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- PDB-2ldy: Solution structure of the RMM-CTD domains of human LINE-1 ORF1p -

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Basic information

Entry
Database: PDB / ID: 2ldy
TitleSolution structure of the RMM-CTD domains of human LINE-1 ORF1p
ComponentsORF1 codes for a 40 kDa product
KeywordsRNA BINDING PROTEIN / Nucleic acid chaperone / Genome evolution
Function / homology
Function and homology information


retrotransposition / cytoplasmic stress granule / cytoplasmic ribonucleoprotein granule / single-stranded DNA binding / single-stranded RNA binding / ribonucleoprotein complex / nucleotide binding / nucleolus / identical protein binding / cytoplasm
Similarity search - Function
L1 transposable element, RRM domain / L1 transposable element, C-terminal domain / L1 transposable element, trimerization domain / L1 transposable element trimerization domain / Transposase, L1 / L1 transposable element, dsRBD-like domain / L1 transposable element, C-terminal domain / L1 transposable element, RRM domain / L1 transposable element RBD-like domain / L1 transposable element dsRBD-like domain ...L1 transposable element, RRM domain / L1 transposable element, C-terminal domain / L1 transposable element, trimerization domain / L1 transposable element trimerization domain / Transposase, L1 / L1 transposable element, dsRBD-like domain / L1 transposable element, C-terminal domain / L1 transposable element, RRM domain / L1 transposable element RBD-like domain / L1 transposable element dsRBD-like domain / Rec A Protein; domain 2 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
LINE-1 retrotransposable element ORF1 protein / LINE-1 retrotransposable element ORF1 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsminimized average structure, model 1
Model type detailsminimized average
AuthorsColes, M. / Truffault, V.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Trimeric structure and flexibility of the L1ORF1 protein in human L1 retrotransposition.
Authors: Khazina, E. / Truffault, V. / Buttner, R. / Schmidt, S. / Coles, M. / Weichenrieder, O.
History
DepositionJun 3, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
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_ref_seq_dif.details
Revision 1.2May 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: ORF1 codes for a 40 kDa product


Theoretical massNumber of molelcules
Total (without water)21,5171
Polymers21,5171
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 200structures with the least restraint violations
RepresentativeModel #1minimized average structure

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Components

#1: Protein ORF1 codes for a 40 kDa product


Mass: 21516.865 Da / Num. of mol.: 1 / Fragment: sequence database residues 157-330
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta2 / References: UniProt: Q15605, UniProt: Q9UN81*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1223D 1H-13C NOESY
1323D CNH-NOESY
1413D NNH-NOESY
1523D HN(CA)CB
1623D HBHA(CO)NH
1723D C(CO)NH
1823D CCH-TOCSY
1923D HNCO
11012D 15N-filtered 1H-1H NOESY
11133D 1H-15N NOESY
11243D 1H-13C NOESY
11343D CNH-NOESY
11433D NNH-NOESY
11543D CCH-NOESY
11643D HN(CA)CB
11743D CBCA(CO)NH
11843D C(CO)NH
11943D CCH-TOCSY
12043D HNCO
12132D 15N-filteres 1H-1H NOESY
12253D 1H-15N NOESY
12363D 1H-13C NOESY
12463D CNH-NOESY
12553D NNH-NOESY
12663D CCH-NOESY
12763D HN(CA)CB
12863D CBCA(CO)NH
12963D C(CO)NH
13063D CCH-TOCSY
13163D HNCO
13252D 15N-filteres 1H-1H NOESY
NMR detailsText: Structures of the RMM and CTD domains were first determined separately, and data compared to that for the two-domain construct

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6 mM [U-100% 15N] L1ORF1p-RMM, 5 mM Tris, 300 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
20.8 mM [U-100% 13C; U-100% 15N] L1ORF1p-RMM, 5 mM Tris, 300 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
30.8 mM [U-100% 15N] L1ORF1p-CTD, 5 mM Tris, 300 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
40.8 mM [U-100% 13C; U-100% 15N] L1ORF1p-CTD, 5 mM Tris, 300 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
50.8 mM [U-100% 15N] L1ORF1p RMM-CTD, 5 mM Tris, 300 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
60.8 mM [U-100% 13C; U-100% 15N] L1ORF1p RMM-CTD, 5 mM Tris, 300 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mML1ORF1p-RMM-1[U-100% 15N]1
5 mMTris-21
300 mMsodium chloride-31
0.8 mML1ORF1p-RMM-4[U-100% 13C; U-100% 15N]2
5 mMTris-52
300 mMsodium chloride-62
0.8 mML1ORF1p-CTD-7[U-100% 15N]3
5 mMTris-83
300 mMsodium chloride-93
0.8 mML1ORF1p-CTD-10[U-100% 13C; U-100% 15N]4
5 mMTris-114
300 mMsodium chloride-124
0.8 mML1ORF1p RMM-CTD-13[U-100% 15N]5
5 mMTris-145
300 mMsodium chloride-155
0.8 mML1ORF1p RMM-CTD-16[U-100% 13C; U-100% 15N]6
5 mMTris-176
300 mMsodium chloride-186
Sample conditionsIonic strength: 300 / pH: 8.0 / Pressure: ambient / Temperature: 291 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
Sparky3.113Goddardchemical shift assignment
Sparky3.113Goddarddata analysis
X-PLOR NIH2.21Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.21Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: Refinement with conformational database potential
NMR constraintsProtein chi angle constraints total count: 98 / Protein other angle constraints total count: 43 / Protein phi angle constraints total count: 176 / Protein psi angle constraints total count: 191
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 21 / Maximum lower distance constraint violation: 0.05 Å / Maximum torsion angle constraint violation: 0.35 ° / Maximum upper distance constraint violation: 0.077 Å
NMR ensemble rmsDistance rms dev: 0.012 Å / Distance rms dev error: 0.0001 Å

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