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- PDB-2m3g: Structure of Anabaena Sensory Rhodopsin Determined by Solid State... -

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Basic information

Entry
Database: PDB / ID: 2m3g
TitleStructure of Anabaena Sensory Rhodopsin Determined by Solid State NMR Spectroscopy
ComponentsAnabaena Sensory Rhodopsin
KeywordsMEMBRANE PROTEIN / Solid state NMR / Anabaena Sensory Rhodopsin / MAS NMR / Trimers
Function / homology
Function and homology information


monoatomic ion channel activity / photoreceptor activity / phototransduction / membrane
Similarity search - Function
Bacterial rhodopsins signature 1. / Rhodopsin, retinal binding site / Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
RETINAL / Bacteriorhodopsin
Similarity search - Component
Biological speciesNostoc sp. PCC 7120 (bacteria)
MethodSOLID-STATE NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsWang, S. / Munro, R.A. / Shi, L. / Kawamura, I. / Okitsu, T. / Wada, A. / Kim, S. / Jung, K. / Brown, L.S. / Ladizhansky, V.
CitationJournal: Nat.Methods / Year: 2013
Title: Solid-state NMR spectroscopy structure determination of a lipid-embedded heptahelical membrane protein.
Authors: Wang, S. / Munro, R.A. / Shi, L. / Kawamura, I. / Okitsu, T. / Wada, A. / Kim, S.Y. / Jung, K.H. / Brown, L.S. / Ladizhansky, V.
History
DepositionJan 17, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2013Group: Database references
Revision 1.2Oct 9, 2013Group: Database references
Revision 1.3Jun 17, 2015Group: Non-polymer description / Structure summary
Revision 1.4Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anabaena Sensory Rhodopsin
B: Anabaena Sensory Rhodopsin
C: Anabaena Sensory Rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,5886
Polymers81,7353
Non-polymers8533
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Anabaena Sensory Rhodopsin


Mass: 27244.834 Da / Num. of mol.: 3 / Fragment: UNP residues 1-229
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. PCC 7120 (bacteria) / Strain: PCC7120 / Gene: alr3165 / Plasmid: pMS107 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codonplus-RIL / References: UniProt: Q8YSC4
#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H28O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NCA
1212D NCO
1313D CONCA
1413D NCACX
1513D NCOCX
1612D CC (DARR)
1722D NCA
1822D NCO
1923D NCACX
11023D NCOCX
11122D CC (DARR)
11232D NCA
11332D NCO
11433D NCACX
11533D NCOCX
11632D CC (DARR)
1173CHHC
1183HBR2-NCOCX

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Sample preparation

Details
Solution-IDContentsSolvent system
12 w/v [U-100% 13C; U-100% 15N] ASR, 0.9 w/v [U-100% 13C; U-100% 15N] DMPC, 0.1 w/v [U-100% 13C; U-100% 15N] DMPA, DMPC/DMPADMPC/DMPA
22 w/v alternately labeled by 2-13C glycerol and U- 15N ASR, 0.9 w/v [U-100% 13C; U-100% 15N] DMPC, 0.1 w/v [U-100% 13C; U-100% 15N] DMPA, DMPC/DMPADMPC/DMPA
32 w/v 1,3-C13-glycerol labeled and U-N15 labeled ASR, 0.9 w/v [U-100% 13C; U-100% 15N] DMPC, 0.1 w/v [U-100% 13C; U-100% 15N] DMPA, DMPC/DMPADMPC/DMPA
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 w/vASR-1[U-100% 13C; U-100% 15N]1
0.9 w/vDMPC-2[U-100% 13C; U-100% 15N]1
0.1 w/vDMPA-3[U-100% 13C; U-100% 15N]1
2 w/vASR-4alternately labeled by 2-13C glycerol and U- 15N2
0.9 w/vDMPC-5[U-100% 13C; U-100% 15N]2
0.1 w/vDMPA-6[U-100% 13C; U-100% 15N]2
2 w/vASR-71,3-C13-glycerol labeled and U-N15 labeled3
0.9 w/vDMPC-8[U-100% 13C; U-100% 15N]3
0.1 w/vDMPA-9[U-100% 13C; U-100% 15N]3
Sample conditionspH: 9 / Pressure: 1 atm / Temperature: 278 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Zhengrong and Baxprocessing
CARAKeller and Wuthrichdata analysis
CARAKeller and Wuthrichchemical shift assignment
ARIALinge, O'Donoghue and Nilgesstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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