[English] 日本語
Yorodumi
- PDB-5ky5: mouse POFUT1 in complex with EGF(+) and GDP -

+
Open data


ID or keywords:

Loading...

-
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 / fucosyltransferase activity / protein O-linked fucosylation / peptide-O-fucosyltransferase activity / fucose metabolic process / regulation of Notch signaling pathway / protein O-linked glycosylation / somitogenesis / Notch signaling pathway / heart development ...peptide-O-fucosyltransferase / fucosyltransferase activity / protein O-linked fucosylation / peptide-O-fucosyltransferase activity / fucose metabolic process / regulation of Notch signaling pathway / protein O-linked glycosylation / somitogenesis / Notch signaling pathway / heart development / nervous system 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
Revision 1.4Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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-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

-
Non-polymers , 3 types, 450 molecules

#4: Chemical ChemComp-GDP / GUANOSINE-5'-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


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


Mass: 18.015 Da / Num. of mol.: 448 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
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