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- PDB-5ky3: mouse POFUT1 in complex with mouse Factor VII EGF1 mutant (T101A)... -

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Basic information

Entry
Database: PDB / ID: 5ky3
Titlemouse POFUT1 in complex with mouse Factor VII EGF1 mutant (T101A) and GDP-fucose
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 / fucosyltransferase activity / peptide-O-fucosyltransferase activity / fucose metabolic process / coagulation factor VIIa / response to Thyroid stimulating hormone ...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 / fucosyltransferase activity / peptide-O-fucosyltransferase activity / fucose metabolic process / coagulation factor VIIa / response to Thyroid stimulating hormone / response to astaxanthin / response to thyrotropin-releasing hormone / response to 2,3,7,8-tetrachlorodibenzodioxine / regulation of Notch signaling pathway / response to genistein / serine-type peptidase complex / response to carbon dioxide / response to vitamin K / response to thyroxine / positive regulation of platelet-derived growth factor receptor signaling pathway / positive regulation of leukocyte chemotaxis / protein O-linked glycosylation / response to cholesterol / response to growth hormone / positive regulation of positive chemotaxis / positive regulation of blood coagulation / positive regulation of TOR signaling / animal organ regeneration / somitogenesis / Notch signaling pathway / protein processing / response to estrogen / circadian rhythm / blood coagulation / nervous system development / response to estradiol / heart development / angiogenesis / vesicle / response to hypoxia / signaling receptor binding / serine-type endopeptidase activity / 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 ...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 / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / 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-BETA-L-FUCOPYRANOSE / 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: 1.53 Å
AuthorsLi, Z. / Rini, J.M.
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 21, 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 1.3Jul 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 1.4Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)45,9716
Polymers44,8472
Non-polymers1,1244
Water7,332407
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-7 kcal/mol
Surface area16850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.150, 66.869, 110.061
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 / Production host: Homo sapiens (human) / References: UniProt: Q91ZW2, peptide-O-fucosyltransferase
#2: Protein/peptide Coagulation factor VII / Serum prothrombin conversion accelerator


Mass: 4389.862 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
#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
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, 409 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-GFB / GUANOSINE-5'-DIPHOSPHATE-BETA-L-FUCOPYRANOSE


Mass: 589.342 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H25N5O15P2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.14 Å3/Da / Density % sol: 42.51 %
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: 1.526→50 Å / Num. obs: 59408 / % possible obs: 100 % / Redundancy: 7.2 % / Biso Wilson estimate: 18.4 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.083 / Net I/σ(I): 12.2
Reflection shellResolution: 1.53→1.58 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.3 / CC1/2: 0.806 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→47.127 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1636 2914 5.02 %0
Rwork0.1477 55126 --
obs0.1485 58040 98.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.85 Å2 / Biso mean: 31.4295 Å2 / Biso min: 12.61 Å2
Refinement stepCycle: final / Resolution: 1.53→47.127 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3048 0 100 407 3555
Biso mean--29.83 37.03 -
Num. residues----391
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073313
X-RAY DIFFRACTIONf_angle_d1.1174545
X-RAY DIFFRACTIONf_chiral_restr0.058486
X-RAY DIFFRACTIONf_plane_restr0.007580
X-RAY DIFFRACTIONf_dihedral_angle_d12.6591976
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.53-1.55510.29661240.24942154227883
1.5551-1.58190.25781120.21852460257292
1.5819-1.61070.221440.20212514265897
1.6107-1.64170.21081310.19382618274999
1.6417-1.67520.2081330.184226622795100
1.6752-1.71160.21051520.167225792731100
1.7116-1.75140.18441440.164826332777100
1.7514-1.79520.17311240.155226562780100
1.7952-1.84370.19371340.15426562790100
1.8437-1.8980.17191520.154925952747100
1.898-1.95930.20371320.152726562788100
1.9593-2.02930.17351240.147526712795100
2.0293-2.11050.17341460.143526482794100
2.1105-2.20660.1751130.139726792792100
2.2066-2.32290.14691440.140526392783100
2.3229-2.46850.13981520.136126732825100
2.4685-2.6590.17751570.138126692826100
2.659-2.92660.16521530.14626732826100
2.9266-3.350.1591420.146126962838100
3.35-4.22020.14231660.132227292895100
4.2202-47.14970.14021350.14662866300199
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)
11.15640.13950.20841.44630.76391.1323-0.0146-0.03990.06140.0125-0.14910.17380.0239-0.1270.1360.1533-0.00330.00230.1383-0.04140.144811.285538.483324.0996
23.71930.45210.51711.87590.79391.0602-0.16340.11040.5325-0.3537-0.07810.2305-0.4362-0.0430.15550.30520.0201-0.06060.1582-0.02120.23611.978153.732919.1533
30.7668-0.192-0.17321.88461.14751.4605-0.02380.0802-0.0378-0.0493-0.06070.0216-0.0248-0.06290.06950.11930.0056-0.0010.13930.00050.119116.870429.979315.0364
42.3269-0.7204-0.23111.51580.97452.4847-0.01180.3754-0.1404-0.1191-0.09620.0052-0.0790.04080.06020.1329-0.00160.00580.1703-0.03430.133919.803419.99274.5101
53.07750.4907-2.84485.5761-2.01225.9908-0.03990.62120.6911-0.75940.0455-0.6565-0.66780.44010.04230.5876-0.04350.04570.41810.00750.542314.265545.3573.3756
64.73564.88781.1296.02812.7476.2389-1.0511.12120.5929-1.73220.55040.8174-0.1442-0.13670.36410.8178-0.06-0.15890.43320.02020.46993.494342.0135-0.118
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 121 )A31 - 121
2X-RAY DIFFRACTION2chain 'A' and (resid 122 through 186 )A122 - 186
3X-RAY DIFFRACTION3chain 'A' and (resid 187 through 259 )A187 - 259
4X-RAY DIFFRACTION4chain 'A' and (resid 260 through 384 )A260 - 384
5X-RAY DIFFRACTION5chain 'B' and (resid 90 through 112 )B90 - 112
6X-RAY DIFFRACTION6chain 'B' and (resid 113 through 126 )B113 - 126

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