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- PDB-6drf: Structure of human Retinal Degeneration 3(RD3) Protein -

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Basic information

Entry
Database: PDB / ID: 6drf
TitleStructure of human Retinal Degeneration 3(RD3) Protein
ComponentsProtein RD3
KeywordsSIGNALING PROTEIN / Sensory transduction / Vision
Function / homology
Function and homology information


negative regulation of guanylate cyclase activity / cone photoreceptor outer segment / rod photoreceptor outer segment / response to stimulus / photoreceptor outer segment / visual perception / photoreceptor inner segment / protein transport / retina development in camera-type eye / endosome ...negative regulation of guanylate cyclase activity / cone photoreceptor outer segment / rod photoreceptor outer segment / response to stimulus / photoreceptor outer segment / visual perception / photoreceptor inner segment / protein transport / retina development in camera-type eye / endosome / perinuclear region of cytoplasm / nucleus / cytoplasm
Similarity search - Function
Retinal degeneration protein 3 / RD3 protein
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsYu, Q. / Lim, S. / Peshenko, I. / Cudia, D. / Dizhoor, A.M. / Ames, J.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)EY012347 United States
CitationJournal: J. Biol. Chem. / Year: 2019
Title: Retinal degeneration 3 (RD3) protein, a retinal guanylyl cyclase regulator, forms a monomeric and elongated four-helix bundle.
Authors: Peshenko, I.V. / Yu, Q. / Lim, S. / Cudia, D. / Dizhoor, A.M. / Ames, J.B.
History
DepositionJun 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 2.0Feb 27, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / citation ...atom_site / citation / citation_author / pdbx_poly_seq_scheme / pdbx_validate_close_contact / pdbx_validate_torsion / struct_conf / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.auth_seq_id / _citation.country ..._atom_site.auth_seq_id / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_torsion.auth_seq_id / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_seq_id / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq_dif.pdbx_auth_seq_num
Revision 2.1Dec 11, 2019Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 2.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 2.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein RD3


Theoretical massNumber of molelcules
Total (without water)16,6021
Polymers16,6021
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10560 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein RD3 / Retinal degeneration protein 3


Mass: 16601.789 Da / Num. of mol.: 1 / Fragment: residues 19-153 / Mutation: R68D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RD3, C1orf36 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Z3Z2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
122isotropic13D HNCA
132isotropic13D HN(CA)CB
142isotropic13D CBCA(CO)NH
152isotropic13D HNCO
172isotropic13D (H)CCH-TOCSY
162isotropic13D CC(CO)NH
182isotropic13D (H)CC(CO)NH
191isotropic13D 1H-15N NOESY
1102isotropic13D 1H-13C NOESY
1111isotropic13D 1H-15N TOCSY
1122isotropic12D 1H-13C HSQC

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.9 mM [U-15N] human RD3, 20 mM D11 TRIS, 3 mM D10 DTT, 50 uM D12 EDTA, 0.04 % w/v sodium azide, 93% H2O/7% D2OThe added 0.04% w/v NaN3 was used to preserve sample over series of 2D NMR experiments.15N_RD393% H2O/7% D2O
solution20.9 mM [U-13C; U-15N] human RD3, 20 mM d11 TRIS, 3 mM d10 DTT, 50 uM d12 EDTA, 0.04 % w/v sodium azide, 93% H2O/7% D2OThe added NaN3 was used to preserve sample over series of 3D NMR experiments.15N,13C_RD393% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.9 mMhuman RD3[U-15N]1
20 mMTRISD111
3 mMDTTD101
50 uMEDTAD121
0.04 % w/vsodium azidenatural abundance1
0.9 mMhuman RD3[U-13C; U-15N]2
20 mMTRISd112
3 mMDTTd102
50 uMEDTAd122
0.04 % w/vsodium azidenatural abundance2
Sample conditionsIonic strength: 20 mM / Label: RD3 / pH: 7.4 / Pressure: 1 atm / Temperature: 296 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe8.9Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.134Goddardchemical shift assignment
X-PLOR NIH2.47Schwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIH2.47Schwieters, Kuszewski, Tjandra and Clorestructure calculation
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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