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- PDB-5ky5: mouse POFUT1 in complex with EGF(+) and GDP -

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Basic information

Entry
Database: PDB / ID: 5ky5
Titlemouse POFUT1 in complex with 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 / Laminin / Laminin / Ribbon / Rossmann fold / 3-Layer(aba) Sandwich ...GDP-fucose protein O-fucosyltransferase 1 / GDP-fucose protein O-fucosyltransferase / GDP-fucose protein O-fucosyltransferase / Rossmann fold - #11340 / Rossmann fold - #11350 / Laminin / Laminin / Ribbon / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
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: 1.5 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

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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)45,5466
Polymers44,5692
Non-polymers9784
Water8,071448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-16 kcal/mol
Surface area17410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.080, 67.030, 111.100
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 EGF(+)


Mass: 4111.439 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Gene: F7, Cf7 / Production host: Escherichia coli (E. coli)
#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

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Non-polymers , 3 types, 450 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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 448 / 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: 2.18 Å3/Da / Density % sol: 43.46 %
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: 1.5→50 Å / Num. obs: 63046 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 18.8 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.109 / Net I/σ(I): 9.5
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.092 / Mean I/σ(I) obs: 1.7 / CC1/2: 0.696 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_2341refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 1.5→47.156 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.9
RfactorNum. reflection% reflectionSelection details
Rfree0.1728 3167 5.02 %0
Rwork0.1575 ---
obs0.1583 63044 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 115.44 Å2 / Biso mean: 30.7758 Å2 / Biso min: 11.12 Å2
Refinement stepCycle: final / Resolution: 1.5→47.156 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3107 0 108 448 3663
Biso mean--40.21 34.41 -
Num. residues----392
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093303
X-RAY DIFFRACTIONf_angle_d1.1184511
X-RAY DIFFRACTIONf_chiral_restr0.056479
X-RAY DIFFRACTIONf_plane_restr0.007581
X-RAY DIFFRACTIONf_dihedral_angle_d15.2021974
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.5-1.52240.31051450.274925622707
1.5224-1.54620.2561310.241325632694
1.5462-1.57150.23411370.22626012738
1.5715-1.59860.2341250.211525592684
1.5986-1.62770.25391410.200425702711
1.6277-1.6590.24451240.198925612685
1.659-1.69290.19581430.182525822725
1.6929-1.72970.2081330.17925862719
1.7297-1.76990.21941540.17425582712
1.7699-1.81420.15191220.175826012723
1.8142-1.86320.21441340.162825752709
1.8632-1.91810.18761480.158625822730
1.9181-1.980.18961240.153725912715
1.98-2.05070.17731200.155826042724
2.0507-2.13290.17221370.153225852722
2.1329-2.22990.15751170.147826322749
2.2299-2.34750.16021490.148425792728
2.3475-2.49460.16871550.144126242779
2.4946-2.68710.1651440.145225982742
2.6871-2.95750.16441530.158526142767
2.9575-3.38540.16221360.158126562792
3.3854-4.26480.14761620.1426712833
4.2648-47.17930.16381330.14828232956
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)
11.02570.07680.20251.92340.84941.9121-0.0116-0.05020.05040.0962-0.18760.22780.0831-0.27510.18680.1422-0.0032-0.00130.1186-0.03780.138411.445237.932124.139
25.42850.66270.67622.68541.02631.573-0.21420.47980.6297-0.3327-0.0590.2679-0.5512-0.10780.25180.32490.0237-0.0980.20660.00540.239211.539153.255519.6813
30.8877-0.4639-0.01722.59842.02561.96980.02340.2440.079-0.2228-0.0232-0.0813-0.26850.06980.01860.1251-0.0137-0.01650.17570.03810.140319.510230.575510.1977
42.5679-0.2497-0.30192.37881.21423.3273-0.06380.4371-0.32540.0224-0.07260.15220.2684-0.09520.12250.1006-0.01640.0130.1609-0.03710.142118.08715.70735.9554
59.1597-0.5929-2.41374.8367-0.70757.50530.36270.20541.3215-0.7307-0.2975-0.329-1.26510.527-0.07420.5134-0.04560.03640.25760.05750.33215.455846.14154.092
67.3202-0.63550.35122.0049-2.47036.8946-0.10020.73260.4253-0.94490.1980.9672-0.6058-0.68020.10850.44360.093-0.16680.4140.02370.3243.120540.92640.3463
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 121 )A33 - 121
2X-RAY DIFFRACTION2chain 'A' and (resid 122 through 186 )A122 - 186
3X-RAY DIFFRACTION3chain 'A' and (resid 187 through 291 )A187 - 291
4X-RAY DIFFRACTION4chain 'A' and (resid 292 through 384 )A292 - 384
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 26 )B1 - 26
6X-RAY DIFFRACTION6chain 'B' and (resid 27 through 40 )B27 - 40

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