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- PDB-5ky2: mouse POFUT1 in complex with O-glucosylated mouse Factor VII EGF1... -

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Basic information

Entry
Database: PDB / ID: 5ky2
Titlemouse POFUT1 in complex with O-glucosylated mouse Factor VII EGF1 and GDP
Components
  • Coagulation factor VII
  • GDP-fucose protein O-fucosyltransferase 1
KeywordsTRANSFERASE / glycosyltransferase
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 / Laminin / Laminin ...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 / Laminin / Laminin / 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 / Ribbon / 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 / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
beta-D-glucopyranose / 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 / molecular replacement / Resolution: 1.47 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 1.4Jan 8, 2020Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _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: GDP-fucose protein O-fucosyltransferase 1
B: Coagulation factor VII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2199
Polymers44,8772
Non-polymers1,3427
Water6,738374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-9 kcal/mol
Surface area17220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.965, 67.138, 109.357
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 , 2 types, 2 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 / 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 (E. coli) / References: UniProt: P70375, coagulation factor VIIa

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Sugars , 2 types, 3 molecules

#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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
#6: 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, 378 molecules

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


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 374 / 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: 42.13 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 20% PEG2000 MME, 50 mM Tris pH 8.5

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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: 1.47→50 Å / Num. obs: 66097 / % possible obs: 100 % / Redundancy: 7.2 % / Biso Wilson estimate: 18 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.123 / Net I/σ(I): 8.3
Reflection shellResolution: 1.47→1.52 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.524 / Mean I/σ(I) obs: 1 / CC1/2: 0.466 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.47→46.935 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.98
RfactorNum. reflection% reflectionSelection details
Rfree0.1749 3135 5.02 %0
Rwork0.1532 ---
obs0.1543 62405 94.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 120.85 Å2 / Biso mean: 30.2703 Å2 / Biso min: 10.89 Å2
Refinement stepCycle: final / Resolution: 1.47→46.935 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3133 0 158 374 3665
Biso mean--36.92 33.76 -
Num. residues----395
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083488
X-RAY DIFFRACTIONf_angle_d1.2834765
X-RAY DIFFRACTIONf_chiral_restr0.07504
X-RAY DIFFRACTIONf_plane_restr0.007618
X-RAY DIFFRACTIONf_dihedral_angle_d15.3461299
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4705-1.49340.3083720.37091330140247
1.4934-1.51790.31931080.32072013212172
1.5179-1.54410.28531250.27282337246284
1.5441-1.57220.27611300.24192572270291
1.5722-1.60240.22251310.21472652278395
1.6024-1.63510.24431590.20822758291798
1.6351-1.67070.22571350.19462791292699
1.6707-1.70960.23671620.182127762938100
1.7096-1.75230.21831540.171528082962100
1.7523-1.79970.17581390.159428332972100
1.7997-1.85260.18121440.15228342978100
1.8526-1.91240.17821520.145527942946100
1.9124-1.98080.17551370.143228572994100
1.9808-2.06010.17171420.138928362978100
2.0601-2.15390.15341350.133428332968100
2.1539-2.26740.16341440.140128563000100
2.2674-2.40950.14741620.133928232985100
2.4095-2.59550.18451680.135228513019100
2.5955-2.85670.15161560.144428613017100
2.8567-3.26990.17281620.144828953057100
3.2699-4.11940.15751720.134128893061100
4.1194-46.95930.16151460.160530713217100
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)
10.9470.0780.1671.69090.96881.4514-0.0174-0.07450.05880.0215-0.12770.1940.0125-0.15490.12670.105-0.0037-0.00420.1078-0.02370.114311.037239.139224.0361
26.4452-0.7148-1.25112.95170.76822.05360.11260.83381.0998-0.5294-0.03550.2643-0.841-0.2886-0.0140.38040.0109-0.1190.23730.07820.36189.600958.503716.1846
30.64980.01170.03622.02151.05451.0628-0.05450.04040.0652-0.1081-0.01710.055-0.1542-0.00110.05840.118-0.0112-0.01310.13260.01220.117215.591738.689517.2066
43.1262-0.7138-0.19071.95841.22392.9594-0.03970.4826-0.0329-0.2312-0.0394-0.0501-0.14820.14740.06430.1187-0.01380.01270.188-0.00370.105120.156220.6183.9687
54.1855-0.9914-0.02631.6362-1.17954.96870.05620.09261.3538-0.5548-0.0569-1.0886-1.691.23980.05620.605-0.17580.03730.33360.03860.596119.07850.52077.3011
64.05010.6007-0.91383.370.39396.9447-0.06530.2970.4729-0.5345-0.2160.124-0.6621-0.14350.26060.33450.0502-0.06590.19760.00250.26368.155444.37486.7728
73.0634-0.41643.48117.4917-1.53324.1156-0.17421.24760.5269-1.4320.0428-0.9926-0.5940.74420.05950.6022-0.02780.13730.38630.09360.357316.814944.75330.4166
83.8536-1.465-0.66994.2409-3.34345.9891-0.18520.52630.4768-1.0952-0.03110.7507-0.3437-0.22370.15410.6740.1094-0.22160.27890.00650.33123.224542.1538-0.3926
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 124 )A30 - 124
2X-RAY DIFFRACTION2chain 'A' and (resid 125 through 144 )A125 - 144
3X-RAY DIFFRACTION3chain 'A' and (resid 145 through 254 )A145 - 254
4X-RAY DIFFRACTION4chain 'A' and (resid 255 through 384 )A255 - 384
5X-RAY DIFFRACTION5chain 'B' and (resid 87 through 93 )B87 - 93
6X-RAY DIFFRACTION6chain 'B' and (resid 94 through 100 )B94 - 100
7X-RAY DIFFRACTION7chain 'B' and (resid 101 through 112 )B101 - 112
8X-RAY DIFFRACTION8chain 'B' and (resid 113 through 126 )B113 - 126

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