[English] 日本語
Yorodumi
- PDB-4xpf: X-ray structure of Drosophila dopamine transporter with subsiteB ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xpf
TitleX-ray structure of Drosophila dopamine transporter with subsiteB mutations (D121G/S426M) bound to RTI-55
Components
  • (ANTIBODY FRAGMENT ...) x 2
  • Dopamine transporter-protein
Keywordstransport protein/inhibitor / all alpha-helical integral membrane protein / transport protein-inhibitor complex
Function / homology
Function and homology information


Dopamine clearance from the synaptic cleft / SLC-mediated transport of neurotransmitters / circadian sleep/wake cycle / response to odorant / cocaine binding / norepinephrine transport / dopamine:sodium symporter activity / regulation of presynaptic cytosolic calcium ion concentration / dopamine transport / sleep ...Dopamine clearance from the synaptic cleft / SLC-mediated transport of neurotransmitters / circadian sleep/wake cycle / response to odorant / cocaine binding / norepinephrine transport / dopamine:sodium symporter activity / regulation of presynaptic cytosolic calcium ion concentration / dopamine transport / sleep / neuronal cell body membrane / dopamine uptake involved in synaptic transmission / amino acid transport / sodium ion transmembrane transport / adult locomotory behavior / presynaptic membrane / axon / metal ion binding / plasma membrane
Similarity search - Function
Sodium:neurotransmitter symporter family signature 2. / Sodium:neurotransmitter symporter family signature 1. / Sodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile. / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-42F / CHOLESTEROL / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / Sodium-dependent dopamine transporter
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.273 Å
Model detailsD.melanogaster DAT construct with mutations V74A, D121G, L415A, S426M, with N-terminal deletion 1- ...D.melanogaster DAT construct with mutations V74A, D121G, L415A, S426M, with N-terminal deletion 1-20, EL2 deletion between 164-206 and C-terminal thrombin insertion at residues 602-607. Molecule crystallized in complexed with antibody fragment-9D5 using hanging-drop vapour diffusion method.
AuthorsPenmatsa, A. / Wang, K.H. / Gouaux, E.
CitationJournal: Nature / Year: 2015
Title: Neurotransmitter and psychostimulant recognition by the dopamine transporter.
Authors: Wang, K.H. / Penmatsa, A. / Gouaux, E.
History
DepositionJan 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2Aug 26, 2015Group: Structure summary
Revision 1.3Sep 27, 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 / pdbx_struct_oper_list / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dopamine transporter-protein
L: ANTIBODY FRAGMENT HEAVY CHAIN-PROTEIN, 9D5-HEAVY CHAIN
H: ANTIBODY FRAGMENT LIGHT CHAIN-PROTEIN, 9D5-LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,57211
Polymers112,6883
Non-polymers1,8858
Water1086
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.415, 140.312, 166.962
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Antibody , 2 types, 2 molecules LH

#2: Antibody ANTIBODY FRAGMENT HEAVY CHAIN-PROTEIN, 9D5-HEAVY CHAIN


Mass: 25840.607 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: hybridoma cells / Cell line (production host): hybridoma / Production host: Mus musculus (house mouse)
#3: Antibody ANTIBODY FRAGMENT LIGHT CHAIN-PROTEIN, 9D5-LIGHT CHAIN


Mass: 25921.338 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: hybridoma cells / Cell line (production host): hybridoma / Production host: Mus musculus (house mouse)

-
Protein / Sugars , 2 types, 2 molecules A

#1: Protein Dopamine transporter-protein


Mass: 60925.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: dDAT / Plasmid: pEG BacMam / Cell line (production host): GnTI-, HEK293s / Production host: Homo sapiens (human) / References: UniProt: Q7K4Y6*PLUS
#4: Sugar ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C22H42O11 / Comment: detergent*YM

-
Non-polymers , 6 types, 13 molecules

#5: Chemical ChemComp-P4G / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE


Mass: 162.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O3
#6: Chemical ChemComp-42F / methyl (1R,2S,3S,5S)-3-(4-iodophenyl)-8-methyl-8-azabicyclo[3.2.1]octane-2-carboxylate


Mass: 385.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H20INO2
#7: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#9: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.37 Å3/Da / Density % sol: 77.11 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.8 / Details: PEG 400 39%, Bicine 0.1M

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.24 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 24, 2013
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 3.27→50 Å / Num. obs: 32190 / % possible obs: 89.4 % / Redundancy: 3.9 % / Biso Wilson estimate: 114.2 Å2 / Rmerge(I) obs: 0.12 / Χ2: 3.345 / Net I/av σ(I): 18.721 / Net I/σ(I): 9 / Num. measured all: 126634
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allΧ2% possible allRmerge(I) obs
3.27-3.393.432152.68691.3
3.39-3.523.832702.92792.3
3.52-3.683.832563.21291.80.838
3.68-3.883.832802.99691.50.743
3.88-4.123.932293.093910.432
4.12-4.44432533.23990.90.218
4.44-4.884.132203.45689.70.147
4.88-5.594.232013.45688.50.121
5.59-7.044.331683.56386.70.106
7.04-50430984.657810.06

-
Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data reduction
PDB_EXTRACT3.15data extraction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M48

4m48


Resolution: 3.273→48.324 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.19 / Stereochemistry target values: ML
Details: Residue H CYS 134 and Residue H GLY 139 are not properly linked: distance between C and N is 10.88.
RfactorNum. reflection% reflection
Rfree0.2962 1605 5.01 %
Rwork0.2412 30434 -
obs0.2439 32039 89.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 307.85 Å2 / Biso mean: 110.3196 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 3.273→48.324 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7385 0 141 6 7532
Biso mean--124.13 99.41 -
Num. residues----961
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057735
X-RAY DIFFRACTIONf_angle_d0.9210559
X-RAY DIFFRACTIONf_chiral_restr0.0371188
X-RAY DIFFRACTIONf_plane_restr0.0041301
X-RAY DIFFRACTIONf_dihedral_angle_d13.9072686
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2733-3.37890.44221360.40772728286489
3.3789-3.49970.43631750.39292772294792
3.4997-3.63970.40091510.35262819297092
3.6397-3.80530.38721410.35782774291591
3.8053-4.00580.35451470.30792795294291
4.0058-4.25670.33091440.23392810295491
4.2567-4.58510.24991520.18852788294091
4.5851-5.04610.25411310.18092800293189
5.0461-5.77520.24541430.19962754289788
5.7752-7.27220.26931290.23342742287186
7.2722-48.32890.27051560.21482652280881

+
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