[English] 日本語
Yorodumi
- PDB-9ftr: Drosophila golgi alpha-mannosidase II (dGMII) in complex with ami... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ftr
TitleDrosophila golgi alpha-mannosidase II (dGMII) in complex with amide modified swainsonine-configured alkyl indolizidine
ComponentsAlpha-mannosidase 2
KeywordsHYDROLASE / Inhibitor / glycosyl hydrolase
Function / homology
Function and homology information


mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase / mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity / rhodopsin biosynthetic process / encapsulation of foreign target / Reactions specific to the complex N-glycan synthesis pathway / mannosidase activity / alpha-mannosidase activity / N-glycan processing / mannose metabolic process / Golgi stack ...mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase / mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity / rhodopsin biosynthetic process / encapsulation of foreign target / Reactions specific to the complex N-glycan synthesis pathway / mannosidase activity / alpha-mannosidase activity / N-glycan processing / mannose metabolic process / Golgi stack / protein glycosylation / carbohydrate binding / Golgi membrane / endoplasmic reticulum / metal ion binding
Similarity search - Function
Alpha-mannosidase 2, C-terminal sub-domain / Glycosyl hydrolases family 38 C-terminal sub-domain / : / Lysosomal alpha-mannosidase-like, central domain / : / Glycoside hydrolase family 38, N-terminal domain / Glycosyl hydrolase family 38, C-terminal / Glycoside hydrolase family 38, central domain / Glycoside hydrolase family 38, central domain superfamily / Glycosyl hydrolases family 38 N-terminal domain ...Alpha-mannosidase 2, C-terminal sub-domain / Glycosyl hydrolases family 38 C-terminal sub-domain / : / Lysosomal alpha-mannosidase-like, central domain / : / Glycoside hydrolase family 38, N-terminal domain / Glycosyl hydrolase family 38, C-terminal / Glycoside hydrolase family 38, central domain / Glycoside hydrolase family 38, central domain superfamily / Glycosyl hydrolases family 38 N-terminal domain / Glycosyl hydrolases family 38 C-terminal domain / Alpha mannosidase middle domain / Alpha mannosidase, middle domain / Glycoside hydrolase families 57/38, central domain superfamily / Glycoside hydrolase 38, N-terminal domain superfamily / Glycoside hydrolase/deacetylase, beta/alpha-barrel / Galactose mutarotase-like domain superfamily / Glycosyl hydrolase, all-beta
Similarity search - Domain/homology
: / Alpha-mannosidase 2
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsBennett, M. / Koemans, T. / Overkleeft, H.S. / Davies, G.J.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: Chem.Commun.(Camb.) / Year: 2024
Title: Structure-guided design of C3-branched swainsonine as potent and selective human Golgi alpha-mannosidase (GMII) inhibitor.
Authors: Koemans, T. / Bennett, M. / Ferraz, M.J. / Armstrong, Z. / Artola, M. / Aerts, J.M.F.G. / Codee, J.D.C. / Overkleeft, H.S. / Davies, G.J.
History
DepositionJun 25, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alpha-mannosidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,92625
Polymers118,2081
Non-polymers1,71824
Water5,567309
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint68 kcal/mol
Surface area34030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.113, 91.939, 133.241
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Alpha-mannosidase 2 / Golgi alpha-mannosidase II / Man II / Golgi alpha-mannosidase IIa / Mannosyl-oligosaccharide 1 / 3- ...Golgi alpha-mannosidase II / Man II / Golgi alpha-mannosidase IIa / Mannosyl-oligosaccharide 1 / 3-1 / 6-alpha-mannosidase


Mass: 118208.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: alpha-Man-IIa, GmII, CG18802 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q24451, mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase
#2: Chemical ChemComp-A1IGB / amide modified swainsonine-configured alkyl indolizidine / (1S,2R,3S,8R,8aR)-1,2,8-tris(oxidanyl)-N-pentyl-2,3,4,5,6,7,8,8a-octahydro-1H-indolizin-4-ium-3-carboxamide


Mass: 287.375 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H27N2O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM succinate pH 7.0 and 6-12% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.14→57.681 Å / Num. obs: 61056 / % possible obs: 100 % / Redundancy: 1.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.045 / Net I/σ(I): 9.6
Reflection shellResolution: 2.14→2.2 Å / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 1 / Num. unique obs: 4448 / CC1/2: 0.682 / Rpim(I) all: 0.352 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.14→57.681 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.915 / SU B: 7.499 / SU ML: 0.184 / Cross valid method: NONE / ESU R: 0.219 / ESU R Free: 0.209 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2589 1578 2.585 %
Rwork0.1794 59478 -
all0.181 --
obs-61056 99.989 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 37.487 Å2
Baniso -1Baniso -2Baniso -3
1--1.64 Å20 Å2-0 Å2
2--0.729 Å2-0 Å2
3---0.911 Å2
Refinement stepCycle: LAST / Resolution: 2.14→57.681 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7902 0 107 309 8318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0128233
X-RAY DIFFRACTIONr_angle_refined_deg2.581.82611155
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3495996
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.114551
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.391101294
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.21210385
X-RAY DIFFRACTIONr_chiral_restr0.1830.21206
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.026369
X-RAY DIFFRACTIONr_nbd_refined0.1960.23755
X-RAY DIFFRACTIONr_nbtor_refined0.2980.25412
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2491
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.5170.242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.680.25
X-RAY DIFFRACTIONr_mcbond_it5.0623.713999
X-RAY DIFFRACTIONr_mcangle_it6.46.6514990
X-RAY DIFFRACTIONr_scbond_it6.3083.7214234
X-RAY DIFFRACTIONr_scangle_it8.0486.7286165
X-RAY DIFFRACTIONr_lrange_it8.92637.82312303
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.14-2.1960.3051290.27243130.27344420.9260.941000.26
2.196-2.2560.4061040.27542360.27843400.8780.9391000.258
2.256-2.3210.3141130.26841020.26942150.930.9451000.246
2.321-2.3920.279900.22840040.22940940.9440.9611000.2
2.392-2.470.2571190.21839090.21940280.9560.9661000.187
2.47-2.5570.2891060.20937320.21138380.9390.9681000.172
2.557-2.6530.275800.19636250.19837050.9490.9731000.162
2.653-2.7610.3021030.19235000.19536030.9430.9741000.156
2.761-2.8840.267760.1833790.18234550.9570.9781000.146
2.884-3.0240.263950.17832000.18132950.9520.9791000.147
3.024-3.1870.294850.18230780.18531640.9450.97899.96840.155
3.187-3.380.297890.18228840.18629730.9470.981000.155
3.38-3.6130.222800.17427340.17528140.9720.9831000.152
3.613-3.9010.273630.17125660.17326290.9510.9841000.151
3.901-4.2710.213520.1423990.14224510.9730.9891000.123
4.271-4.7720.233470.1221600.12222070.9650.9921000.106
4.772-5.5040.159440.12419110.12519550.9830.9911000.111
5.504-6.7260.253500.1716410.17316930.970.98699.88190.154
6.726-9.4480.203310.16613000.16713310.9780.9861000.152
9.448-57.6810.24220.1997880.1998100.9530.9741000.198

+
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