[English] 日本語
Yorodumi
- PDB-6zgb: glutamate transporter homologue Glttk in complex with a photo cag... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zgb
Titleglutamate transporter homologue Glttk in complex with a photo cage compound
ComponentsProton/glutamate symporter, SDF family
KeywordsTRANSPORT PROTEIN / glutamate transporter / photo cage / membrane protein
Function / homology
Function and homology information


dicarboxylic acid transport / symporter activity / membrane / plasma membrane
Similarity search - Function
Proton glutamate symport protein / Sodium:dicarboxylate symporter / Sodium:dicarboxylate symporter / Sodium:dicarboxylate symporter, conserved site / Sodium:dicarboxylate symporter superfamily / Sodium:dicarboxylate symporter family / Sodium:dicarboxylate symporter family signature 1. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Chem-QJW / Proton/glutamate symporter, SDF family
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsArkhipova, V. / Slotboom, D.J. / Guskov, A.
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Structural Aspects of Photopharmacology: Insight into the Binding of Photoswitchable and Photocaged Inhibitors to the Glutamate Transporter Homologue.
Authors: Arkhipova, V. / Fu, H. / Hoorens, M.W.H. / Trinco, G. / Lameijer, L.N. / Marin, E. / Feringa, B.L. / Poelarends, G.J. / Szymanski, W. / Slotboom, D.J. / Guskov, A.
History
DepositionJun 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Proton/glutamate symporter, SDF family
B: Proton/glutamate symporter, SDF family
C: Proton/glutamate symporter, SDF family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,48311
Polymers140,0563
Non-polymers1,4278
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: scanning transmission electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8430 Å2
ΔGint-59 kcal/mol
Surface area49330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.740, 115.740, 308.490
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 8 through 186 or resid 188 through 430))
21(chain B and (resid 8 through 186 or resid 188 through 430))
31(chain C and (resid 8 through 186 or resid 188 through 430))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGLEULEU(chain A and (resid 8 through 186 or resid 188 through 430))AA8 - 1868 - 186
12VALVALSERSER(chain A and (resid 8 through 186 or resid 188 through 430))AA188 - 430188 - 430
21ARGARGLEULEU(chain B and (resid 8 through 186 or resid 188 through 430))BB8 - 1868 - 186
22VALVALSERSER(chain B and (resid 8 through 186 or resid 188 through 430))BB188 - 430188 - 430
31ARGARGLEULEU(chain C and (resid 8 through 186 or resid 188 through 430))CC8 - 1868 - 186
32VALVALSERSER(chain C and (resid 8 through 186 or resid 188 through 430))CC188 - 430188 - 430

-
Components

#1: Protein Proton/glutamate symporter, SDF family


Mass: 46685.363 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: 8 His tag at C-terminus
Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
Gene: TK0986 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JID0
#2: Chemical ChemComp-QJW / (2~{S},3~{S})-2-azanyl-3-[(2-nitrophenyl)methoxy]butanedioic acid


Mass: 284.222 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H12N2O7
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.26 Å3/Da / Density % sol: 71.12 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 27%PEG350MME, 100 mM Tris 8.0, 40 mM NaCl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 40350 / % possible obs: 99.7 % / Redundancy: 7.58 % / CC1/2: 0.998 / Net I/σ(I): 9.16
Reflection shellResolution: 3.2→3.28 Å / Redundancy: 7.83 % / Num. unique obs: 2923 / CC1/2: 0.145 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DWY

5dwy


Resolution: 3.2→45.748 Å / SU ML: 0.58 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.04
RfactorNum. reflection% reflection
Rfree0.2745 2017 5.01 %
Rwork0.2319 --
obs0.234 40289 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 356.89 Å2 / Biso mean: 153.2887 Å2 / Biso min: 72.05 Å2
Refinement stepCycle: final / Resolution: 3.2→45.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9474 0 98 0 9572
Biso mean--193.13 --
Num. residues----1271
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5643X-RAY DIFFRACTION16.033TORSIONAL
12B5643X-RAY DIFFRACTION16.033TORSIONAL
13C5643X-RAY DIFFRACTION16.033TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.2-3.27990.48231410.43072677100
3.2799-3.36860.44941420.40532698100
3.3686-3.46770.45091430.37462710100
3.4677-3.57960.3751420.30992697100
3.5796-3.70750.31420.27682714100
3.7075-3.85580.30531440.24312719100
3.8558-4.03120.26961410.23482692100
4.0312-4.24360.29741430.21512726100
4.2436-4.50930.2441430.18222711100
4.5093-4.85710.23281450.1803273699
4.8571-5.34520.24381440.1887272899
5.3452-6.11710.27331470.22752782100
6.1171-7.70090.25741480.23722808100
7.7009-450.25381520.2255287498
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)
12.1247-1.2446-0.27851.70930.81914.4274-0.23540.2393-0.1527-0.4957-0.03250.1157-0.7752-0.34750.21081.4441-0.0573-0.00420.86190.05370.752442.52917.078918.5584
22.14290.96120.93183.77050.50221.5119-0.69220.4261-0.0025-0.70620.6694-0.4318-0.4570.6669-0.02420.9254-0.09140.19921.1997-0.18880.825877.2151-9.758624.7053
32.0751-1.2331.10692.47010.80955.4017-0.08260.1016-0.0664-0.3107-0.5549-0.04040.5471-0.55650.54281.2819-0.39280.19251.2528-0.17330.833736.0445-25.494228.1164
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 7 through 431)A7 - 431
2X-RAY DIFFRACTION2(chain 'B' and resid 8 through 430)B8 - 430
3X-RAY DIFFRACTION3(chain 'C' and resid 8 through 430)C8 - 430

+
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