[English] 日本語
Yorodumi
- PDB-6nqt: GalNac-T2 soaked with UDP-sugar -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6nqt
TitleGalNac-T2 soaked with UDP-sugar
ComponentsPolypeptide N-acetylgalactosaminyltransferase 2
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Inhibitor / Complex / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
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-LR7 / : / Polypeptide N-acetylgalactosaminyltransferase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsFernandez, D. / Bertozzi, C.R. / Schumann, B. / Agbay, A.
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
DepositionJan 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
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 / _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
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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
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)392,72418
Polymers388,4376
Non-polymers4,28612
Water3,405189
1
A: Polypeptide N-acetylgalactosaminyltransferase 2
C: Polypeptide N-acetylgalactosaminyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,9086
Polymers129,4792
Non-polymers1,4294
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-10 kcal/mol
Surface area38480 Å2
MethodPISA
2
B: Polypeptide N-acetylgalactosaminyltransferase 2
D: Polypeptide N-acetylgalactosaminyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,9086
Polymers129,4792
Non-polymers1,4294
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-19 kcal/mol
Surface area38800 Å2
MethodPISA
3
F: Polypeptide N-acetylgalactosaminyltransferase 2
hetero molecules

E: Polypeptide N-acetylgalactosaminyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,9086
Polymers129,4792
Non-polymers1,4294
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445x-1/2,-y-1/2,-z1
Buried area3250 Å2
ΔGint-27 kcal/mol
Surface area38900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.575, 120.126, 247.389
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: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALASNASNAA76 - 56876 - 568
21VALVALASNASNBB76 - 56876 - 568
12LYSLYSLEULEUAA75 - 56975 - 569
22LYSLYSLEULEUCC75 - 56975 - 569
13LYSLYSLEULEUAA75 - 56975 - 569
23LYSLYSLEULEUDD75 - 56975 - 569
14LYSLYSLEULEUAA75 - 56975 - 569
24LYSLYSLEULEUEE75 - 56975 - 569
15ASNASNASNASNAA82 - 56882 - 568
25ASNASNASNASNFF82 - 56882 - 568
16VALVALLEULEUBB76 - 56976 - 569
26VALVALLEULEUCC76 - 56976 - 569
17VALVALASNASNBB76 - 56876 - 568
27VALVALASNASNDD76 - 56876 - 568
18VALVALLEULEUBB76 - 56976 - 569
28VALVALLEULEUEE76 - 56976 - 569
19ASNASNASNASNBB82 - 56882 - 568
29ASNASNASNASNFF82 - 56882 - 568
110LYSLYSLEULEUCC75 - 56975 - 569
210LYSLYSLEULEUDD75 - 56975 - 569
111LYSLYSLEULEUCC75 - 56975 - 569
211LYSLYSLEULEUEE75 - 56975 - 569
112ASNASNASNASNCC82 - 56882 - 568
212ASNASNASNASNFF82 - 56882 - 568
113LYSLYSLEULEUDD75 - 56975 - 569
213LYSLYSLEULEUEE75 - 56975 - 569
114ASNASNASNASNDD82 - 56882 - 568
214ASNASNASNASNFF82 - 56882 - 568
115ASNASNLEULEUEE82 - 56982 - 569
215ASNASNLEULEUFF82 - 56982 - 569

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

-
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: 64739.562 Da / Num. of mol.: 6 / Mutation: ILE253A, LEU310A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GALNT2 / Cell line (production host): HEK293 / Organ (production host): Kidney / Production host: Homo sapiens (human)
References: UniProt: Q10471, polypeptide N-acetylgalactosaminyltransferase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-LR7 / [[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{R},6~{R})-3-(hex-5-ynoylamino)-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl] hydrogen phosphate


Mass: 659.428 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H31N3O17P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHE AUTHORS STATE THAT ATOM C1' IN LR7 IN CHAIN D HAS A WEAK DENSITY, AND THIS IS THE BEST THEY COULD MODEL.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9753 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9753 Å / Relative weight: 1
ReflectionResolution: 3.05→39 Å / Num. obs: 64645 / % possible obs: 97.1 % / Redundancy: 3 % / Biso Wilson estimate: 44.5 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.09 / Net I/σ(I): 7.7
Reflection shellResolution: 3.05→3.21 Å / Redundancy: 3 % / Rmerge(I) obs: 0.771 / Num. unique obs: 9466 / CC1/2: 0.646 / Rpim(I) all: 0.521 / % possible all: 98.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4d0t

4d0t


Resolution: 3.05→20.7 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.859 / SU B: 30.728 / SU ML: 0.522 / Cross valid method: THROUGHOUT / ESU R Free: 0.553 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28596 3345 5.2 %RANDOM
Rwork0.23123 ---
obs0.23408 61083 96.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.875 Å2
Baniso -1Baniso -2Baniso -3
1-5.99 Å20 Å20 Å2
2---0.89 Å20 Å2
3----5.1 Å2
Refinement stepCycle: 1 / Resolution: 3.05→20.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22685 0 264 189 23138
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01923505
X-RAY DIFFRACTIONr_bond_other_d0.0070.0220903
X-RAY DIFFRACTIONr_angle_refined_deg2.061.9431966
X-RAY DIFFRACTIONr_angle_other_deg1.2232.98948225
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.374.9592961
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.61323.4441089
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.426153652
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.17915192
X-RAY DIFFRACTIONr_chiral_restr0.1380.23471
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02126512
X-RAY DIFFRACTIONr_gen_planes_other0.0020.025017
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_it4.3096.60811760
X-RAY DIFFRACTIONr_mcbond_other4.3096.60811759
X-RAY DIFFRACTIONr_mcangle_it6.8789.90614679
X-RAY DIFFRACTIONr_mcangle_other6.8789.90614680
X-RAY DIFFRACTIONr_scbond_it3.8316.62311745
X-RAY DIFFRACTIONr_scbond_other3.8316.62411746
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1089.88317288
X-RAY DIFFRACTIONr_long_range_B_refined9.48476.79226244
X-RAY DIFFRACTIONr_long_range_B_other9.48376.79226245
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)
11A280480.16
12B280480.16
21A284320.16
22C284320.16
31A281940.16
32D281940.16
41A267180.18
42E267180.18
51A251220.18
52F251220.18
61B272960.17
62C272960.17
71B272120.17
72D272120.17
81B258780.18
82E258780.18
91B244440.19
92F244440.19
101C274060.16
102D274060.16
111C262640.17
112E262640.17
121C246500.18
122F246500.18
131D260060.17
132E260060.17
141D246480.18
142F246480.18
151E237080.19
152F237080.19
LS refinement shellResolution: 3.05→3.127 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 242 -
Rwork0.366 4436 -
obs--97.87 %

+
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