[English] 日本語
Yorodumi
- PDB-4p3j: Apo inward-facing state of the glutamate transporter homologue Gl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4p3j
TitleApo inward-facing state of the glutamate transporter homologue GltPh in alkali-free conditions
ComponentsGltPh
KeywordsTRANSPORT PROTEIN / membrane protein / sodium-couple asparate transporter / inward-facing state / apo form / alkali-free conditions
Function / homology
Function and homology information


amino acid:sodium symporter activity / L-aspartate transmembrane transport / L-aspartate transmembrane transporter activity / L-aspartate import across plasma membrane / chloride transmembrane transporter activity / protein homotrimerization / chloride transmembrane transport / identical protein binding / metal ion binding / 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
: / Glutamate transporter homolog
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsVerdon, G. / Boudker, O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health (NINDS)NS064357 United States
CitationJournal: Elife / Year: 2014
Title: Coupled ion binding and structural transitions along the transport cycle of glutamate transporters.
Authors: Verdon, G. / Oh, S. / Serio, R.N. / Boudker, O.
History
DepositionMar 8, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 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: GltPh
B: GltPh
C: GltPh
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,4506
Polymers133,8483
Non-polymers6023
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7150 Å2
ΔGint-147 kcal/mol
Surface area47300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.948, 196.843, 207.484
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
12A
22B
32C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A6 - 255
2111B6 - 255
3111C6 - 255
1211A315 - 416
2211B315 - 416
3211C315 - 416
1121A255 - 314
2121B255 - 314
3121C255 - 314

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.330127, -0.815525, -0.475327), (0.820192, -0.497076, 0.283197), (-0.467228, -0.296368, 0.832985)64.1804, 2.8138, 22.68006
3given(-0.353956, 0.813119, -0.462118), (-0.808494, -0.514409, -0.285867), (-0.470162, 0.272435, 0.83948)30.53713, 60.85577, 10.82581

-
Components

#1: Protein GltPh / 425aa long hypothetical proton glutamate symport protein


Mass: 44615.910 Da / Num. of mol.: 3 / Fragment: Residues 1-417
Mutation: D37H, K40H, K55C, K125H, K132H, K223H, K264H, C321A, A364C, E368H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
Gene: PH1295 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): DH10 / References: UniProt: O59010
#2: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Hg

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 4.08 Å3/Da / Density % sol: 69.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: PEG 400 Potassium Citrate Potassium Chloride Magnesium Chloride

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.5→100 Å / Num. obs: 50777 / % possible obs: 94.4 % / Redundancy: 3.3 % / Net I/σ(I): 13.7
Reflection shellResolution: 3.5→3.56 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.881 / Mean I/σ(I) obs: 1.24

-
Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P19

4p19


Resolution: 3.5→15 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.913 / SU B: 82.173 / SU ML: 0.549 / Cross valid method: THROUGHOUT / ESU R Free: 0.602 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27845 1353 5 %RANDOM
Rwork0.26317 ---
obs0.26395 25446 95.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 144.258 Å2
Baniso -1Baniso -2Baniso -3
1-1.82 Å20 Å20 Å2
2--6.38 Å20 Å2
3----8.2 Å2
Refinement stepCycle: 1 / Resolution: 3.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9088 0 3 0 9091
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0199265
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1161.98112643
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.85351227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.91723.741278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.604151490
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.551524
X-RAY DIFFRACTIONr_chiral_restr0.0770.21594
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216656
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: tight thermal / Weight position: 0.5

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A25726.65
11B25728.48
11C25729.9
22A44215.73
22B44215.07
22C44226.35
LS refinement shellResolution: 3.5→3.586 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 73 -
Rwork0.355 1723 -
obs--93.2 %
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)
11.14110.63160.40932.0484-0.4830.58370.2746-0.5950.12510.0592-0.3075-0.0641-0.0727-0.28190.0330.3774-0.06240.17770.3686-0.12610.329637.461136.6613-30.4686
21.60710.13890.00350.15550.18280.93150.3745-0.3948-0.04110.159-0.2745-0.00050.08940.0181-0.10.2857-0.2821-0.02590.49340.01220.195861.316620.9937-22.1455
30.989-0.04730.4920.2147-0.06230.51410.2222-0.3411-0.26270.0696-0.17010.08120.3244-0.1852-0.05210.3795-0.277-0.10080.37070.13260.351736.40326.8535-30.9345
41.28440.2079-2.12850.8512-0.16244.44320.0787-0.30620.3187-0.1373-0.18920.195-0.0960.13140.11060.15550.1240.11210.3928-0.24620.570522.079741.9104-32.0963
50.595-0.609-0.43971.16110.96913.0130.1604-0.24570.2976-0.0217-0.2215-0.1260.4323-0.15470.06110.2582-0.2510.06250.5616-0.19550.316771.806631.0682-14.4776
61.2603-0.26850.32470.06760.06133.19950.2868-0.5462-0.7517-0.08890.14050.17230.0251-0.5047-0.42730.465-0.1421-0.18960.36240.46970.625938.491-8.8029-26.7431
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 76
2X-RAY DIFFRACTION1A130 - 221
3X-RAY DIFFRACTION2B1 - 76
4X-RAY DIFFRACTION2B130 - 221
5X-RAY DIFFRACTION3C1 - 76
6X-RAY DIFFRACTION3C130 - 221
7X-RAY DIFFRACTION4A77 - 129
8X-RAY DIFFRACTION4A222 - 417
10X-RAY DIFFRACTION5B77 - 129
11X-RAY DIFFRACTION5B222 - 416
13X-RAY DIFFRACTION6C77 - 129
14X-RAY DIFFRACTION6C222 - 416
9X-RAY DIFFRACTION4A501
12X-RAY DIFFRACTION5B501
15X-RAY DIFFRACTION6C501

+
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