[English] 日本語
Yorodumi
- PDB-6m2l: Crystal structure of Plasmodium falciparum hexose transporter PfH... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6m2l
TitleCrystal structure of Plasmodium falciparum hexose transporter PfHT1 bound with C3361
ComponentsHexose transporter 1Glucose transporter
KeywordsTRANSPORT PROTEIN / MFS / hexose transporter / inhibitor / Plasmodium falciparum
Function / homology
Function and homology information


transmembrane transporter activity / carbohydrate transport / membrane
Similarity search - Function
Glucose transporter GLUT / Sugar/inositol transporter / Sugar transport proteins signature 2. / Sugar transport proteins signature 1. / Major facilitator, sugar transporter-like / Sugar (and other) transporter / Sugar transporter, conserved site / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
Chem-F00 / Hexose transporter 1
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsJiang, X. / Yuan, Y.Y. / Zhang, S. / Wang, N. / Yan, C.Y. / Yan, N.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31630017 China
National Natural Science Foundation of China (NSFC)81861138009 China
CitationJournal: Cell / Year: 2020
Title: Structural Basis for Blocking Sugar Uptake into the Malaria Parasite Plasmodium falciparum.
Authors: Jiang, X. / Yuan, Y. / Huang, J. / Zhang, S. / Luo, S. / Wang, N. / Pu, D. / Zhao, N. / Tang, Q. / Hirata, K. / Yang, X. / Jiao, Y. / Sakata-Kato, T. / Wu, J.W. / Yan, C. / Kato, N. / Yin, H. / Yan, N.
History
DepositionFeb 27, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hexose transporter 1
B: Hexose transporter 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,6014
Polymers112,9372
Non-polymers6652
Water0
1
A: Hexose transporter 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8012
Polymers56,4681
Non-polymers3321
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hexose transporter 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8012
Polymers56,4681
Non-polymers3321
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.432, 102.432, 248.305
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122

-
Components

#1: Protein Hexose transporter 1 / Glucose transporter / PfHT1 / Putative sugar transporter


Mass: 56468.301 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: ht1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O97467
#2: Chemical ChemComp-F00 / (2S,3R,4S,5R,6R)-6-(hydroxymethyl)-4-undec-10-enoxy-oxane-2,3,5-triol


Mass: 332.432 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H32O6 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.34 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.2
Details: 0.1 M NH4Cl, 0.1 M Na3Citrate pH 5.2, 28% PEG500MME

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.7→50 Å / Num. obs: 14879 / % possible obs: 99.8 % / Redundancy: 82.38 % / CC1/2: 0.998 / Net I/σ(I): 10.69
Reflection shellResolution: 3.7→3.9 Å / Num. unique obs: 2116 / CC1/2: 0.869

-
Processing

Software
NameVersionClassification
PHENIX1.8.3_1479refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZW9

4zw9


Resolution: 3.7→19.959 Å / SU ML: 0.81 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 42.37
RfactorNum. reflection% reflection
Rfree0.3823 1477 10.05 %
Rwork0.3367 --
obs0.3412 14692 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 330.56 Å2 / Biso mean: 113.99 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 3.7→19.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6757 0 46 0 6803
Biso mean--93.98 --
Num. residues----895
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036965
X-RAY DIFFRACTIONf_angle_d0.7149491
X-RAY DIFFRACTIONf_chiral_restr0.0241178
X-RAY DIFFRACTIONf_plane_restr0.0031136
X-RAY DIFFRACTIONf_dihedral_angle_d13.1552364
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.7002-3.81880.42721390.41721174100
3.8188-3.95430.45821290.39761172100
3.9543-4.11130.40471360.39991172100
4.1113-4.29660.43751500.40211158100
4.2966-4.52070.43311230.38931190100
4.5207-4.80020.41411190.371199100
4.8002-5.16490.41581360.34691200100
5.1649-5.67380.41821410.35971182100
5.6738-6.47020.41491420.34561203100
6.4702-8.06140.38951210.33021260100
8.0614-19.9590.2561410.2253130599
Refinement TLS params.Method: refined / Origin x: -23.3925 Å / Origin y: -74.6374 Å / Origin z: 0.0634 Å
111213212223313233
T0.9569 Å2-0.4877 Å20.1532 Å2-0.6934 Å20.1228 Å2--0.5998 Å2
L0.349 °20.04 °2-0.1439 °2-1.8845 °2-1.3212 °2--1.5781 °2
S-0.0912 Å °-0.2296 Å °0.1938 Å °-0.5409 Å °0.2472 Å °-0.0726 Å °-0.2412 Å °0.0136 Å °0.0268 Å °
Refinement TLS groupSelection details: all

+
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