris 8.5 / Temp details: room temperature

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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: Apr 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.328→47.039 Å / Num. obs: 87243 / % possible obs: 98 % / Redundancy: 7.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.107 / Net I/σ(I): 9.2
Reflection shellResolution: 1.33→1.38 Å / Redundancy: 5.7 % / Rmerge(I) obs: 1.024 / Mean I/σ(I) obs: 1.2 / CC1/2: 0.467 / % possible all: 87

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.33→47.039 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 17.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1697 4306 5 %0
Rwork0.152 81798 --
obs0.1529 86104 96.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.24 Å2 / Biso mean: 23.2376 Å2 / Biso min: 7.15 Å2
Refinement stepCycle: final / Resolution: 1.33→47.039 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3073 0 100 503 3676
Biso mean--28.04 29.47 -
Num. residues----388
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053304
X-RAY DIFFRACTIONf_angle_d0.9014518
X-RAY DIFFRACTIONf_chiral_restr0.066480
X-RAY DIFFRACTIONf_plane_restr0.006580
X-RAY DIFFRACTIONf_dihedral_angle_d17.8681226
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.33-1.34510.3564880.33471716180462
1.3451-1.36090.36821200.28692263238381
1.3609-1.37750.2751400.25212496263691
1.3775-1.3950.2411220.23262694281696
1.395-1.41330.24121440.2142720286498
1.4133-1.43270.2081310.20542745287698
1.4327-1.45320.21151390.19162765290498
1.4532-1.47490.21081430.19012711285498
1.4749-1.49790.19131670.17682695286299
1.4979-1.52250.18641520.16792736288899
1.5225-1.54870.20531350.15712774290999
1.5487-1.57690.15771440.15352756290099
1.5769-1.60720.17631420.15312740288299
1.6072-1.640.18091440.1522775291999
1.64-1.67570.16381390.15292790292999
1.6757-1.71470.19741500.14982745289599
1.7147-1.75760.17511600.15612757291799
1.7576-1.80510.17791370.15372815295299
1.8051-1.85820.18741460.15162782292899
1.8582-1.91820.1521550.14372768292399
1.9182-1.98670.15891290.143928152944100
1.9867-2.06630.16271450.138228022947100
2.0663-2.16030.14311350.132728302965100
2.1603-2.27420.14861360.136828332969100
2.2742-2.41670.13941700.132827982968100
2.4167-2.60330.15431610.132528252986100
2.6033-2.86520.15271590.141428372996100
2.8652-3.27970.15881570.14228663023100
3.2797-4.13170.15611720.138728903062100
4.1317-47.06850.16661440.152230593203100
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)
10.7810.31670.28411.18410.6841.0268-0.0278-0.07660.09810.0413-0.13170.1798-0.0004-0.12840.14920.09810.0009-0.00160.095-0.03610.102411.22938.424423.9906
21.68160.38940.50611.00680.72650.8121-0.25090.09330.4543-0.3065-0.03790.2378-0.4587-0.01640.130.2850.0054-0.09420.1427-0.01980.246211.853153.527419.4147
30.77260.31490.20431.99920.97811.1285-0.0385-0.0277-0.00310.0726-0.0157-0.01880.00680.00130.05180.07360.0066-0.00260.08690.00120.05917.533633.172521.5293
42.2235-0.59530.04431.4770.79432.0242-0.03010.2569-0.0323-0.0994-0.05910.0131-0.060.05120.0530.0755-0.01010.00770.1081-0.00840.060819.217120.0924.2838
57.2873-2.67241.28996.84024.08084.1332-0.04270.29820.8493-0.4040.0073-0.1463-0.73330.13540.02330.32-0.0075-0.06780.12280.03370.201411.32546.27477.3673
61.4407-0.74270.15551.18721.12833.70680.2494-0.08820.7645-0.0349-0.1367-0.5301-1.31371.2177-0.1350.3554-0.09970.00050.26720.05740.278517.934243.24922.1464
74.1991-1.94942.80251.79290.0934.8894-0.09840.95021.1458-1.06770.0761-0.9346-0.88340.91690.00850.5189-0.1060.09340.32010.09140.411815.752546.08-0.1974
82.6368-1.7306-0.66071.7221-1.19774.7107-0.12670.47860.4593-0.6844-0.09560.5465-0.4638-0.16240.1860.37080.042-0.13970.18010.00940.26633.522741.74670.0067
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 32 through 121 )A32 - 121
2X-RAY DIFFRACTION2chain 'A' and (resid 122 through 186 )A122 - 186
3X-RAY DIFFRACTION3chain 'A' and (resid 187 through 234 )A187 - 234
4X-RAY DIFFRACTION4chain 'A' and (resid 235 through 384 )A235 - 384
5X-RAY DIFFRACTION5chain 'B' and (resid 89 through 100 )B89 - 100
6X-RAY DIFFRACTION6chain 'B' and (resid 101 through 105 )B101 - 105
7X-RAY DIFFRACTION7chain 'B' and (resid 106 through 112 )B106 - 112
8X-RAY DIFFRACTION8chain 'B' and (resid 113 through 126 )B113 - 126

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