[English] 日本語
Yorodumi
- PDB-5ndf: Small-molecule inhibition of ppGalNAc-Ts selectively reduces muci... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ndf
TitleSmall-molecule inhibition of ppGalNAc-Ts selectively reduces mucin-type O-glycosylation
ComponentsPolypeptide N-acetylgalactosaminyltransferase 2
KeywordsTRANSFERASE / GalNAc-T2 Inhibition Flavonoids Mucin-type O-glycosylation Alzheimer disease
Function / homology
Function and homology information


protein O-linked glycosylation via threonine / protein O-linked glycosylation via serine / polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / protein O-linked GalNAcylation / O-linked glycosylation of mucins / Golgi stack / protein O-linked glycosylation / COPI-independent Golgi-to-ER retrograde traffic / Golgi cisterna membrane ...protein O-linked glycosylation via threonine / protein O-linked glycosylation via serine / polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / protein O-linked GalNAcylation / O-linked glycosylation of mucins / Golgi stack / protein O-linked glycosylation / COPI-independent Golgi-to-ER retrograde traffic / Golgi cisterna membrane / positive regulation of immunoglobulin production / protein maturation / manganese ion binding / carbohydrate binding / Golgi membrane / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / extracellular region / membrane
Similarity search - Function
N-acetylgalactosaminyltransferase / Glycosyltransferase 2-like / Glycosyl transferase family 2 / Ricin-type beta-trefoil lectin domain / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A ...N-acetylgalactosaminyltransferase / Glycosyltransferase 2-like / Glycosyl transferase family 2 / Ricin-type beta-trefoil lectin domain / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-LU2 / : / URIDINE-5'-DIPHOSPHATE / Polypeptide N-acetylgalactosaminyltransferase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHurtado-Guerrero, R. / De las Rivas, M.
Funding support Spain, 2items
OrganizationGrant numberCountry
MICINNBFU2016-75633-P Spain
MICINNCTQ2013-44367-C2-2-P Spain
CitationJournal: J. Biol. Chem. / Year: 2017
Title: The small molecule luteolin inhibits N-acetyl-alpha-galactosaminyltransferases and reduces mucin-type O-glycosylation of amyloid precursor protein.
Authors: Liu, F. / Xu, K. / Xu, Z. / de Las Rivas, M. / Wang, C. / Li, X. / Lu, J. / Zhou, Y. / Delso, I. / Merino, P. / Hurtado-Guerrero, R. / Zhang, Y. / Wu, F.
History
DepositionMar 8, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Polypeptide N-acetylgalactosaminyltransferase 2
B: Polypeptide N-acetylgalactosaminyltransferase 2
C: Polypeptide N-acetylgalactosaminyltransferase 2
D: Polypeptide N-acetylgalactosaminyltransferase 2
E: Polypeptide N-acetylgalactosaminyltransferase 2
F: Polypeptide N-acetylgalactosaminyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)393,18231
Polymers388,9486
Non-polymers4,23425
Water15,277848
1
E: Polypeptide N-acetylgalactosaminyltransferase 2
hetero molecules

C: Polypeptide N-acetylgalactosaminyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,6928
Polymers129,6492
Non-polymers1,0426
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_535x+1/2,-y-3/2,-z1
2
F: Polypeptide N-acetylgalactosaminyltransferase 2
hetero molecules

D: Polypeptide N-acetylgalactosaminyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,9789
Polymers129,6492
Non-polymers1,3297
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
3
A: Polypeptide N-acetylgalactosaminyltransferase 2
B: Polypeptide N-acetylgalactosaminyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,51214
Polymers129,6492
Non-polymers1,86312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6030 Å2
ΔGint-25 kcal/mol
Surface area38930 Å2
MethodPISA
4
C: Polypeptide N-acetylgalactosaminyltransferase 2
hetero molecules

E: Polypeptide N-acetylgalactosaminyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,6928
Polymers129,6492
Non-polymers1,0426
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_435x-1/2,-y-3/2,-z1
Buried area5470 Å2
ΔGint-39 kcal/mol
Surface area39080 Å2
MethodPISA
5
D: Polypeptide N-acetylgalactosaminyltransferase 2
hetero molecules

F: Polypeptide N-acetylgalactosaminyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,9789
Polymers129,6492
Non-polymers1,3297
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area5250 Å2
ΔGint-37 kcal/mol
Surface area39270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.980, 123.111, 248.152
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUAA75 - 56975 - 569
21LEULEUBB75 - 56975 - 569
12LEULEUAA75 - 56975 - 569
22LEULEUCC75 - 56975 - 569
13LEULEUAA75 - 56975 - 569
23LEULEUDD75 - 56975 - 569
14PHEPHEAA75 - 56575 - 565
24PHEPHEEE75 - 56575 - 565
15LEULEUAA75 - 56975 - 569
25LEULEUFF75 - 56975 - 569
16LEULEUBB75 - 56975 - 569
26LEULEUCC75 - 56975 - 569
17LEULEUBB75 - 56975 - 569
27LEULEUDD75 - 56975 - 569
18PHEPHEBB75 - 56575 - 565
28PHEPHEEE75 - 56575 - 565
19LEULEUBB75 - 56975 - 569
29LEULEUFF75 - 56975 - 569
110LEULEUCC75 - 56975 - 569
210LEULEUDD75 - 56975 - 569
111PHEPHECC75 - 56575 - 565
211PHEPHEEE75 - 56575 - 565
112LEULEUCC75 - 56975 - 569
212LEULEUFF75 - 56975 - 569
113PHEPHEDD75 - 56575 - 565
213PHEPHEEE75 - 56575 - 565
114LEULEUDD75 - 56975 - 569
214LEULEUFF75 - 56975 - 569
115PHEPHEEE75 - 56575 - 565
215PHEPHEFF75 - 56575 - 565

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

-
Components

-
Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Polypeptide N-acetylgalactosaminyltransferase 2 / Polypeptide GalNAc transferase 2 / pp-GaNTase 2 / Protein-UDP acetylgalactosaminyltransferase 2 / ...Polypeptide GalNAc transferase 2 / pp-GaNTase 2 / Protein-UDP acetylgalactosaminyltransferase 2 / UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 2


Mass: 64824.703 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GALNT2 / Production host: Komagataella pastoris (fungus)
References: UniProt: Q10471, polypeptide N-acetylgalactosaminyltransferase

-
Non-polymers , 5 types, 873 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-LU2 / 2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4H-chromen-4-one / Luteolin


Mass: 286.236 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H10O6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 848 / 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: 2.3 Å3/Da / Density % sol: 46.45 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 10% PEG 8000, 6% ethylene glycol, 100 mM Hepes pH 7

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.3→124.08 Å / Num. obs: 151903 / % possible obs: 95.5 % / Redundancy: 6.7 % / Rpim(I) all: 0.05 / Net I/σ(I): 10.3
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 1.6 / Rpim(I) all: 0.535 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FFV

2ffv


Resolution: 2.3→124.08 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / SU B: 9.027 / SU ML: 0.206 / Cross valid method: THROUGHOUT / ESU R: 0.361 / ESU R Free: 0.244 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25149 4316 2.8 %RANDOM
Rwork0.21311 ---
obs0.2142 147500 95.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 53.476 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2---0.2 Å20 Å2
3---0.24 Å2
Refinement stepCycle: 1 / Resolution: 2.3→124.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23778 0 259 848 24885
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01924594
X-RAY DIFFRACTIONr_bond_other_d0.0020.0222423
X-RAY DIFFRACTIONr_angle_refined_deg1.7291.95533335
X-RAY DIFFRACTIONr_angle_other_deg1.059351888
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.30852987
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.81823.2951217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.612154165
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.26815234
X-RAY DIFFRACTIONr_chiral_restr0.1130.23500
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02127468
X-RAY DIFFRACTIONr_gen_planes_other0.0020.025314
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.5155.18311888
X-RAY DIFFRACTIONr_mcbond_other4.5155.18311887
X-RAY DIFFRACTIONr_mcangle_it6.5587.76814856
X-RAY DIFFRACTIONr_mcangle_other6.5587.76814857
X-RAY DIFFRACTIONr_scbond_it5.1965.69612706
X-RAY DIFFRACTIONr_scbond_other5.1965.69612707
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.9538.32318466
X-RAY DIFFRACTIONr_long_range_B_refined10.72359.59927779
X-RAY DIFFRACTIONr_long_range_B_other10.72559.627780
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A330240.04
12B330240.04
21A329240.05
22C329240.05
31A332300.04
32D332300.04
41A329040.04
42E329040.04
51A330760.04
52F330760.04
61B329280.05
62C329280.05
71B329920.04
72D329920.04
81B326480.04
82E326480.04
91B329520.04
92F329520.04
101C329300.05
102D329300.05
111C326900.04
112E326900.04
121C330380.04
122F330380.04
131D328140.04
132E328140.04
141D330480.04
142F330480.04
151E327880.04
152F327880.04
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 320 -
Rwork0.349 11236 -
obs--99.3 %

+
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