[English] 日本語
Yorodumi
- PDB-7q4i: Crystal structure of DmC1GalT1 in complex with UDP-Mn2+ and the A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7q4i
TitleCrystal structure of DmC1GalT1 in complex with UDP-Mn2+ and the APD-TGalNAc-RP
Components
  • Glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase 1
  • Mucin-1
KeywordsTRANSFERASE / C1GalT1 / T-synthase / T antigen / Tn antigen / mucin-type O-glycosylation
Function / homology
Function and homology information


N-acetylgalactosaminide beta-1,3-galactosyltransferase / glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase activity / O-glycan processing, core 1 / beta-1,3-galactosyltransferase activity / O-linked glycosylation of mucins / negative regulation of hematopoietic stem cell differentiation / central nervous system morphogenesis / Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 ...N-acetylgalactosaminide beta-1,3-galactosyltransferase / glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase activity / O-glycan processing, core 1 / beta-1,3-galactosyltransferase activity / O-linked glycosylation of mucins / negative regulation of hematopoietic stem cell differentiation / central nervous system morphogenesis / Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis / glycolipid biosynthetic process / O-linked glycosylation of mucins / negative regulation of cell adhesion mediated by integrin / regulation of filopodium assembly / negative regulation of transcription by competitive promoter binding / muscle cell development / neuromuscular junction development / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Dectin-2 family / protein glycosylation / DNA damage response, signal transduction by p53 class mediator / localization / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / transcription coregulator activity / Golgi lumen / p53 binding / Interleukin-4 and Interleukin-13 signaling / vesicle / membrane => GO:0016020 / apical plasma membrane / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / metal ion binding / nucleus / plasma membrane
Similarity search - Function
Glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase 1 / Fringe-like / Fringe-like / Domain found in sea urchin sperm protein, enterokinase, agrin / SEA domain superfamily / SEA domain profile. / SEA domain / SEA domain
Similarity search - Domain/homology
2-acetamido-2-deoxy-alpha-D-galactopyranose / : / URIDINE-5'-DIPHOSPHATE / Mucin-1 / Glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase 1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGonzalez-Ramirez, A.M. / Coelho, H. / Companon, I. / Grosso, A.S. / Yang, Z. / Narimatsu, Y. / Clausen, H. / Marcelo, F. / Corzana, F. / Hurtado-Guerrero, R.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2019-105451GB-I00 Spain
CitationJournal: Nat Commun / Year: 2022
Title: Structural basis for the synthesis of the core 1 structure by C1GalT1.
Authors: Gonzalez-Ramirez, A.M. / Grosso, A.S. / Yang, Z. / Companon, I. / Coelho, H. / Narimatsu, Y. / Clausen, H. / Marcelo, F. / Corzana, F. / Hurtado-Guerrero, R.
History
DepositionOct 31, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase 1
B: Glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase 1
G: Mucin-1
F: Mucin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,39013
Polymers73,8434
Non-polymers1,5479
Water1,33374
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9570 Å2
ΔGint-46 kcal/mol
Surface area22510 Å2
Unit cell
Length a, b, c (Å)50.241, 80.445, 71.949
Angle α, β, γ (deg.)90.00, 93.19, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 0 / Auth seq-ID: 87 - 364 / Label seq-ID: 15 - 292

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

-
Protein / Protein/peptide / Sugars , 3 types, 6 molecules ABGF

#1: Protein Glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase 1 / / Core 1 O-glycan T-synthase / Core 1 UDP-galactose:N-acetylgalactosamine-alpha-R beta 1 / 3- ...Core 1 O-glycan T-synthase / Core 1 UDP-galactose:N-acetylgalactosamine-alpha-R beta 1 / 3-galactosyltransferase 1 / Core 1 beta1 / C1GalT1 / Core 1 beta3-Gal-T1


Mass: 36265.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: C1GalTA, CG9520 / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
References: UniProt: Q7K237, N-acetylgalactosaminide beta-1,3-galactosyltransferase
#2: Protein/peptide Mucin-1 / / MUC-1 / Breast carcinoma-associated antigen DF3 / Cancer antigen 15-3 / CA 15-3 / Carcinoma- ...MUC-1 / Breast carcinoma-associated antigen DF3 / Cancer antigen 15-3 / CA 15-3 / Carcinoma-associated mucin / Episialin / H23AG / Krebs von den Lungen-6 / KL-6 / PEMT / Peanut-reactive urinary mucin / PUM / Polymorphic epithelial mucin / PEM / Tumor-associated epithelial membrane antigen / EMA / Tumor-associated mucin


Mass: 655.724 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P15941
#6: Sugar ChemComp-A2G / 2-acetamido-2-deoxy-alpha-D-galactopyranose / N-acetyl-alpha-D-galactosamine / 2-acetamido-2-deoxy-alpha-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE / N-Acetylgalactosamine


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-galactopyranosamineCOMMON NAMEGMML 1.0
a-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 4 types, 81 molecules

#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


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


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: potassium thiocyanate, Polyethylene glycol monomethyl ether 2,000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9919 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9919 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 22437 / % possible obs: 99.8 % / Redundancy: 3.4 % / CC1/2: 0.981 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.091 / Net I/σ(I): 7.1
Reflection shellResolution: 2.4→2.53 Å / Rmerge(I) obs: 0.825 / Num. unique obs: 3241 / CC1/2: 0.412 / Rpim(I) all: 0.526

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AF-Q9NS00-F1-model_v1.pdb

Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.92 / SU B: 8.877 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.624 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23466 841 3.8 %RANDOM
Rwork0.17547 ---
obs0.1778 21579 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.346 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å2-2.71 Å2
2--0.25 Å2-0 Å2
3----0.1 Å2
Refinement stepCycle: 1 / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4570 0 178 74 4822
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0134899
X-RAY DIFFRACTIONr_bond_other_d0.0030.0164434
X-RAY DIFFRACTIONr_angle_refined_deg1.7691.6956657
X-RAY DIFFRACTIONr_angle_other_deg1.421.63310243
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6365560
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.38622.113265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.22615782
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7481529
X-RAY DIFFRACTIONr_chiral_restr0.080.2604
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025448
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021168
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_it2.8263.1892242
X-RAY DIFFRACTIONr_mcbond_other2.8253.1862240
X-RAY DIFFRACTIONr_mcangle_it4.3414.7742797
X-RAY DIFFRACTIONr_mcangle_other4.3414.7762798
X-RAY DIFFRACTIONr_scbond_it3.6223.5822657
X-RAY DIFFRACTIONr_scbond_other3.6223.5822658
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6655.213860
X-RAY DIFFRACTIONr_long_range_B_refined7.61336.3365415
X-RAY DIFFRACTIONr_long_range_B_other7.61336.3245405
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 9246 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 49 -
Rwork0.226 1585 -
obs--99.88 %

+
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