[English] 日本語
Yorodumi
- PDB-6e7i: Human ppGalNAcT2 I253A/L310A Mutant with EA2 and UDP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6e7i
TitleHuman ppGalNAcT2 I253A/L310A Mutant with EA2 and UDP
Components
  • EA2
  • Polypeptide N-acetylgalactosaminyltransferase 2
KeywordsTRANSFERASE / glycosyltransferase / glycosylation / bump-hole / galnac
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 / O-glycan processing / O-linked glycosylation of mucins / regulation of sensory perception of pain / peptidase inhibitor activity / Golgi stack / protein O-linked glycosylation ...protein O-linked glycosylation via threonine / protein O-linked glycosylation via serine / polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / O-glycan processing / O-linked glycosylation of mucins / regulation of sensory perception of pain / peptidase inhibitor activity / Golgi stack / protein O-linked glycosylation / COPI-independent Golgi-to-ER retrograde traffic / positive regulation of immunoglobulin production / Golgi cisterna membrane / endopeptidase inhibitor activity / 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
: / URIDINE-5'-DIPHOSPHATE / Polypeptide N-acetylgalactosaminyltransferase 2 / Apomucin
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBertozzi, C.R. / Schumann, B. / Agbay, A.J.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI)NIH R01 CA200423 United States
CitationJournal: Mol.Cell / Year: 2020
Title: Bump-and-Hole Engineering Identifies Specific Substrates of Glycosyltransferases in Living Cells.
Authors: Schumann, B. / Malaker, S.A. / Wisnovsky, S.P. / Debets, M.F. / Agbay, A.J. / Fernandez, D. / Wagner, L.J.S. / Lin, L. / Li, Z. / Choi, J. / Fox, D.M. / Peh, J. / Gray, M.A. / Pedram, K. / ...Authors: Schumann, B. / Malaker, S.A. / Wisnovsky, S.P. / Debets, M.F. / Agbay, A.J. / Fernandez, D. / Wagner, L.J.S. / Lin, L. / Li, Z. / Choi, J. / Fox, D.M. / Peh, J. / Gray, M.A. / Pedram, K. / Kohler, J.J. / Mrksich, M. / Bertozzi, C.R.
History
DepositionJul 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2Oct 11, 2023Group: 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
Revision 1.3Oct 16, 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
P: EA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4484
Polymers61,9892
Non-polymers4592
Water5,891327
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-28 kcal/mol
Surface area21800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.310, 69.310, 169.780
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
Components

#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: 60670.133 Da / Num. of mol.: 1 / Mutation: I253A,L310A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GALNT2 / Cell line (production host): HEK293 - FreeStyle 293-F / Production host: Homo sapiens (human)
References: UniProt: Q10471, polypeptide N-acetylgalactosaminyltransferase
#2: Protein/peptide EA2


Mass: 1318.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: Q62605
#3: 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
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG8000, HEPES

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 22, 2017
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.8→60.02 Å / Num. obs: 42632 / % possible obs: 92.1 % / Redundancy: 2 % / Biso Wilson estimate: 11.8 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 5.3
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 0.715 / Num. unique obs: 5819 / % possible all: 93.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FFU

2ffu


Resolution: 1.8→56.66 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.922 / SU B: 3.397 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.139 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2155 1998 5.1 %RANDOM
Rwork0.16719 ---
obs0.1696 37096 91.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.453 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å2-0.09 Å20 Å2
2---0.17 Å20 Å2
3---0.56 Å2
Refinement stepCycle: 1 / Resolution: 1.8→56.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3955 25 1 327 4308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0144086
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173551
X-RAY DIFFRACTIONr_angle_refined_deg1.6051.6645549
X-RAY DIFFRACTIONr_angle_other_deg1.0131.6418334
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.995503
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.95421.703229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.28215672
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3591533
X-RAY DIFFRACTIONr_chiral_restr0.0860.2510
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024644
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02764
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_it1.5791.6062012
X-RAY DIFFRACTIONr_mcbond_other1.5741.6052011
X-RAY DIFFRACTIONr_mcangle_it2.4432.4012512
X-RAY DIFFRACTIONr_mcangle_other2.4432.4022513
X-RAY DIFFRACTIONr_scbond_it1.9881.7512074
X-RAY DIFFRACTIONr_scbond_other1.9891.7512075
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0412.5563037
X-RAY DIFFRACTIONr_long_range_B_refined4.43618.5854639
X-RAY DIFFRACTIONr_long_range_B_other4.36218.3814576
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 142 -
Rwork0.249 2876 -
obs--94.76 %

+
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