[English] 日本語
Yorodumi
- PDB-9ep0: Dolichyl phosphate mannose synthase in complex with donor (GDP-Ma... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ep0
TitleDolichyl phosphate mannose synthase in complex with donor (GDP-Man) and traces of acceptor (Dol55P) and product (Dol55P-Man)
ComponentsDolichol monophosphate mannose synthase
KeywordsTRANSFERASE / Dolichyl phosphate mannose synthase / enzyme / integral membrane protein / protein glycosylation / glycosylphosphatidylinositol synthesis / GDP-mannose / dolichyl monophosphate / dolichol monophosphate mannose / donor-acceptor and product complex
Function / homology
Function and homology information


dolichyl-phosphate beta-D-mannosyltransferase / dolichyl-phosphate beta-D-mannosyltransferase activity / dolichol phosphate mannose biosynthetic process / GPI anchor biosynthetic process / dolichol-linked oligosaccharide biosynthetic process / protein O-linked glycosylation via mannose / polysaccharide biosynthetic process / metal ion binding / plasma membrane
Similarity search - Function
GtrA-like protein / DPM1-like / GtrA/DPMS, transmembrane domain / Glycosyltransferase 2-like / Glycosyl transferase family 2 / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
ETHYL DIHYDROGEN PHOSPHATE / GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE / dolichyl phosphate mannose / Dolichol-phosphate mannosyltransferase
Similarity search - Component
Biological speciesPyrococcus furiosus DSM 3638 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsGandini, R. / Keskitalo, M.M. / Reichenbach, T. / Divne, C.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council2017-03877 Sweden
Swedish Research Council2013-5717 Sweden
CitationJournal: To be published
Title: Crystal structure of Pyrococcus furiosus dolichylphosphate mannose synthase in complex with substrates (GDP-Man and DolP) and traces of a flipped glycolipid product (DolP-Man)
Authors: Gandini, R. / Keskitalo, M. / Reichenbach, T. / Divne, C.
History
DepositionMar 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dolichol monophosphate mannose synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4525
Polymers42,6851
Non-polymers1,7674
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, The protein is a monomer in solution (SEC) and in the crystal
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-21 kcal/mol
Surface area17760 Å2
Unit cell
Length a, b, c (Å)87.800, 145.250, 99.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Dolichol monophosphate mannose synthase


Mass: 42684.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal hexa-histdine tag and TEV protease cleavage site added by the expression plasmid
Source: (gene. exp.) Pyrococcus furiosus DSM 3638 (archaea) / Strain: DSM 3638 / Gene: PF0058 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli B (bacteria) / References: UniProt: Q8U4M3
#2: Chemical ChemComp-GDD / GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE


Mass: 605.341 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H25N5O16P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EFS / ETHYL DIHYDROGEN PHOSPHATE


Mass: 126.048 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H7O4P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MJC / dolichyl phosphate mannose


Mass: 1011.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C61H103O9P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.7 Å3/Da / Density % sol: 66.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M potassium chloride, 0.1 M trisodium citrate (pH 5.5), 37% (v/v) pentaerythritol propoxylate (5/4 PO/OH), 50 mM Hepes (pH 7.5), 150 mM NaCl, 10% (v/v) glycerol, 0.05% LDAO, 5 mM GDP- ...Details: 0.2 M potassium chloride, 0.1 M trisodium citrate (pH 5.5), 37% (v/v) pentaerythritol propoxylate (5/4 PO/OH), 50 mM Hepes (pH 7.5), 150 mM NaCl, 10% (v/v) glycerol, 0.05% LDAO, 5 mM GDP-mannose, 5 mM MgCl2, 0.25 mM C55 dolichyl phosphate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.9→43.9 Å / Num. obs: 14327 / % possible obs: 99.6 % / Redundancy: 13.2 % / Biso Wilson estimate: 89.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.133 / Net I/σ(I): 15.4
Reflection shellResolution: 2.9→3 Å / Redundancy: 13.7 % / Num. unique obs: 1357 / CC1/2: 0.715 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→43.9 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 37.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3006 1442 10.07 %
Rwork0.2369 --
obs0.2429 14315 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→43.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2771 0 88 0 2859
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092924
X-RAY DIFFRACTIONf_angle_d1.1833963
X-RAY DIFFRACTIONf_dihedral_angle_d10.17423
X-RAY DIFFRACTIONf_chiral_restr0.058452
X-RAY DIFFRACTIONf_plane_restr0.015476
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-30.51551360.50241257X-RAY DIFFRACTION99
3-3.120.43491510.37591245X-RAY DIFFRACTION99
3.12-3.270.41021400.31071290X-RAY DIFFRACTION99
3.27-3.440.35421370.27541250X-RAY DIFFRACTION100
3.44-3.650.34411470.26391271X-RAY DIFFRACTION100
3.65-3.940.30221440.23861277X-RAY DIFFRACTION100
3.94-4.330.32291430.21881292X-RAY DIFFRACTION100
4.33-4.960.26171400.19271309X-RAY DIFFRACTION100
4.96-6.240.24571500.22211308X-RAY DIFFRACTION100

+
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