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- PDB-5ky7: mouse POFUT1 in complex with O-glucosylated EGF(+) and GDP -

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Basic information

Entry
Database: PDB / ID: 5ky7
Titlemouse POFUT1 in complex with O-glucosylated EGF(+) and GDP
Components
  • EGF(+)
  • GDP-fucose protein O-fucosyltransferase 1
KeywordsTRANSFERASE / glycosyltransferase
Function / homology
Function and homology information


peptide-O-fucosyltransferase / protein O-linked fucosylation / peptide-O-fucosyltransferase activity / fucosyltransferase activity / fucose metabolic process / regulation of Notch signaling pathway / protein O-linked glycosylation / somitogenesis / Notch signaling pathway / nervous system development ...peptide-O-fucosyltransferase / protein O-linked fucosylation / peptide-O-fucosyltransferase activity / fucosyltransferase activity / fucose metabolic process / regulation of Notch signaling pathway / protein O-linked glycosylation / somitogenesis / Notch signaling pathway / nervous system development / heart development / angiogenesis / endoplasmic reticulum / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
beta-D-glucopyranose / GUANOSINE-5'-DIPHOSPHATE / GDP-fucose protein O-fucosyltransferase 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 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 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: EGF(+)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6346
Polymers44,5692
Non-polymers1,0664
Water5,639313
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-9 kcal/mol
Surface area16410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.890, 66.440, 108.360
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 EGF(+)


Mass: 4111.439 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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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
#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 , 2 types, 314 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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.1 Å3/Da / Density % sol: 41.3 %
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: Dec 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 49185 / % possible obs: 98 % / Redundancy: 5.7 % / Biso Wilson estimate: 20.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.064 / Net I/σ(I): 13.5
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.805 / Mean I/σ(I) obs: 2.2 / CC1/2: 0.765 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 1.6→46.801 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2157 2467 5.02 %0
Rwork0.1953 46717 --
obs0.1964 49184 97.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 155.38 Å2 / Biso mean: 37.7969 Å2 / Biso min: 12.17 Å2
Refinement stepCycle: final / Resolution: 1.6→46.801 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2979 0 115 313 3407
Biso mean--44.26 39.55 -
Num. residues----385
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053162
X-RAY DIFFRACTIONf_angle_d1.1284326
X-RAY DIFFRACTIONf_chiral_restr0.061469
X-RAY DIFFRACTIONf_plane_restr0.006554
X-RAY DIFFRACTIONf_dihedral_angle_d14.921856
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.63080.31411290.28862546267597
1.6308-1.66410.29861310.26422527265897
1.6641-1.70030.30191360.25412518265497
1.7003-1.73990.30191450.2512558270397
1.7399-1.78340.23081280.24212541266997
1.7834-1.83160.27081260.23112570269698
1.8316-1.88550.26421480.23392546269498
1.8855-1.94630.25031210.22842578269998
1.9463-2.01590.23561220.21382595271798
2.0159-2.09660.21951370.20862569270698
2.0966-2.1920.20561180.20192596271498
2.192-2.30760.25341410.19782604274599
2.3076-2.45220.22251530.20022624277799
2.4522-2.64150.19961480.18582606275498
2.6415-2.90730.22141500.19112631278199
2.9073-3.32790.18441400.17812653279399
3.3279-4.19240.18021620.16592664282699
4.1924-46.82070.20661320.18342791292397
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)
10.1212-0.02440.10560.460.21110.4328-0.3296-0.27370.6265-0.1462-0.2810.1196-0.3265-0.529-0.19820.29370.0878-0.2260.3275-0.2110.39729.814540.677123.581
21.2520.83480.44190.76690.68780.8999-0.088-0.19470.3672-0.0712-0.03750.1725-0.3774-0.10270.31750.46570.1553-0.38670.3643-0.38910.5973.400648.683822.5391
30.89411.095-0.16451.69390.53891.5814-0.08920.0302-0.3879-0.05170.0094-0.4499-0.00280.0579-0.07290.6599-0.1175-0.35970.27280.04250.758624.465753.601821.3789
41.3422-0.14310.50881.47251.07322.1459-0.06820.22180.0809-0.0801-0.094-0.0641-0.03280.07980.06560.1477-0.0101-0.01570.1710.02470.126918.185323.41288.1164
53.7339-2.211.285.71692.64473.0654-0.25640.16990.9998-0.43030.0217-0.502-0.61390.27850.2570.4988-0.0166-0.24110.25750.05150.529311.946444.60516.5072
60.5031-0.3856-0.79421.7114-0.52765.1469-0.02830.58810.5391-0.4674-0.27880.4421-0.6114-0.23230.19010.56860.0383-0.29010.33950.05740.54925.448342.02610.8719
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 152 )A33 - 152
2X-RAY DIFFRACTION2chain 'A' and (resid 153 through 170 )A153 - 170
3X-RAY DIFFRACTION3chain 'A' and (resid 171 through 186 )A171 - 186
4X-RAY DIFFRACTION4chain 'A' and (resid 187 through 384 )A187 - 384
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 19 )B3 - 19
6X-RAY DIFFRACTION6chain 'B' and (resid 20 through 40 )B20 - 40

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