[English] 日本語
Yorodumi
- PDB-6eje: Human Xylosyltransferase 1 in complex with peptide PAAEGSGEQDFT -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6eje
TitleHuman Xylosyltransferase 1 in complex with peptide PAAEGSGEQDFT
Components
  • Syndecan-1Syndecan 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 / chondroitin sulfate proteoglycan biosynthetic process / chondroitin sulfate biosynthetic process / Defective B3GALT6 causes EDSP2 and SEMDJL1 / Defective B4GALT7 causes EDS, progeroid type / Defective B3GAT3 causes JDSSDHD / Defective EXT2 causes exostoses 2 ...myoblast development / protein xylosyltransferase / protein xylosyltransferase activity / striated muscle cell development / chondroitin sulfate proteoglycan biosynthetic process / chondroitin sulfate biosynthetic process / 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 / Golgi cis cisterna / A tetrasaccharide linker sequence is required for GAG synthesis / heparan sulfate proteoglycan biosynthetic process / HS-GAG biosynthesis / glycosaminoglycan biosynthetic process / proteoglycan biosynthetic process / glycosaminoglycan metabolic process / HS-GAG degradation / positive regulation of extracellular exosome assembly / Sertoli cell development / embryonic skeletal system development / Respiratory syncytial virus (RSV) attachment and entry / positive regulation of exosomal secretion / cargo receptor activity / RSV-host interactions / ossification involved in bone maturation / ureteric bud development / Syndecan interactions / Other interleukin signaling / canonical Wnt signaling pathway / Retinoid metabolism and transport / response to glucocorticoid / response to cAMP / lysosomal lumen / receptor-mediated endocytosis / Cell surface interactions at the vascular wall / response to hydrogen peroxide / response to toxic substance / Golgi lumen / response to calcium ion / cell migration / Attachment and Entry / external side of plasma membrane / Golgi membrane / cell surface / protein-containing complex / extracellular space / extracellular exosome / identical protein binding / metal ion 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / 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 / Phosphate


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 / Water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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)

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more