[English] 日本語
Yorodumi
- PDB-5oge: Crystal structure of a nucleotide sugar transporter -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5oge
TitleCrystal structure of a nucleotide sugar transporter
ComponentsGDP-mannose transporter 1
KeywordsMEMBRANE PROTEIN / SLC35 / Golgi transporter
Function / homology
Function and homology information


GDP-mannose transmembrane transporter activity / GDP-mannose transmembrane transport / antiporter activity / cytoplasmic vesicle membrane / Golgi membrane / endoplasmic reticulum membrane / Golgi apparatus / mitochondrion
Similarity search - Function
UAA transporter / UAA transporter family / :
Similarity search - Domain/homology
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / GDP-mannose transporter 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.22 Å
AuthorsNewstead, S. / Parker, J.L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust102890/Z/13/Z United Kingdom
CitationJournal: Nature / Year: 2017
Title: Structural basis of nucleotide sugar transport across the Golgi membrane.
Authors: Parker, J.L. / Newstead, S.
History
DepositionJul 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation
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.pdbx_database_id_PubMed / _citation.year
Revision 1.2Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GDP-mannose transporter 1
B: GDP-mannose transporter 1
C: GDP-mannose transporter 1
D: GDP-mannose transporter 1
E: GDP-mannose transporter 1
F: GDP-mannose transporter 1
G: GDP-mannose transporter 1
H: GDP-mannose transporter 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)300,63520
Polymers296,3568
Non-polymers4,27812
Water00
1
A: GDP-mannose transporter 1
E: GDP-mannose transporter 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8727
Polymers74,0892
Non-polymers1,7835
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-19 kcal/mol
Surface area31370 Å2
MethodPISA
2
B: GDP-mannose transporter 1
hetero molecules

G: GDP-mannose transporter 1


Theoretical massNumber of molelcules
Total (without water)74,8024
Polymers74,0892
Non-polymers7132
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area1480 Å2
ΔGint-16 kcal/mol
Surface area31850 Å2
MethodPISA
3
C: GDP-mannose transporter 1

H: GDP-mannose transporter 1


Theoretical massNumber of molelcules
Total (without water)74,0892
Polymers74,0892
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area1140 Å2
ΔGint-14 kcal/mol
Surface area31070 Å2
MethodPISA
4
D: GDP-mannose transporter 1
F: GDP-mannose transporter 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8727
Polymers74,0892
Non-polymers1,7835
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-20 kcal/mol
Surface area32070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.570, 102.910, 181.410
Angle α, β, γ (deg.)89.92, 90.12, 90.06
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
GDP-mannose transporter 1 / GMT 1 / Low dye-binding protein 3 / Morphogenesis checkpoint-dependent protein 3 / Vanadate ...GMT 1 / Low dye-binding protein 3 / Morphogenesis checkpoint-dependent protein 3 / Vanadate resistance glycosylation protein 4


Mass: 37044.504 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: VRG4, GOG5, LDB3, MCD3, VAN2, VIG4, YGL225W / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): BJ5460 / References: UniProt: P40107
#2: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C21H40O4

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.16 %
Crystal growTemperature: 277 K / Method: lipidic cubic phase / pH: 5
Details: 26 - 30 % (v/v) PEG 400, 0.1 M sodium citrate pH 5.0 and 75 mM sodium chloride or sodium acetate

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 2.7 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.7 Å / Relative weight: 1
ReflectionResolution: 3.22→45.35 Å / Num. obs: 48151 / % possible obs: 90.3 % / Redundancy: 8.4 % / Biso Wilson estimate: 112.71 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.07 / Net I/σ(I): 8.9
Reflection shellResolution: 3.22→3.3 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.688 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2345 / CC1/2: 0.564 / Rpim(I) all: 0.688 / % possible all: 60.1

-
Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.22→45.35 Å / Cor.coef. Fo:Fc: 0.876 / Cor.coef. Fo:Fc free: 0.844 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.607
RfactorNum. reflection% reflectionSelection details
Rfree0.306 2328 4.83 %RANDOM
Rwork0.28 ---
obs0.281 48149 90.3 %-
Displacement parametersBiso mean: 97.43 Å2
Baniso -1Baniso -2Baniso -3
1-18.2152 Å22.9935 Å27.848 Å2
2---31.1612 Å27.6712 Å2
3---12.946 Å2
Refine analyzeLuzzati coordinate error obs: 0 Å
Refinement stepCycle: 1 / Resolution: 3.22→45.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18836 0 300 0 19136
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00919996HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0227519HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6679SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes303HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2820HARMONIC5
X-RAY DIFFRACTIONt_it19996HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.05
X-RAY DIFFRACTIONt_other_torsion22.4
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2675SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact23664SEMIHARMONIC4
LS refinement shellResolution: 3.22→3.3 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 153 6.54 %
Rwork0.271 2188 -
all0.275 2341 -
obs--60.16 %
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)
10.9259-0.1357-0.27380.45350.34692.0875-0.0291-0.02150.0158-0.11870.093-0.0282-0.1966-0.1428-0.0639-0.0986-0.0185-0.0525-0.1617-0.0333-0.1969-45.3088-49.095233.7087
20.8229-0.03530.20660.7155-0.69262.09-0.03030.0129-0.0505-0.13770.05290.06670.19560.0949-0.0226-0.1105-0.0002-0.0703-0.1295-0.0527-0.2132-41.4746-55.7349124.4102
30.75560.1741-0.40130.6-1.02621.7592-0.0115-0.0290.13950.10440.03260.0784-0.12890.1116-0.0211-0.1479-0.0226-0.0408-0.1028-0.0729-0.2047-41.4444-100.604359.5493
41.1354-0.0698-0.08440.78430.52861.7036-0.0278-0.0552-0.05060.17470.055-0.07660.127-0.1477-0.0272-0.0633-0.0457-0.0908-0.1828-0.0408-0.2227-45.393-106.8529150.1904
50.11150.06-0.20021.01070.1142.8037-0.0431-0.1438-0.05130.12060.0311-0.11640.07360.05440.012-0.2276-0.0215-0.0539-0.1123-0.0903-0.1463-25.1028-46.91975.9834
60.61120.14920.2870.63650.29292.237-0.01470.05160.0298-0.10560.01-0.1256-0.10140.06650.0046-0.1835-0.0252-0.0157-0.1238-0.0929-0.1702-25.2521-109.1237108.0626
70.54310.08130.12551.1381-0.31292.2982-0.0095-0.08760.03570.13920.03260.1099-0.0683-0.0497-0.0231-0.18010.0321-0.044-0.15260.0105-0.1911-16.4373-58.1685166.5592
80.7279-0.3122-0.26670.6905-0.28622.0324-0.02840.1241-0.0508-0.13580.0230.14020.0732-0.0710.0054-0.13570.005-0.0922-0.13890.0179-0.1781-16.3092-98.275917.3442
90.4020.2986-0.26320.00220.56860.55630.03380.14130.1479-0.1024-0.06970.0743-0.084-0.07370.03590.0127-0.02980.11-0.0091-0.15150.274-39.6829-74.1515102.2766
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ G|* }
8X-RAY DIFFRACTION8{ H|* }
9X-RAY DIFFRACTION9{ I|401-404, B|401-402, D|401-405, E|401 }

+
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