[English] 日本語
Yorodumi
- PDB-8qj3: Receptor Sd-Amt1 (OFF-state) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8qj3
TitleReceptor Sd-Amt1 (OFF-state)
ComponentsAmmonium transporter
KeywordsSIGNALING PROTEIN / Ammonium receptor / OFF-state / Shewanella denitrificans / Sd-Amt1 / diguanylate cyclase / Amt
Function / homology
Function and homology information


ammonium homeostasis / ammonium channel activity / plasma membrane
Similarity search - Function
Ammonium transporter / Ammonium transporter AmtB-like domain / Ammonium Transporter Family / Ammonium/urea transporter / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / Reverse transcriptase/Diguanylate cyclase domain
Similarity search - Domain/homology
Ammonium transporter
Similarity search - Component
Biological speciesShewanella denitrificans OS217 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsAndrade, S.L. / Pflueger, T. / Gschell, M.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)AN-676/3 Germany
German Research Foundation (DFG)GRK-2202 Germany
CitationJournal: Sci Adv / Year: 2024
Title: How sensor Amt-like proteins integrate ammonium signals.
Authors: Tobias Pflüger / Mathias Gschell / Lin Zhang / Volodymyr Shnitsar / Annas J Zabadné / Paul Zierep / Stefan Günther / Oliver Einsle / Susana L A Andrade /
Abstract: Unlike aquaporins or potassium channels, ammonium transporters (Amts) uniquely discriminate ammonium from potassium and water. This feature has certainly contributed to their repurposing as ammonium ...Unlike aquaporins or potassium channels, ammonium transporters (Amts) uniquely discriminate ammonium from potassium and water. This feature has certainly contributed to their repurposing as ammonium receptors during evolution. Here, we describe the ammonium receptor Sd-Amt1, where an Amt module connects to a cytoplasmic diguanylate cyclase transducer module via an HAMP domain. Structures of the protein with and without bound ammonium were determined to 1.7- and 1.9-Ångstrom resolution, depicting the ON and OFF states of the receptor and confirming the presence of a binding site for two ammonium cations that is pivotal for signal perception and receptor activation. The transducer domain was disordered in the crystals, and an AlphaFold2 prediction suggests that the helices linking both domains are flexible. While the sensor domain retains the trimeric fold formed by all Amt family members, the HAMP domains interact as pairs and serve to dimerize the transducer domain upon activation.
History
DepositionSep 12, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ammonium transporter
B: Ammonium transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,7656
Polymers141,6732
Non-polymers1,0924
Water6,720373
1
A: Ammonium transporter
hetero molecules

A: Ammonium transporter
hetero molecules

A: Ammonium transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,6166
Polymers212,5103
Non-polymers1063
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area11400 Å2
ΔGint-197 kcal/mol
Surface area35790 Å2
MethodPISA
2
B: Ammonium transporter
hetero molecules

B: Ammonium transporter
hetero molecules

B: Ammonium transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,68012
Polymers212,5103
Non-polymers3,1709
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area15670 Å2
ΔGint-209 kcal/mol
Surface area36080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.757, 114.757, 278.565
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-955-

HOH

21B-950-

HOH

-
Components

#1: Protein Ammonium transporter


Mass: 70836.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella denitrificans OS217 (bacteria)
Strain: OS217 / Gene: Sden_0766 / Details (production host): C-terminal His-tag / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: Q12R70
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#3: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M Bis/Tris pH 6.5 with 25 % (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.9→93.61 Å / Num. obs: 107695 / % possible obs: 99.8 % / Redundancy: 5.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.033 / Rrim(I) all: 0.08 / Net I/σ(I): 14.8 / Num. measured all: 624924
Reflection shellResolution: 1.9→1.93 Å / % possible obs: 97.4 % / Redundancy: 5.7 % / Rmerge(I) obs: 1.351 / Num. measured all: 29533 / Num. unique obs: 5208 / CC1/2: 0.404 / Rpim(I) all: 0.621 / Rrim(I) all: 1.487 / Net I/σ(I) obs: 1.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→48.97 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.739 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1844 5231 4.9 %RANDOM
Rwork0.16222 ---
obs0.16332 101232 98.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.026 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20.26 Å2-0 Å2
2--0.52 Å20 Å2
3----1.68 Å2
Refinement stepCycle: 1 / Resolution: 1.9→48.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6068 0 72 374 6514
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0116448
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166170
X-RAY DIFFRACTIONr_angle_refined_deg1.8151.6158796
X-RAY DIFFRACTIONr_angle_other_deg0.6281.55614121
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.35837
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.691524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.10210971
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0930.21030
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.027639
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021605
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_it2.3891.543297
X-RAY DIFFRACTIONr_mcbond_other2.3871.5393296
X-RAY DIFFRACTIONr_mcangle_it3.6322.7544151
X-RAY DIFFRACTIONr_mcangle_other3.6322.7554152
X-RAY DIFFRACTIONr_scbond_it3.1121.9983151
X-RAY DIFFRACTIONr_scbond_other3.1111.9983152
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8463.524646
X-RAY DIFFRACTIONr_long_range_B_refined7.1817.147963
X-RAY DIFFRACTIONr_long_range_B_other7.09316.317846
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 311 -
Rwork0.265 6492 -
obs--85.13 %
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)
10.4442-0.03520.10650.5339-0.10480.48670.0365-0.0526-0.03150.05340.00130.19180.0397-0.1584-0.03790.0163-0.01590.0290.06780.01440.107537.990128.5827-23.9572
20.55050.0421-0.25010.55460.03660.65090.0243-0.04570.17150.05090.0022-0.091-0.10490.0658-0.02650.0469-0.0172-0.01030.0141-0.02210.10997.921118.270422.8596
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 401
2X-RAY DIFFRACTION2B2 - 702

+
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