[English] 日本語
Yorodumi
- PDB-6jkc: Crystal structure of tetrameric PepTSo2 in P4212 space group -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6jkc
TitleCrystal structure of tetrameric PepTSo2 in P4212 space group
ComponentsProton:oligopeptide symporter POT family
KeywordsMEMBRANE PROTEIN / Peptide transporter / LCP crystallization
Function / homology
Function and homology information


dipeptide transmembrane transport / tripeptide transmembrane transporter activity / peptide:proton symporter activity / dipeptide transmembrane transporter activity / membrane / identical protein binding
Similarity search - Function
Dipeptide/tripeptide permease / MFS general substrate transporter like domains / Proton-dependent oligopeptide transporter family / POT family / Growth Hormone; Chain: A; / MFS transporter superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Proton:oligopeptide symporter POT family
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsNagamura, R. / Fukuda, M. / Ishitani, R. / Nureki, O.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science24227004 Japan
Japan Society for the Promotion of Science25291011 Japan
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2019
Title: Structural basis for oligomerization of the prokaryotic peptide transporter PepT.
Authors: Reina Nagamura / Masahiro Fukuda / Akihiro Kawamoto / Kyoko Matoba / Naoshi Dohmae / Ryuichiro Ishitani / Junichi Takagi / Osamu Nureki /
Abstract: Proton-dependent oligopeptide transporters (POTs) belong to the major facilitator superfamily (MFS) and transport dipeptides and tripeptides from the extracellular environment into the target cell. ...Proton-dependent oligopeptide transporters (POTs) belong to the major facilitator superfamily (MFS) and transport dipeptides and tripeptides from the extracellular environment into the target cell. The human POTs PepT1 and PepT2 are also involved in the absorption of various orally ingested drugs. Previously reported structures revealed that the bacterial POTs possess 14 helices, of which H1-H6 and H7-H12 constitute the typical MFS fold and the residual two helices are involved in the cytoplasmic linker. PepT from Shewanella oneidensis is a unique POT which reportedly assembles as a 200 kDa tetramer. Although the previously reported structures suggested the importance of H12 for tetramer formation, the structural basis for the PepT-specific oligomerization remains unclear owing to the lack of a high-resolution tetrameric structure. In this study, the expression and purification conditions for tetrameric PepT were optimized. A single-particle cryo-EM analysis revealed the tetrameric structure of PepT incorporated into Salipro nanoparticles at 4.1 Å resolution. Furthermore, a combination of lipidic cubic phase (LCP) crystallization and an automated data-processing system for multiple microcrystals enabled crystal structures of PepT to be determined at resolutions of 3.5 and 3.9 Å. The present structures in a lipid bilayer revealed the detailed mechanism for the tetrameric assembly of PepT, in which a characteristic extracellular loop (ECL) interacts with two asparagine residues on H12 which were reported to be important for tetramerization and plays an essential role in oligomeric assembly. This study provides valuable insights into the oligomerization mechanism of this MFS-type transporter, which will further pave the way for understanding other oligomeric membrane proteins.
History
DepositionFeb 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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: Proton:oligopeptide symporter POT family


Theoretical massNumber of molelcules
Total (without water)57,6271
Polymers57,6271
Non-polymers00
Water0
1
A: Proton:oligopeptide symporter POT family

A: Proton:oligopeptide symporter POT family

A: Proton:oligopeptide symporter POT family

A: Proton:oligopeptide symporter POT family


Theoretical massNumber of molelcules
Total (without water)230,5064
Polymers230,5064
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_745-x+2,-y-1,z1
crystal symmetry operation3_535-y+1/2,x-3/2,z1
crystal symmetry operation4_655y+3/2,-x+1/2,z1
Buried area5450 Å2
ΔGint-54 kcal/mol
Surface area77890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.410, 119.410, 104.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Space group name HallP4ab2ab
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z
#3: y+1/2,-x+1/2,z
#4: x+1/2,-y+1/2,-z
#5: -x+1/2,y+1/2,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z

-
Components

#1: Protein Proton:oligopeptide symporter POT family


Mass: 57626.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: UniProt ID: Q8EHE6
Source: (gene. exp.) Shewanella oneidensis (strain MR-1) (bacteria)
Strain: MR-1 / Gene: SO_1277 / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta 2 (DE3) / References: UniProt: Q8EHE6

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 66.64 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 4
Details: 40% PEG 200, 100 mM NaCl, 100 mM Na acetate, pH 4.0

-
Data collection

DiffractionMean temperature: 100 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 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→47.53 Å / Num. obs: 8312 / % possible obs: 83 % / Redundancy: 3.6 % / Biso Wilson estimate: 79.72 Å2 / CC1/2: 0.961 / Rmerge(I) obs: 0.284 / Rrim(I) all: 0.328 / Net I/σ(I): 5.49
Reflection shellResolution: 3.5→3.71 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.359 / Num. unique obs: 1295 / CC1/2: 0.293 / Rrim(I) all: 1.586 / % possible all: 83.4

-
Processing

Software
NameVersionClassification
REFMACrefinement
PHENIX1.14_3260refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LEP

4lep


Resolution: 3.5→47.53 Å / SU ML: 0.4697 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.8325
RfactorNum. reflection% reflection
Rfree0.303 429 5.22 %
Rwork0.2672 --
obs0.269 8223 82.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 65.71 Å2
Refinement stepCycle: LAST / Resolution: 3.5→47.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3498 0 0 0 3498
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00283586
X-RAY DIFFRACTIONf_angle_d0.55384888
X-RAY DIFFRACTIONf_chiral_restr0.038572
X-RAY DIFFRACTIONf_plane_restr0.0042597
X-RAY DIFFRACTIONf_dihedral_angle_d12.62132028
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.630.4103360.3602733X-RAY DIFFRACTION78.71
3.63-3.770.3732390.3081749X-RAY DIFFRACTION81.24
3.77-3.940.3011390.2875784X-RAY DIFFRACTION84.93
3.94-4.150.3877350.2995795X-RAY DIFFRACTION84.18
4.15-4.410.275330.2767780X-RAY DIFFRACTION82.71
4.41-4.750.3765410.2807787X-RAY DIFFRACTION84.84
4.75-5.230.2928440.2685791X-RAY DIFFRACTION83.33
5.23-5.980.2823570.2974769X-RAY DIFFRACTION82.68
5.98-7.530.2964610.2409753X-RAY DIFFRACTION79.41
7.53-47.80.2302440.1952853X-RAY DIFFRACTION81.47

+
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