[English] 日本語
Yorodumi
- PDB-2j0b: Structure of the catalytic domain of mouse Manic Fringe in comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2j0b
TitleStructure of the catalytic domain of mouse Manic Fringe in complex with UDP and manganese
ComponentsBETA-1,3-N-ACETYLGLUCOSAMINYLTRANSFERASE MANIC FRINGE
KeywordsTRANSFERASE / GLYCOSYLTRANSFERASE / DEVELOPMENTAL PROTEIN / TRANSMEMBRANE / GOLGI APPARATUS / NOTCH SIGNALING / MEMBRANE / GLYCOPROTEIN / SIGNAL-ANCHOR
Function / homology
Function and homology information


O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase / O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase activity / marginal zone B cell differentiation / regulation of Notch signaling pathway / pattern specification process / blastocyst formation / positive regulation of Notch signaling pathway / Golgi membrane / metal ion binding
Similarity search - Function
Fringe / Fringe-like / Fringe-like / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A - #50 / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / : / URIDINE-5'-DIPHOSPHATE / Beta-1,3-N-acetylglucosaminyltransferase manic fringe
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.1 Å
AuthorsJinek, M. / Chen, Y.-W. / Clausen, H. / Cohen, S.M. / Conti, E.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2006
Title: Structural Insights Into the Notch-Modifying Glycosyltransferase Fringe
Authors: Jinek, M. / Chen, Y.-W. / Clausen, H. / Cohen, S.M. / Conti, E.
History
DepositionAug 1, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 16, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status ...exptl_crystal_grow / pdbx_database_status / reflns / reflns_shell
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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 / _struct_conn.ptnr2_label_seq_id
Remark 650 HELIX THE FOLLOWING HELIX RECORDS HAVE BEEN REMOVED AT AUTHORS REQUEST: HELIX 5 5 ILE A 82 GLN A ... HELIX THE FOLLOWING HELIX RECORDS HAVE BEEN REMOVED AT AUTHORS REQUEST: HELIX 5 5 ILE A 82 GLN A 84 5 HELIX 9 9 GLY A 197 ALA A 199 5

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BETA-1,3-N-ACETYLGLUCOSAMINYLTRANSFERASE MANIC FRINGE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1445
Polymers31,5491
Non-polymers5944
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)161.760, 40.970, 38.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2048-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein BETA-1,3-N-ACETYLGLUCOSAMINYLTRANSFERASE MANIC FRINGE / MANIC FRINGE / O-FUCOSYLPEPTIDE 3-BETA-N-ACETYLGLUCOSAMINYLTRANSFERASE


Mass: 31549.287 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 45-321 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: ENGINEERED MUTATION TO REMOVE GLYCOSYLATION SITE / Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: O09008, O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase

-
Non-polymers , 5 types, 89 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, ASN 109 TO GLN ENGINEERED RESIDUE IN CHAIN A, ASN 185 TO GLN
Has protein modificationY
Sequence detailsTHE PROTEIN SEQUENCE ALIGNS WITH UNIPROT ENTRY O09008. THE SEQUENCE 42-44(GLY-PRO-MET) IN 2J0B IS ...THE PROTEIN SEQUENCE ALIGNS WITH UNIPROT ENTRY O09008. THE SEQUENCE 42-44(GLY-PRO-MET) IN 2J0B IS NOT PRESENT IN THE UNIPROT ENTRY BUT IS DERIVED FROM THE EXPRESSION VECTOR. IN ADDITION, THERE IS A MUTATION AT RESIDUE 185 (ASN TO GLN)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.8 %
Description: LIGAND SOAK, STRUCTURE OBTAINED THROUGH FOURIER DIFFERENCE
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.2 M POTASSIUM SULFATE, 20% PEG 3350, pH 6.50

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9195
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 9, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9195 Å / Relative weight: 1
ReflectionResolution: 2.1→81.6 Å / Num. obs: 15588 / % possible obs: 99.6 % / Observed criterion σ(I): 3 / Redundancy: 5.9 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 13.6
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 4.4 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.1→80.85 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.922 / SU B: 8.307 / SU ML: 0.115 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.221 781 5 %RANDOM
Rwork0.177 ---
obs0.18 14817 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.05 Å2
Baniso -1Baniso -2Baniso -3
1--1.04 Å20 Å20 Å2
2--0.55 Å20 Å2
3---0.49 Å2
Refinement stepCycle: LAST / Resolution: 2.1→80.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1942 0 32 85 2059
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222035
X-RAY DIFFRACTIONr_bond_other_d0.0020.021383
X-RAY DIFFRACTIONr_angle_refined_deg1.7731.9782777
X-RAY DIFFRACTIONr_angle_other_deg1.0753.0043352
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4745242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.88223.29791
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.38415324
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3311513
X-RAY DIFFRACTIONr_chiral_restr0.1250.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022209
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02423
X-RAY DIFFRACTIONr_nbd_refined0.2280.2438
X-RAY DIFFRACTIONr_nbd_other0.2140.21491
X-RAY DIFFRACTIONr_nbtor_refined0.1890.2997
X-RAY DIFFRACTIONr_nbtor_other0.0960.21062
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2106
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.220.25
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2480.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1270.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0451.51216
X-RAY DIFFRACTIONr_mcbond_other0.2671.5485
X-RAY DIFFRACTIONr_mcangle_it1.93321967
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7583824
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.414.5809
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 84 -
Rwork0.191 1087 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 23.686 Å / Origin y: -0.189 Å / Origin z: 34.727 Å
111213212223313233
T-0.0599 Å20.0127 Å2-0.0014 Å2--0.1267 Å20.0023 Å2---0.1135 Å2
L3.2746 °20.0705 °20.5172 °2-1.0801 °2-0.0138 °2--1.1202 °2
S0.0037 Å °0.0003 Å °-0.1809 Å °0.0273 Å °-0.0067 Å °0.037 Å °0.0382 Å °-0.1125 Å °0.0031 Å °

+
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