[English] 日本語
Yorodumi
- PDB-4d2d: Structure of a tri peptide bound POT family peptide transporter -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4d2d
TitleStructure of a tri peptide bound POT family peptide transporter
Components
  • ALANINE-TRIPEPTIDE
  • DI-OR TRIPEPTIDE\:H+ SYMPORTER
KeywordsTRANSPORT PROTEIN / MAJOR FACILITATOR SUPERFAMILY / PROTON OLIGOPEPTIDE TRANSPORTER (POT) FAMILY / PEPTIDE TRANSPORTER / TRIPEPTIDE COMPLEX
Function / homology
Function and homology information


oligopeptide transport / peptide transmembrane transporter activity / identical protein binding / plasma membrane
Similarity search - Function
: / Dipeptide/tripeptide permease / PTR2 family proton/oligopeptide symporters signature 1. / MFS general substrate transporter like domains / PTR2 family proton/oligopeptide symporters signature 2. / PTR2 family proton/oligopeptide symporter, conserved site / Proton-dependent oligopeptide transporter family / POT family / Growth Hormone; Chain: A; / Major facilitator superfamily domain ...: / Dipeptide/tripeptide permease / PTR2 family proton/oligopeptide symporters signature 1. / MFS general substrate transporter like domains / PTR2 family proton/oligopeptide symporters signature 2. / PTR2 family proton/oligopeptide symporter, conserved site / Proton-dependent oligopeptide transporter family / POT family / Growth Hormone; Chain: A; / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / (2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / PHOSPHATE ION / Di-/tripeptide transporter
Similarity search - Component
Biological speciesSTREPTOCOCCUS THERMOPHILUS (bacteria)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.522 Å
AuthorsLyons, J.A. / Parker, J.L. / Solcan, N. / Brinth, A. / Li, D. / Shah, S.T.A. / Caffrey, M. / Newstead, S.
CitationJournal: Embo Rep. / Year: 2014
Title: Structural Basis for Polyspecificity in the Pot Family of Proton-Coupled Oligopeptide Transporters.
Authors: Lyons, J.A. / Parker, J.L. / Solcan, N. / Brinth, A. / Li, D. / Shah, S.T. / Caffrey, M. / Newstead, S.
History
DepositionMay 9, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Database references
Revision 1.2Sep 25, 2019Group: Data collection / Experimental preparation / Other / Category: exptl_crystal_grow / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DI-OR TRIPEPTIDE\:H+ SYMPORTER
B: ALANINE-TRIPEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9349
Polymers53,9522
Non-polymers1,9827
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-6.9 kcal/mol
Surface area21790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.380, 110.700, 110.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

-
Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein DI-OR TRIPEPTIDE\:H+ SYMPORTER / DI- OR TRIPEPTIDE PROTON SYMPORTER


Mass: 53721.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS THERMOPHILUS (bacteria) / Strain: LMG 18311 / Plasmid: PWALDO-GFPD / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: Q5M4H8
#2: Protein/peptide ALANINE-TRIPEPTIDE


Mass: 231.249 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

-
Non-polymers , 4 types, 52 molecules

#3: Chemical ChemComp-78M / (2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / 7.8 MONOACYLGLYCEROL


Mass: 314.460 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H34O4
#4: Chemical ChemComp-78N / (2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / 7.8 MONOACYLGLYCEROL (2R)


Mass: 314.460 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H34O4
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.3 % / Description: NONE
Crystal growMethod: lipidic cubic phase / pH: 7
Details: 16-23 %(V/V) PEG 400, 0.1 M HEPES PH 7.0, 0.15-0.55 M NH4H2PO4 AND 10 MM TRI-ALANINE. CRYSTALS WERE GROWN BY THE LCP METHOD WITH 7.8 MAG AS HOSTING LIPID.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 2, 2012 / Details: K-B PAIR OF BIOMORPH MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.52→75.56 Å / Num. obs: 21341 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 44.26 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.4
Reflection shellResolution: 2.52→2.59 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.2 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4APS

4aps


Resolution: 2.522→75.556 Å / SU ML: 0.29 / σ(F): 1.34 / Phase error: 24.67 / Stereochemistry target values: ML
Details: RESIDUES 1-5, 272-275, 414-419, 479-491 ARE DISORDERED TRIPEPTIDE WAS MODELED WITH ITS C-TERMINUS ORIENTATED TOWARDS THE EXTRACELLULAR SIDE. SEE PAPER FOR FURTHER DISCUSSION.
RfactorNum. reflection% reflection
Rfree0.2422 1102 5.2 %
Rwork0.1981 --
obs0.2005 21332 98.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.229 Å2
Refinement stepCycle: LAST / Resolution: 2.522→75.556 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3598 0 137 45 3780
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033833
X-RAY DIFFRACTIONf_angle_d0.825186
X-RAY DIFFRACTIONf_dihedral_angle_d15.3251352
X-RAY DIFFRACTIONf_chiral_restr0.029591
X-RAY DIFFRACTIONf_plane_restr0.004620
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5217-2.63650.30151170.22282519X-RAY DIFFRACTION99
2.6365-2.77550.25851360.21552506X-RAY DIFFRACTION99
2.7755-2.94940.24481190.20952539X-RAY DIFFRACTION99
2.9494-3.17710.2751420.21182536X-RAY DIFFRACTION99
3.1771-3.49680.27081450.21532519X-RAY DIFFRACTION99
3.4968-4.00280.23531450.19412550X-RAY DIFFRACTION99
4.0028-5.04290.23141620.18892532X-RAY DIFFRACTION98
5.0429-75.590.21451360.18262529X-RAY DIFFRACTION94

+
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