[English] 日本語
Yorodumi
- PDB-5vcr: Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransf... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vcr
TitleAlpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase with bound uranium dioxide
ComponentsAlpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase
KeywordsTRANSFERASE / glycosyltransferase / MGAT2 / Complex N-gly / Branched acceptor
Function / homology
Function and homology information


alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase / alpha-1,6-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity / Defective MGAT2 causes CDG-2a / Reactions specific to the complex N-glycan synthesis pathway / oligosaccharide biosynthetic process / protein N-linked glycosylation via asparagine / Golgi stack / protein N-linked glycosylation / manganese ion binding / Maturation of spike protein ...alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase / alpha-1,6-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity / Defective MGAT2 causes CDG-2a / Reactions specific to the complex N-glycan synthesis pathway / oligosaccharide biosynthetic process / protein N-linked glycosylation via asparagine / Golgi stack / protein N-linked glycosylation / manganese ion binding / Maturation of spike protein / viral protein processing / Golgi membrane / Golgi apparatus / protein homodimerization activity / membrane
Similarity search - Function
N-acetylglucosaminyltransferase II / N-acetylglucosaminyltransferase II (MGAT2) / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
URANYL (VI) ION / Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.992 Å
AuthorsSanders, J.H. / Kadirvelraj, R. / Wood, Z.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1P01GM107012-02 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: HumanN-acetylglucosaminyltransferase II substrate recognition uses a modular architecture that includes a convergent exosite.
Authors: Kadirvelraj, R. / Yang, J.Y. / Sanders, J.H. / Liu, L. / Ramiah, A. / Prabhakar, P.K. / Boons, G.J. / Wood, Z.A. / Moremen, K.W.
History
DepositionMar 31, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / 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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 2, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3May 16, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase
B: Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,14710
Polymers96,6962
Non-polymers1,4508
Water5,296294
1
A: Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1455
Polymers48,3481
Non-polymers7974
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0025
Polymers48,3481
Non-polymers6544
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.670, 105.670, 171.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-712-

HOH

-
Components

-
Protein / Sugars , 2 types, 3 molecules AB

#1: Protein Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase / Beta-1 / 2-N-acetylglucosaminyltransferase II / GlcNAc-T II / GNT-II / Mannoside ...Beta-1 / 2-N-acetylglucosaminyltransferase II / GlcNAc-T II / GNT-II / Mannoside acetylglucosaminyltransferase 2 / N-glycosyl-oligosaccharide-glycoprotein N-acetylglucosaminyltransferase II


Mass: 48348.117 Da / Num. of mol.: 2 / Fragment: UNP residues 29-447
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MGAT2 / Production host: Homo sapiens (human)
References: UniProt: Q10469, alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 4 types, 301 molecules

#2: Chemical
ChemComp-IUM / URANYL (VI) ION / Uranyl


Mass: 270.028 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O2U
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.4 M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.74 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Dec 13, 2015
RadiationMonochromator: Rosenbaum-Rock double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.74 Å / Relative weight: 1
ReflectionResolution: 1.992→56.397 Å / Num. obs: 126205 / % possible obs: 99 % / Redundancy: 14.1 % / Net I/σ(I): 17.7
Reflection shellHighest resolution: 1.992 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementResolution: 1.992→56.397 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.34
RfactorNum. reflection% reflection
Rfree0.208 6294 5 %
Rwork0.1766 --
obs0.1782 125828 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.992→56.397 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5768 0 32 294 6094
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0175995
X-RAY DIFFRACTIONf_angle_d1.4568153
X-RAY DIFFRACTIONf_dihedral_angle_d12.83539
X-RAY DIFFRACTIONf_chiral_restr0.087864
X-RAY DIFFRACTIONf_plane_restr0.011029
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9922-2.01480.40821500.3712863X-RAY DIFFRACTION71
2.0148-2.03850.30382030.30533944X-RAY DIFFRACTION98
2.0385-2.06340.29422120.27594004X-RAY DIFFRACTION100
2.0634-2.08950.28842100.26364022X-RAY DIFFRACTION100
2.0895-2.1170.23042140.21964020X-RAY DIFFRACTION100
2.117-2.1460.25652090.20644049X-RAY DIFFRACTION100
2.146-2.17660.25732090.20143996X-RAY DIFFRACTION100
2.1766-2.20910.21342140.19554058X-RAY DIFFRACTION100
2.2091-2.24370.26832180.18754012X-RAY DIFFRACTION100
2.2437-2.28040.23552120.17874026X-RAY DIFFRACTION100
2.2804-2.31980.23422110.17054044X-RAY DIFFRACTION100
2.3198-2.36190.19852140.16823991X-RAY DIFFRACTION100
2.3619-2.40740.20532100.17014054X-RAY DIFFRACTION100
2.4074-2.45650.21712140.1724057X-RAY DIFFRACTION100
2.4565-2.50990.26212040.16923971X-RAY DIFFRACTION100
2.5099-2.56830.23052160.17154063X-RAY DIFFRACTION100
2.5683-2.63250.21342110.17124018X-RAY DIFFRACTION100
2.6325-2.70370.23962110.174019X-RAY DIFFRACTION100
2.7037-2.78330.2292100.16634050X-RAY DIFFRACTION100
2.7833-2.87310.19932110.15644006X-RAY DIFFRACTION100
2.8731-2.97580.21142170.17164025X-RAY DIFFRACTION100
2.9758-3.09490.24692110.18514031X-RAY DIFFRACTION100
3.0949-3.23580.24052090.18114019X-RAY DIFFRACTION100
3.2358-3.40640.17552170.16714054X-RAY DIFFRACTION100
3.4064-3.61970.17092120.15413989X-RAY DIFFRACTION100
3.6197-3.89920.18322200.14934036X-RAY DIFFRACTION100
3.8992-4.29140.16192180.1384034X-RAY DIFFRACTION100
4.2914-4.91210.14692070.14044001X-RAY DIFFRACTION100
4.9121-6.18750.20722150.18114038X-RAY DIFFRACTION100
6.1875-56.420.21742050.22524040X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.17890.0808-0.38874.1699-0.10572.6287-0.0394-0.0270.1559-0.09990.11850.0774-0.2720.0146-0.04920.328-0.0310.06330.18480.02450.266250.481589.017575.7205
21.0788-2.38010.68817.5985-0.26261.1656-0.01890.25150.0469-0.2915-0.0299-0.3714-0.03040.11240.05730.2395-0.05930.11570.2574-0.01280.329155.217183.435572.067
37.1126-0.2048-2.47653.04761.51075.1784-0.29090.2075-0.6985-0.0056-0.05630.2220.5106-0.1040.31090.3752-0.00280.05650.2913-0.04460.507958.864954.222169.7481
44.6086-0.1353-0.78153.07850.08741.72230.10710.10490.03890.0273-0.08860.509-0.1195-0.3617-0.01750.2762-0.00020.05760.30150.00960.351835.924780.170481.5316
54.4031-1.5970.37833.6801-0.24611.8373-0.0566-0.0395-0.12090.1083-0.00020.2719-0.0085-0.10590.04710.2181-0.03020.06950.24090.00490.339238.985670.313983.2237
67.84873.1698-3.50997.1286-1.3197.3062-0.15821.09180.695-0.93580.2691.231-0.6286-0.5594-0.11730.52360.0472-0.1640.66850.07010.787223.502687.825771.3595
77.7721-2.122-4.23092.89881.76263.116-0.20650.1287-0.61550.07050.1035-0.0380.0875-0.02660.10660.24420.00050.02080.16570.08850.188445.238664.182181.8359
85.224-1.4833-0.06376.5144-0.45662.5192-0.0431-0.09330.02570.1304-0.08650.18230.0671-0.15930.10550.2371-0.08060.07240.2273-0.03240.292860.792103.00874.2002
98.367-1.15734.44131.7774-1.01933.1468-0.12820.1146-0.02380.1535-0.0259-0.2410.00860.28380.15110.2966-0.00920.07950.2779-0.02240.291486.1064104.407475.5124
102.6723-0.2046-0.42164.25981.38322.907-0.08980.2240.5305-0.3102-0.01580.1401-0.2995-0.10040.05720.3123-0.0154-0.02540.25170.03190.420862.4401122.87267.3358
113.8709-1.0906-0.36622.54220.35321.2379-0.03350.1780.4822-0.1426-0.0577-0.023-0.1239-0.09160.09140.3116-0.05490.00840.2417-0.01140.363672.5346121.077168.6543
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 84 through 157 )
2X-RAY DIFFRACTION2chain 'A' and (resid 158 through 191 )
3X-RAY DIFFRACTION3chain 'A' and (resid 192 through 224 )
4X-RAY DIFFRACTION4chain 'A' and (resid 225 through 324 )
5X-RAY DIFFRACTION5chain 'A' and (resid 325 through 388 )
6X-RAY DIFFRACTION6chain 'A' and (resid 389 through 415 )
7X-RAY DIFFRACTION7chain 'A' and (resid 416 through 445 )
8X-RAY DIFFRACTION8chain 'B' and (resid 84 through 176 )
9X-RAY DIFFRACTION9chain 'B' and (resid 177 through 243 )
10X-RAY DIFFRACTION10chain 'B' and (resid 244 through 324 )
11X-RAY DIFFRACTION11chain 'B' and (resid 325 through 444 )

+
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