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- PDB-6eje: Human Xylosyltransferase 1 in complex with peptide PAAEGSGEQDFT -

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Basic information

Entry
Database: PDB / ID: 6eje
TitleHuman Xylosyltransferase 1 in complex with peptide PAAEGSGEQDFT
Components
  • Syndecan-1
  • Xylosyltransferase 1
KeywordsTRANSFERASE / Proteoglycan / Glycosyltransferase / Golgi / Xylosyltransferase
Function / homology
Function and homology information


myoblast development / protein xylosyltransferase / protein xylosyltransferase activity / striated muscle cell development / Golgi cis cisterna / Defective B3GALT6 causes EDSP2 and SEMDJL1 / Defective B4GALT7 causes EDS, progeroid type / Defective B3GAT3 causes JDSSDHD / Defective EXT2 causes exostoses 2 / Defective EXT1 causes exostoses 1, TRPS2 and CHDS ...myoblast development / protein xylosyltransferase / protein xylosyltransferase activity / striated muscle cell development / Golgi cis cisterna / Defective B3GALT6 causes EDSP2 and SEMDJL1 / Defective B4GALT7 causes EDS, progeroid type / Defective B3GAT3 causes JDSSDHD / Defective EXT2 causes exostoses 2 / Defective EXT1 causes exostoses 1, TRPS2 and CHDS / Glycosaminoglycan-protein linkage region biosynthesis / glycosaminoglycan biosynthetic process / HS-GAG biosynthesis / proteoglycan biosynthetic process / positive regulation of extracellular exosome assembly / chondroitin sulfate proteoglycan biosynthetic process / glycosaminoglycan metabolic process / heparan sulfate proteoglycan biosynthetic process / HS-GAG degradation / embryonic skeletal system development / positive regulation of exosomal secretion / cargo receptor activity / ossification involved in bone maturation / Other interleukin signaling / Syndecan interactions / RSV-host interactions / Respiratory syncytial virus (RSV) attachment and entry / canonical Wnt signaling pathway / Retinoid metabolism and transport / lysosomal lumen / receptor-mediated endocytosis / Cell surface interactions at the vascular wall / Golgi lumen / cell migration / Attachment and Entry / Golgi membrane / external side of plasma membrane / cell surface / extracellular space / extracellular exosome / metal ion binding / identical protein binding / plasma membrane
Similarity search - Function
Xylosyltransferase, C-terminal / Xylosyltransferase / Xylosyltransferase C terminal / Syndecan / Syndecan, conserved site / Syndecans signature. / Glycosyl transferase, family 14 / Core-2/I-Branching enzyme / Syndecan/Neurexin domain / Syndecan domain ...Xylosyltransferase, C-terminal / Xylosyltransferase / Xylosyltransferase C terminal / Syndecan / Syndecan, conserved site / Syndecans signature. / Glycosyl transferase, family 14 / Core-2/I-Branching enzyme / Syndecan/Neurexin domain / Syndecan domain / Neurexin/syndecan/glycophorin C / putative band 4.1 homologues' binding motif
Similarity search - Domain/homology
PHOSPHATE ION / Syndecan-1 / Xylosyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsBriggs, D.C. / Hohenester, E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust101748/Z/13/Z United Kingdom
CitationJournal: Structure / Year: 2018
Title: Structural Basis for the Initiation of Glycosaminoglycan Biosynthesis by Human Xylosyltransferase 1.
Authors: Briggs, D.C. / Hohenester, E.
History
DepositionSep 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Xylosyltransferase 1
B: Syndecan-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4484
Polymers87,3302
Non-polymers1182
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Activity assay shows this peptide is a substrate for the enzyme
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-20 kcal/mol
Surface area30510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.280, 86.720, 153.470
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Xylosyltransferase 1 / Peptide O-xylosyltransferase 1 / Xylosyltransferase I / XylT-I


Mass: 86122.047 Da / Num. of mol.: 1 / Fragment: UNP residues 232-959
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XYLT1, XT1 / Plasmid: pCEP-Pu / Cell line (production host): HEK293FS / Production host: Homo sapiens (human) / References: UniProt: Q86Y38, protein xylosyltransferase
#2: Protein/peptide Syndecan-1 / SYND1


Mass: 1208.189 Da / Num. of mol.: 1 / Fragment: UNP residues 201-212 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P18827
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
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: 2.56 Å3/Da / Density % sol: 52.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 55-65% Morpheus Precipitant mix 2 (PEG8000 and Ethylene glycol) 0.1M Bicine/Tris buffer at pH 7.5 0.1M of NPS mix (0.033M of each)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 2.43→67.28 Å / Num. obs: 34088 / % possible obs: 98.8 % / Redundancy: 4.3 % / Biso Wilson estimate: 44.42 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.063 / Rrim(I) all: 0.137 / Net I/σ(I): 9.3 / Num. measured all: 147667 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.43-2.494.40.98625290.580.5141.11699.6
10.87-67.2840.0334290.9990.0180.03894.4

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Processing

Software
NameVersionClassification
Aimless0.5.31data scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GAK

2gak


Resolution: 2.43→61.619 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.65
RfactorNum. reflection% reflection
Rfree0.2349 1712 5.03 %
Rwork0.1972 --
obs0.1991 34054 98.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 122.99 Å2 / Biso mean: 50.0257 Å2 / Biso min: 24.17 Å2
Refinement stepCycle: final / Resolution: 2.43→61.619 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5563 0 6 111 5680
Biso mean--62.34 35.47 -
Num. residues----704
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025733
X-RAY DIFFRACTIONf_angle_d0.5067809
X-RAY DIFFRACTIONf_chiral_restr0.04838
X-RAY DIFFRACTIONf_plane_restr0.0031007
X-RAY DIFFRACTIONf_dihedral_angle_d11.4583385
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.43-2.50150.35021660.2882667283399
2.5015-2.58230.33281340.27772681281599
2.5823-2.67460.29541400.27126862826100
2.6746-2.78160.35161230.2662678280199
2.7816-2.90820.32371560.26322677283399
2.9082-3.06160.25831540.23822679283399
3.0616-3.25340.29181640.2242656282099
3.2534-3.50450.25531290.20882664279398
3.5045-3.85720.18561360.17542688282498
3.8572-4.41520.19421280.15472736286498
4.4152-5.56210.18211380.14412717285597
5.5621-61.63870.19031440.18392813295796
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)
11.56190.2407-0.07041.317-0.01970.6314-0.01050.0281-0.2217-0.0431-0.00070.1110.002-0.0969-0.01710.36650.0246-0.0230.3954-0.01670.34470.805223.165152.5572
21.33870.35460.20451.84010.06890.7338-0.0013-0.111-0.2030.1349-0.02080.03250.0956-0.03070.03340.35330.025-0.00360.37010.02160.37954.865219.839159.2455
30.88710.1069-0.25321.04070.07321.19220.0128-0.1080.080.1199-0.03740.1208-0.2783-0.12630.01540.41230.0134-0.04050.4003-0.05240.3809-2.044656.720363.319
47.9966-3.0606-0.58828.2806-0.1837.5549-0.4227-0.39230.1470.48710.399-0.14410.2622-0.08890.03820.6202-0.03980.03430.47110.04970.4535-3.37321.291370.7957
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 253 through 377 )A253 - 377
2X-RAY DIFFRACTION2chain 'A' and (resid 378 through 606 )A378 - 606
3X-RAY DIFFRACTION3chain 'A' and (resid 607 through 959 )A607 - 959
4X-RAY DIFFRACTION4chain 'B' and (resid 205 through 213 )B205 - 213

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