[English] 日本語
Yorodumi
- PDB-7dii: Crystal structure of LeuT in lipidic cubic phase at pH 7 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7dii
TitleCrystal structure of LeuT in lipidic cubic phase at pH 7
ComponentsNa(+):neurotransmitter symporter (Snf family)
KeywordsTRANSPORT PROTEIN / Neurotransmitter transporter / NSS / SLC6
Function / homologynitrogen compound transport / Sodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile. / sodium ion transmembrane transport / plasma membrane / LEUCINE / Na(+):neurotransmitter symporter (Snf family)
Function and homology information
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.403 Å
AuthorsFan, J. / Xiao, Y. / Sun, Z. / Zhou, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770783 China
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Crystal structures of LeuT reveal conformational dynamics in the outward-facing states.
Authors: Fan, J. / Xiao, Y. / Quick, M. / Yang, Y. / Sun, Z. / Javitch, J.A. / Zhou, X.
History
DepositionNov 19, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jul 21, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Nov 29, 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 / 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: Na(+):neurotransmitter symporter (Snf family)
B: Na(+):neurotransmitter symporter (Snf family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,2608
Polymers114,9052
Non-polymers3546
Water1,63991
1
A: Na(+):neurotransmitter symporter (Snf family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6304
Polymers57,4531
Non-polymers1773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Na(+):neurotransmitter symporter (Snf family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6304
Polymers57,4531
Non-polymers1773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.588, 72.184, 80.806
Angle α, β, γ (deg.)100.890, 97.580, 115.160
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 5 through 58 or resid 60...
21(chain B and (resid 5 through 58 or resid 60...

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 5 through 58 or resid 60...AA5 - 585 - 58
12TRPTRPLYSLYS(chain A and (resid 5 through 58 or resid 60...AA60 - 27160 - 271
13ARGARGARGARG(chain A and (resid 5 through 58 or resid 60...AA5 - 5065 - 506
14ARGARGARGARG(chain A and (resid 5 through 58 or resid 60...AA5 - 5065 - 506
15ILEILEVALVAL(chain A and (resid 5 through 58 or resid 60...AA364 - 413364 - 413
16PHEPHEARGARG(chain A and (resid 5 through 58 or resid 60...AA415 - 506415 - 506
17LEULEUHOHHOH(chain A and (resid 5 through 58 or resid 60...AC - I601 - 702
21ARGARGLEULEU(chain B and (resid 5 through 58 or resid 60...BB5 - 585 - 58
22TRPTRPPROPRO(chain B and (resid 5 through 58 or resid 60...BB60 - 13060 - 130
23THRTHRLYSLYS(chain B and (resid 5 through 58 or resid 60...BB135 - 271135 - 271
24GLNGLNPROPRO(chain B and (resid 5 through 58 or resid 60...BB273 - 362273 - 362
25PHEPHEARGARG(chain B and (resid 5 through 58 or resid 60...BB415 - 506415 - 506
26LEULEUHOHHOH(chain B and (resid 5 through 58 or resid 60...BF - J601 - 702

-
Components

#1: Protein Na(+):neurotransmitter symporter (Snf family) / LeuT


Mass: 57452.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: O67854
#2: Chemical ChemComp-LEU / LEUCINE / Leucine


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.53 %
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase / pH: 7
Details: 0.1 M NaCl, 0.1 M Na+-HEPES pH 7.0, 32% (v/v) PEG 350 MME and 1 mM L-Leu

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.403→36.06 Å / Num. obs: 47577 / % possible obs: 96.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 41.35 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.044 / Rrim(I) all: 0.083 / Net I/σ(I): 10.6 / Num. measured all: 164247
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.403-2.4442.90.439680623620.8550.310.5412.296.3
6.509-36.063.50.031823323740.9960.0190.03626.897.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A65

2a65


Resolution: 2.403→32.097 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 23.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2134 2287 4.81 %
Rwork0.192 45229 -
obs0.193 47516 96.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.18 Å2 / Biso mean: 50.9853 Å2 / Biso min: 27.01 Å2
Refinement stepCycle: final / Resolution: 2.403→32.097 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7778 0 22 91 7891
Biso mean--40.07 55.17 -
Num. residues----980
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4534X-RAY DIFFRACTION3.619TORSIONAL
12B4534X-RAY DIFFRACTION3.619TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.403-2.45480.26621190.2601282596
2.4548-2.51190.24921530.2408280696
2.5119-2.57470.25451470.2221280896
2.5747-2.64430.24611450.2101278897
2.6443-2.72210.24041380.2033283297
2.7221-2.80990.20391400.1962287297
2.8099-2.91020.23721450.1947279997
2.9102-3.02670.2451440.1924285997
3.0267-3.16430.20411360.1899282197
3.1643-3.3310.19461500.1893284497
3.331-3.53940.22171410.1922284497
3.5394-3.81230.19891370.1901284897
3.8123-4.19520.21161490.198281297
4.1952-4.80050.22381700.187279296
4.8005-6.04150.21771270.1908286597
6.0415-32.0970.16661460.162281497
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)
10.08830.13890.04010.5186-0.31430.3302-0.1328-0.18780.0255-0.1040.0172-0.01-0.0638-0.120500.4066-0.02660.01020.4414-0.05640.4353-11.2241-13.3841-19.9576
20.27120.10090.14870.0906-0.05470.53850.07340.0044-0.0153-0.0659-0.16420.00240.0336-0.0885-00.38670.00290.01860.35260.01480.3285-13.6491-21.2683-29.4357
30.18950.00130.23560.3798-0.23870.33690.22530.2376-0.0193-0.3246-0.17750.09560.2281-0.1076-00.4044-0.03230.01790.37490.02410.3394-16.802-34.628-30.7347
40.02370.0559-0.0910.1336-0.11790.24270.05540.04870.30380.2891-0.19430.06190.0188-0.1218-0.00010.49390.00440.01260.44130.00960.4136-15.7134-24.5319-10.0298
50.33290.21020.3040.5080.32220.5513-0.034-0.1010.0205-0.0075-0.0223-0.10490.0327-0.13-00.3628-0.01790.03970.38980.02060.3459-7.413-20.2247-19.0985
60.49940.00250.68950.27310.3261.06280.0363-0.00760.0348-0.1475-0.0855-0.0941-0.12940.0024-00.3808-0.00850.03830.3267-0.01060.3626-14.2606-9.5276-33.3732
70.13360.0711-0.00660.08120.07820.12960.47110.02060.2347-0.3931-0.4277-0.0332-0.1654-0.1410.00010.46520.0385-0.00140.4294-0.01720.3269-17.3406-19.268-47.5716
81.97862.97151.92069.55895.64183.3563-0.0087-0.1892-0.0695-0.008-0.01340.0474-0.24810.048-0.02580.4663-0.10220.0370.50150.02620.4207-12.4911-18.4186-24.9731
90.30580.4677-0.02960.4905-0.08190.46820.11330.0773-0.0875-0.0137-0.289-0.07430.0294-0.2153-00.3653-0.0142-0.01460.4358-0.01910.3608-1.94454.0470.4506
100.2439-0.0328-0.00590.3530.45351.1390.0462-0.0584-0.05130.0215-0.0882-0.02290.007-0.0389-00.3241-0.014-0.01270.40050.01460.33183.837810.64599.5633
110.50520.1163-0.5660.40490.18410.73560.02550.03320.02990.0195-0.0695-0.0257-0.0171-0.0301-00.35190.0125-0.00370.31540.01920.32898.973918.29192.4775
120.25220.12790.16540.06650.09660.16630.0367-0.18190.09330.11930.0585-0.16080.10780.184200.4276-0.00550.04420.44840.01650.47269.5213-7.5351-2.7493
130.7137-0.0089-0.10660.22750.42411.19750.03950.0089-0.0892-0.0446-0.11160.003-0.0146-0.1239-00.3199-0.0131-0.01250.3442-0.00660.31331.22629.43256.4424
140.2497-0.236-0.35570.42150.49360.5827-0.0573-0.29530.028-0.0318-0.26830.1520.1694-0.0634-00.4551-0.1130.04270.5817-0.0080.5351-10.4072-5.88279.839
150.07570.02220.08680.24820.05140.06830.0391-0.3992-0.3213-0.0171-0.06910.19880.0702-0.23300.3762-0.0401-0.01480.4897-0.00260.3462-0.115312.321228.0747
168.5297-6.13160.33347.47714.73238.06660.0475-0.03110.1075-0.0367-0.0334-0.05620.09410.0424-0.0460.4565-0.05140.05670.51630.00330.43331.6578.12845.411
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 54 )A5 - 54
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 152 )A55 - 152
3X-RAY DIFFRACTION3chain 'A' and (resid 153 through 190 )A153 - 190
4X-RAY DIFFRACTION4chain 'A' and (resid 191 through 215 )A191 - 215
5X-RAY DIFFRACTION5chain 'A' and (resid 216 through 369 )A216 - 369
6X-RAY DIFFRACTION6chain 'A' and (resid 370 through 481 )A370 - 481
7X-RAY DIFFRACTION7chain 'A' and (resid 482 through 506 )A482 - 506
8X-RAY DIFFRACTION8chain 'A' and (resid 601 through 601 )A601
9X-RAY DIFFRACTION9chain 'B' and (resid 5 through 54 )B5 - 54
10X-RAY DIFFRACTION10chain 'B' and (resid 55 through 152 )B55 - 152
11X-RAY DIFFRACTION11chain 'B' and (resid 153 through 215 )B153 - 215
12X-RAY DIFFRACTION12chain 'B' and (resid 216 through 254 )B216 - 254
13X-RAY DIFFRACTION13chain 'B' and (resid 255 through 437 )B255 - 437
14X-RAY DIFFRACTION14chain 'B' and (resid 438 through 481 )B438 - 481
15X-RAY DIFFRACTION15chain 'B' and (resid 482 through 506 )B482 - 506
16X-RAY DIFFRACTION16chain 'B' and (resid 601 through 601 )B601

+
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