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- PDB-5ux6: Structure of Human POFUT1 in its apo form -

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Basic information

Entry
Database: PDB / ID: 5ux6
TitleStructure of Human POFUT1 in its apo form
ComponentsGDP-fucose protein O-fucosyltransferase 1
KeywordsTRANSFERASE / GDP-fucose / Notch signaling / POFUT1 / T-ALL
Function / homology
Function and homology information


peptide-O-fucosyltransferase / protein O-linked fucosylation / peptide-O-fucosyltransferase activity / fucosyltransferase activity / Pre-NOTCH Processing in the Endoplasmic Reticulum / O-glycan processing / regulation of Notch signaling pathway / fucose metabolic process / protein O-linked glycosylation / somitogenesis ...peptide-O-fucosyltransferase / protein O-linked fucosylation / peptide-O-fucosyltransferase activity / fucosyltransferase activity / Pre-NOTCH Processing in the Endoplasmic Reticulum / O-glycan processing / regulation of Notch signaling pathway / fucose metabolic process / protein O-linked glycosylation / somitogenesis / Notch signaling pathway / nervous system development / heart development / angiogenesis / regulation of DNA-templated transcription / 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
GDP-fucose protein O-fucosyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsXu, X. / McMillan, B. / Blacklow, S.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA092433 United States
CitationJournal: Glycobiology / Year: 2017
Title: Structure of human POFUT1, its requirement in ligand-independent oncogenic Notch signaling, and functional effects of Dowling-Degos mutations.
Authors: McMillan, B.J. / Zimmerman, B. / Egan, E.D. / Lofgren, M. / Xu, X. / Hesser, A. / Blacklow, S.C.
History
DepositionFeb 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jul 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 1.5Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: GDP-fucose protein O-fucosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,2795
Polymers83,7442
Non-polymers5353
Water11,385632
1
A: GDP-fucose protein O-fucosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1853
Polymers41,8721
Non-polymers3132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GDP-fucose protein O-fucosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0932
Polymers41,8721
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.198, 132.236, 72.055
Angle α, β, γ (deg.)90.00, 106.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 41872.039 Da / Num. of mol.: 2 / Mutation: N160A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POFUT1, FUT12, KIAA0180 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9H488, peptide-O-fucosyltransferase
#2: 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
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 632 / 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: 2.79 Å3/Da / Density % sol: 55.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 16.5% v/v PEG3350, 0.05% w/v octyl-beta-D-glucoside, 0.5% v/v glycerol, and 100 mM sodium citrate pH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.087→50 Å / Num. obs: 52549 / % possible obs: 98.2 % / Redundancy: 2.7 % / Net I/σ(I): 7.42
Reflection shellResolution: 2.09→2.2 Å / Redundancy: 2.6 % / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZY4

3zy4


Resolution: 2.09→47.78 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.21
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1993 3.79 %Random selection
Rwork0.182 ---
obs0.184 52549 98.3 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.09→47.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5635 0 34 632 6301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045875
X-RAY DIFFRACTIONf_angle_d0.717989
X-RAY DIFFRACTIONf_dihedral_angle_d13.0933499
X-RAY DIFFRACTIONf_chiral_restr0.044839
X-RAY DIFFRACTIONf_plane_restr0.0041024
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0871-2.13930.36171250.32023498X-RAY DIFFRACTION96
2.1393-2.19710.33541640.29053622X-RAY DIFFRACTION99
2.1971-2.26180.29421240.26013623X-RAY DIFFRACTION99
2.2618-2.33480.2971590.24883622X-RAY DIFFRACTION99
2.3348-2.41820.26971320.23313625X-RAY DIFFRACTION99
2.4182-2.51510.23261530.223624X-RAY DIFFRACTION99
2.5151-2.62950.27061400.20253582X-RAY DIFFRACTION98
2.6295-2.76810.23951390.18793619X-RAY DIFFRACTION98
2.7681-2.94160.2181480.17633604X-RAY DIFFRACTION99
2.9416-3.16860.19741330.16463629X-RAY DIFFRACTION99
3.1686-3.48740.16981500.14343620X-RAY DIFFRACTION99
3.4874-3.99180.18241430.12933649X-RAY DIFFRACTION99
3.9918-5.02840.16761370.1243633X-RAY DIFFRACTION98
5.0284-47.78790.24541460.17373606X-RAY DIFFRACTION97
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)
12.2734-0.4257-0.53352.54920.22212.319-0.04420.3693-0.2019-0.24290.03960.07620.1802-0.2435-0.00370.1993-0.057-0.00170.2236-0.0280.120214.198513.96426.474
20.7562-0.4852-0.59121.00710.51711.3235-0.06240.0221-0.08980.00950.03720.10060.0516-0.03720.03080.1090.0004-0.02750.12460.00010.14298.891121.034328.8299
32.9245-0.79720.22833.0619-0.19393.02090.0260.2173-0.0795-0.1605-0.03510.09160.07130.0758-0.03520.13740.0112-0.00740.1117-0.00180.103510.881158.567715.8646
41.8328-0.303-0.03433.17550.71262.0401-0.03280.08940.0706-0.1581-0.10920.1978-0.332-0.07950.12850.17650.0209-0.03830.18880.0410.14986.282573.593714.9484
51.4119-1.58120.56293.3917-1.12621.5495-0.03090.064-0.1082-0.15130.01030.24060.1015-0.05550.00150.1482-0.0233-0.00360.1195-0.00760.129510.232153.845521.4956
60.69870.08520.08622.6422.04771.5690.01510.05250.0276-0.0179-0.0293-0.2517-0.06530.0659-0.02180.12370.02860.02230.11570.02250.182624.967153.717439.7168
70.565-0.24120.16562.4179-0.73111.7303-0.04540.0131-0.14630.17430.22140.38590.0764-0.5415-0.15030.21920.00110.01750.30910.0230.269414.417360.173544.9083
82.1461-0.06951.01211.8834-0.76062.67880.0191-0.01130.08460.0148-0.0457-0.1348-0.0080.00830.02470.10750.03030.03380.0976-0.01560.135323.025844.045838.0292
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 28 THROUGH 165 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 166 THROUGH 384 )
3X-RAY DIFFRACTION3CHAIN 'B' AND (RESID 28 THROUGH 111 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 112 THROUGH 181 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 182 THROUGH 229 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 230 THROUGH 254 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 255 THROUGH 286 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 287 THROUGH 383 )

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