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- PDB-2ykq: Structure of the human LINE-1 ORF1p trimer -

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Basic information

Entry
Database: PDB / ID: 2ykq
TitleStructure of the human LINE-1 ORF1p trimer
ComponentsLINE-1 ORF1P
KeywordsRNA BINDING PROTEIN / RNA-BINDING PROTEIN / GENOME EVOLUTION / NUCLEIC ACID CHAPERONE / RNP / COILED-COIL
Function / homology
Function and homology information


retrotransposition / cytoplasmic ribonucleoprotein granule / cytoplasmic stress 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 / L1 transposable element, trimerization domain / Rec A Protein; domain 2 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsKhazina, E. / Weichenrieder, O.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Trimeric Structure and Flexibility of the L1Orf1P Protein in Human L1 Retrotransposition
Authors: Khazina, E. / Truffault, V. / Buettner, R. / Schmidt, S. / Coles, M. / Weichenrieder, O.
History
DepositionMay 28, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2011Group: Database references
Revision 1.2Oct 24, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / 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_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LINE-1 ORF1P
B: LINE-1 ORF1P
C: LINE-1 ORF1P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,4535
Polymers82,3823
Non-polymers712
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7170 Å2
ΔGint-44.6 kcal/mol
Surface area34880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.440, 91.640, 107.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein LINE-1 ORF1P / ORF1 CODES FOR A 40 KDA PRODUCT


Mass: 27460.805 Da / Num. of mol.: 3 / Fragment: RESIDUES 104-326 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: THE FOLLOWING RESIDUES ARE SELENOMETHIONINES, M226, M230, M302, M323
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET15B / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): ROSETTA2 / References: UniProt: Q15605, UniProt: Q9UN81*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 104 TO MSE ENGINEERED RESIDUE IN CHAIN A, ARG 105 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, CYS 104 TO MSE ENGINEERED RESIDUE IN CHAIN A, ARG 105 TO ALA ENGINEERED RESIDUE IN CHAIN A, MET 121 TO ALA ENGINEERED RESIDUE IN CHAIN A, MET 125 TO ILE ENGINEERED RESIDUE IN CHAIN A, MET 128 TO ILE ENGINEERED RESIDUE IN CHAIN B, CYS 104 TO MSE ENGINEERED RESIDUE IN CHAIN B, ARG 105 TO ALA ENGINEERED RESIDUE IN CHAIN B, MET 121 TO ALA ENGINEERED RESIDUE IN CHAIN B, MET 125 TO ILE ENGINEERED RESIDUE IN CHAIN B, MET 128 TO ILE ENGINEERED RESIDUE IN CHAIN C, CYS 104 TO MSE ENGINEERED RESIDUE IN CHAIN C, ARG 105 TO ALA ENGINEERED RESIDUE IN CHAIN C, MET 121 TO ALA ENGINEERED RESIDUE IN CHAIN C, MET 125 TO ILE ENGINEERED RESIDUE IN CHAIN C, MET 128 TO ILE
Has protein modificationY
Sequence detailsTHE FOLLOWING RESIDUES HAVE BEEN MUTATED, C104M, R105A, M121A, M125I, M128I. THE LAST 6 AMINO ACIDS ...THE FOLLOWING RESIDUES HAVE BEEN MUTATED, C104M, R105A, M121A, M125I, M128I. THE LAST 6 AMINO ACIDS ARE A HEXAHISTIDINE PURIFICATION TAG.

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growpH: 8.5
Details: 100 MM TRIS-CL PH 8.5, 100 MM MG-ACETATE, 12 % PEG 8000

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9787
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 21, 2009 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 3.1→69.8 Å / Num. obs: 13318 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 68 Å2 / Rsym value: 0.089 / Net I/σ(I): 11.3
Reflection shellResolution: 3.1→3.18 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.59 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2YKO AND 2W7A

2yko

2w7a


Resolution: 3.1→69.805 Å / SU ML: 0.48 / σ(F): 2.01 / Phase error: 26.57 / Stereochemistry target values: ML
Details: SIDE-CHAINS OF THE FOLLOWING RESIDUES WERE TRUNCATED AT CB ATOMS. CHAIN B, RESIDUES 112, 113, 115, 116. CHAIN C, RESIDUES 111 TO 113. THE FOLLOWING RESIDUES ARE DISORDERED. CHAIN A, RESIDUES ...Details: SIDE-CHAINS OF THE FOLLOWING RESIDUES WERE TRUNCATED AT CB ATOMS. CHAIN B, RESIDUES 112, 113, 115, 116. CHAIN C, RESIDUES 111 TO 113. THE FOLLOWING RESIDUES ARE DISORDERED. CHAIN A, RESIDUES 104 TO 111, 191 TO 193, 204 TO 212, 324 TO 332. CHAIN B, RESIDUES 104 TO 111, 190 TO 194, 204 TO 212, 324 TO 332. CHAIN C, RESIDUES 104 TO 110, 192 TO 194, 204 TO 213, 324 TO 332.
RfactorNum. reflection% reflection
Rfree0.2862 671 5 %
Rwork0.2394 --
obs0.2418 13316 99.68 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.233 Å2 / ksol: 0.338 e/Å3
Displacement parametersBiso mean: 76.1 Å2
Baniso -1Baniso -2Baniso -3
1--18.9913 Å20 Å20 Å2
2--1.6686 Å20 Å2
3---17.3227 Å2
Refinement stepCycle: LAST / Resolution: 3.1→69.805 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4946 0 2 0 4948
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025012
X-RAY DIFFRACTIONf_angle_d0.4726715
X-RAY DIFFRACTIONf_dihedral_angle_d9.9972028
X-RAY DIFFRACTIONf_chiral_restr0.031747
X-RAY DIFFRACTIONf_plane_restr0.002869
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.33940.3391430.29732460X-RAY DIFFRACTION100
3.3394-3.67540.34141290.26562499X-RAY DIFFRACTION100
3.6754-4.20720.28821160.24782525X-RAY DIFFRACTION100
4.2072-5.30030.2691320.21682540X-RAY DIFFRACTION100
5.3003-69.82230.25531510.22332621X-RAY DIFFRACTION99
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)
11.9337-2.2049-0.31734.55910.76250.8834-0.1730.0062-0.66990.09890.12970.47130.15220.17050.01360.20780.0139-0.0672-0.1946-0.30710.108857.081989.392620.556
22.4248-1.70911.0636.5398-1.7043.94890.19720.08650.1805-0.57010.05720.1353-0.4349-0.4490.00840.44410.11790.02640.384-0.01920.221138.8092126.10511.06
33.6742-1.4778-1.89114.6438-2.40594.392-0.1664-0.7048-0.37890.11250.04650.55460.0584-0.5299-0.01420.4220.12770.12720.43850.08470.540427.8546112.037637.5958
43.9494-0.02391.46513.4022.58672.7886-0.1766-0.82520.2890.24230.1570.351-0.30010.0941-0.00120.30210.02050.02560.3354-0.07780.283355.4333128.12836.842
51.00351.01232.23457.03123.57365.26720.19730.85680.0781-0.71850.5718-0.27430.13211.61240.8310.27860.076-0.07460.6947-0.03640.308740.9648104.41018.0822
61.2236-0.12630.08720.0180.03550.40560.0556-0.8457-0.26120.02030.82641.4383-0.2337-0.97190.01070.59980.0884-0.12040.48730.18130.801944.666496.945138.8354
72.991.9695-1.20812.68560.06451.0227-0.0986-0.6249-0.6993-0.33670.1785-0.9302-0.41811.4757-0.00870.39590.09280.01850.7591-0.01490.317865.9355110.682225.2031
82.29741.05270.09791.8533-1.92043.04710.05410.1612-0.9912-0.87110.1293-0.14540.59160.20690.00160.51330.0474-0.07090.44580.00380.665728.019796.76512.7627
93.0632-1.68520.1441.0585-0.59893.6508-0.10820.5728-0.11350.0254-0.3154-0.296-0.48290.7723-0.00040.5922-0.12250.13160.65720.01360.459555.85992.20649.2559
102.1985-0.095-0.95890.66081.34383.31510.43120.40130.0986-0.32330.2582-0.1568-0.42310.57430.01420.36450.02310.04430.545-0.04370.526477.01110.393713.7868
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND (RESSEQ 112:156)) OR (CHAIN B AND (RESSEQ 112:156)) OR (CHAIN C AND (RESSEQ 111:156))
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 157:190 OR RESSEQ 194:203 OR RESSEQ 213:252)
3X-RAY DIFFRACTION3CHAIN B AND (RESSEQ 157:189 OR RESSEQ 195:203 OR RESSEQ 213:252)
4X-RAY DIFFRACTION4CHAIN C AND (RESSEQ 157:191 OR RESSEQ 195:203 OR RESSEQ 214:252)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 253:265)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 253:265)
7X-RAY DIFFRACTION7CHAIN C AND (RESSEQ 253:265)
8X-RAY DIFFRACTION8CHAIN A AND (RESSEQ 266:323)
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 266:323)
10X-RAY DIFFRACTION10CHAIN C AND (RESSEQ 266:323)

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