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- PDB-5l0v: human POGLUT1 in complex with 2F-glucose modified EGF(+) and UDP -

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Basic information

Entry
Database: PDB / ID: 5l0v
Titlehuman POGLUT1 in complex with 2F-glucose modified EGF(+) and UDP
Components
  • EGF(+)
  • Protein O-glucosyltransferase 1
KeywordsTRANSFERASE / transferase glycosyltransferase GT-B glucosyltransferase
Function / homology
Function and homology information


EGF-domain serine glucosyltransferase / EGF-domain serine xylosyltransferase / EGF-domain serine glucosyltransferase activity / EGF-domain serine xylosyltransferase activity / muscle tissue development / regulation of gastrulation / protein O-linked glycosylation via serine / UDP-xylosyltransferase activity / Pre-NOTCH Processing in the Endoplasmic Reticulum / UDP-glucosyltransferase activity ...EGF-domain serine glucosyltransferase / EGF-domain serine xylosyltransferase / EGF-domain serine glucosyltransferase activity / EGF-domain serine xylosyltransferase activity / muscle tissue development / regulation of gastrulation / protein O-linked glycosylation via serine / UDP-xylosyltransferase activity / Pre-NOTCH Processing in the Endoplasmic Reticulum / UDP-glucosyltransferase activity / circulatory system development / glucosyltransferase activity / paraxial mesoderm development / axial mesoderm development / protein O-linked glycosylation / positive regulation of Notch signaling pathway / gastrulation / endomembrane system / somitogenesis / endoplasmic reticulum lumen / endoplasmic reticulum
Similarity search - Function
Glycosyl transferase CAP10 domain / Glycosyl transferase family 90 / Putative lipopolysaccharide-modifying enzyme. / Laminin / Laminin / Ribbon / Mainly Beta
Similarity search - Domain/homology
2-deoxy-2-fluoro-beta-D-glucopyranose / URIDINE-5'-DIPHOSPHATE / Protein O-glucosyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.305 Å
AuthorsLi, Z. / Rini, J.M.
CitationJournal: Nat Commun / Year: 2017
Title: Structural basis of Notch O-glucosylation and O-xylosylation by mammalian protein-O-glucosyltransferase 1 (POGLUT1).
Authors: Li, Z. / Fischer, M. / Satkunarajah, M. / Zhou, D. / Withers, S.G. / Rini, J.M.
History
DepositionJul 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 24, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line ..._chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein O-glucosyltransferase 1
B: EGF(+)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,96210
Polymers46,3332
Non-polymers1,6298
Water10,485582
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-25 kcal/mol
Surface area17920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.810, 74.890, 83.020
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 Protein O-glucosyltransferase 1 / CAP10-like 46 kDa protein / hCLP46 / KTEL motif-containing protein 1 / Myelodysplastic syndromes ...CAP10-like 46 kDa protein / hCLP46 / KTEL motif-containing protein 1 / Myelodysplastic syndromes relative protein / O-glucosyltransferase Rumi homolog / hRumi / Protein O-xylosyltransferase


Mass: 42077.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: POGLUT1, C3orf9, CLP46, KTELC1, MDSRP, MDS010, UNQ490/PRO1006
Plasmid: PB-T-PAF / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human)
References: UniProt: Q8NBL1, Transferases; Glycosyltransferases; Hexosyltransferases, protein xylosyltransferase
#2: Protein/peptide EGF(+)


Mass: 4255.569 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pMal / Production host: Escherichia coli BL21(DE3) (bacteria)

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Sugars , 2 types, 5 molecules

#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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
#7: Sugar ChemComp-SHG / 2-deoxy-2-fluoro-beta-D-glucopyranose / 2-deoxy-2-fluoro-beta-D-glucose / 2-deoxy-2-fluoro-D-glucose / 2-deoxy-2-fluoro-glucose


Type: D-saccharide, beta linking / Mass: 182.147 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H11FO5
IdentifierTypeProgram
b-D-Glcp2fluoroIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 585 molecules

#4: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 582 / 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: 2.38 Å3/Da / Density % sol: 48.38 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG5000 MME, 50 mM MES pH 6.5, 10mM CaCl2, 250mM NaCl, 5% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.305→50 Å / Num. obs: 103515 / % possible obs: 96 % / Redundancy: 6.5 % / Biso Wilson estimate: 15.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Net I/σ(I): 19.57
Reflection shellRedundancy: 6.4 % / Rmerge(I) obs: 0.805 / Mean I/σ(I) obs: 2.07 / CC1/2: 0.783 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.305→35.81 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.81
RfactorNum. reflection% reflectionSelection details
Rfree0.1739 5192 5.02 %0
Rwork0.1585 ---
obs0.1593 103505 96.14 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 79.56 Å2 / Biso mean: 25.2504 Å2 / Biso min: 9.52 Å2
Refinement stepCycle: final / Resolution: 1.305→35.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3224 0 167 582 3973
Biso mean--36 32.76 -
Num. residues----396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093459
X-RAY DIFFRACTIONf_angle_d1.184719
X-RAY DIFFRACTIONf_chiral_restr0.08497
X-RAY DIFFRACTIONf_plane_restr0.008601
X-RAY DIFFRACTIONf_dihedral_angle_d15.6311306
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3051-1.320.28671760.266933743550100
1.32-1.33550.26771790.258133893568100
1.3355-1.35180.27111720.256633043476100
1.3518-1.36890.26591920.244833823574100
1.3689-1.38690.21851720.234133583530100
1.3869-1.40590.25041620.22634043566100
1.4059-1.4260.22971670.22233553522100
1.426-1.44730.24021720.214133863558100
1.4473-1.46990.2081610.199334413602100
1.4699-1.4940.21381740.197233533527100
1.494-1.51980.22441650.18933933558100
1.5198-1.54740.2031560.185533643520100
1.5474-1.57720.20211880.176933953583100
1.5772-1.60940.19071740.174134113585100
1.6094-1.64440.18931910.164433703561100
1.6444-1.68260.17611660.1633823548100
1.6826-1.72470.19132010.158633673568100
1.7247-1.77130.18311860.160933993585100
1.7713-1.82340.17442040.156833753579100
1.8234-1.88230.17651510.15862976312798
1.8823-1.94960.1567880.1561676176457
1.9496-2.02760.17931310.15313136326799
2.0276-2.11990.16811770.14933943571100
2.1199-2.23160.14721960.144234143610100
2.2316-2.37140.1491520.14042761291380
2.3714-2.55450.15872070.140533963603100
2.5545-2.81140.15021870.14833084327190
2.8114-3.2180.14831680.15234963664100
3.218-4.05350.16461800.13973120330090
4.0535-35.82390.17681970.151536583855100
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)
12.892-1.43450.5931.6285-0.68751.9734-0.0923-0.1867-0.0930.08060.16370.20450.0641-0.3926-0.07650.1423-0.0320.03110.20590.00110.10893.091330.853134.1471
20.9677-0.25510.31491.8606-1.13692.90480.0429-0.0732-0.1176-0.01090.0034-0.180.54180.4491-0.04450.23770.1488-0.0210.2833-0.00510.210931.309512.647931.4719
32.37120.64480.24422.6468-0.19772.2222-0.0319-0.0835-0.02780.08010.043-0.11960.2340.4004-0.00770.12340.0785-0.00220.1772-0.01140.11227.162720.765728.2825
41.4374-0.63190.49210.7538-0.13181.45380.03660.038-0.0674-0.02910.01840.02710.08870.0233-0.05110.0809-0.00330.01810.0674-0.01330.085313.72428.028316.938
53.30220.4796-0.19811.2511.24722.40090.2880.9785-0.6563-0.2788-0.26620.21750.22670.01940.0220.17390.0154-0.02980.1952-0.08920.16818.436123.45232.1038
61.5156-0.13010.14790.8086-0.08071.50990.00980.0188-0.0836-0.01820.00280.06090.056-0.075-0.01810.0913-0.00610.00250.0753-0.00810.10837.883730.397217.1737
72.348-1.36770.53458.67650.34782.47970.0560.1271-0.4005-0.1533-0.08340.59120.1878-0.34640.02350.1146-0.04080.01340.1844-0.03430.1982-6.875630.058416.4143
82.0735-1.04465.75471.3869-0.33665.8959-0.268-0.35410.57970.15780.03620.0863-0.383-0.24540.2170.1713-0.00620.02590.1293-0.01120.1984.27841.612525.3084
92.2731-1.90710.84323.9447-0.73661.665-0.1467-0.23130.02630.30490.1381-0.39790.12050.39420.01530.16360.0604-0.01780.2629-0.00970.153229.489822.30735.1364
105.9661-2.91140.66882.0031.14226.4583-0.1174-0.1501-0.63540.12860.06810.53780.58130.07470.05480.27660.02110.04260.2165-0.06160.300820.457613.430710.6008
112.450.7181-0.45815.07430.78712.7845-0.03770.0348-0.2883-0.2275-0.0061-0.13210.2410.22140.0320.21090.06380.02410.2183-0.05430.223127.13416.95386.7167
123.8697-0.2306-1.9191.48251.54816.44910.0851-0.03990.5626-0.36080.8222-1.0631-0.67381.3582-0.87080.342-0.10280.13240.5419-0.24250.503435.4823.93475.9482
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 68 )A30 - 68
2X-RAY DIFFRACTION2chain 'A' and (resid 69 through 104 )A69 - 104
3X-RAY DIFFRACTION3chain 'A' and (resid 105 through 139 )A105 - 139
4X-RAY DIFFRACTION4chain 'A' and (resid 140 through 227 )A140 - 227
5X-RAY DIFFRACTION5chain 'A' and (resid 228 through 248 )A228 - 248
6X-RAY DIFFRACTION6chain 'A' and (resid 249 through 311 )A249 - 311
7X-RAY DIFFRACTION7chain 'A' and (resid 312 through 331 )A312 - 331
8X-RAY DIFFRACTION8chain 'A' and (resid 332 through 349 )A332 - 349
9X-RAY DIFFRACTION9chain 'A' and (resid 350 through 385 )A350 - 385
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 7 )B1 - 7
11X-RAY DIFFRACTION11chain 'B' and (resid 8 through 26 )B8 - 26
12X-RAY DIFFRACTION12chain 'B' and (resid 27 through 40 )B27 - 40

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