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

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Basic information

Entry
Database: PDB / ID: 2yko
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 / SAD / Resolution: 2.1 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 1.1Aug 24, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Other
Revision 1.2Sep 14, 2011Group: Database references
Revision 1.3Oct 10, 2012Group: Database references
Revision 1.4Dec 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 1.5Nov 20, 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)84,1415
Polymers84,0703
Non-polymers712
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7240 Å2
ΔGint-47 kcal/mol
Surface area34670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.690, 85.420, 111.450
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: 28023.404 Da / Num. of mol.: 3 / Fragment: RESIDUES 104-330 / 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) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O
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: 2.5 Å3/Da / Density % sol: 51 %
Description: SELENIUM SITES WERE IDENTIFIED IN DATA SET 2, COLLECTED AT 0.97868 A (SE K-EDGE PEAK).
Crystal growpH: 7 / Details: 100 MM NA-HEPES PH7.0, 1.1 M NA-MALONATE

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.971000, 0.979868
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 21, 2009 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9711
20.9798681
ReflectionResolution: 2.1→36.8 Å / Num. obs: 40087 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 2.3 % / Biso Wilson estimate: 36.2 Å2 / Rsym value: 0.049 / Net I/σ(I): 10.9
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2 / Rsym value: 0.49 / % possible all: 97.6

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Processing

Software
NameClassification
XDSdata reduction
XSCALEdata scaling
SHELXphasing
PHASERphasing
PHENIXrefinement
RefinementMethod to determine structure: SAD
Starting model: PDB ENTRIES 2WPQ AND 2W7A

2wpq

2w7a


Resolution: 2.1→36.824 Å / SU ML: 0.28 / σ(F): 2 / Phase error: 24.91 / Stereochemistry target values: ML
Details: HYDROGENS WERE REFINED IN THE RIDING POSITIONS. SIDE-CHAINS OF THE FOLLOWING RESIDUES WERE TRUNCATED AT CB ATOMS. CHAIN A, RESIDUES 110 TO 111. CHAIN B, RESIDUES 114 TO 116. CHAIN C, RESIDUE ...Details: HYDROGENS WERE REFINED IN THE RIDING POSITIONS. SIDE-CHAINS OF THE FOLLOWING RESIDUES WERE TRUNCATED AT CB ATOMS. CHAIN A, RESIDUES 110 TO 111. CHAIN B, RESIDUES 114 TO 116. CHAIN C, RESIDUE 113. THE FOLLOWING RESIDUES WERE MODELED AS DOUBLE CONFORMATIONS. CHAIN A, RESIDUES 155, 220. CHAIN B, RESIDUES 135, 201, 220, 322. CHAIN C, RESIDUES 130, 136, 256. THE FOLLOWING RESIDUES ARE DISORDERED. CHAIN A, RESIDUES 104 TO 109, 190 TO 192, 204 TO 210, 324 TO 336. CHAIN B, RESIDUES 104 TO 113, 167 TO 171, 190 TO 194, 204 TO 210, 324 TO 336. CHAIN C, RESIDUES 104 TO 112, 204 TO 213, 324 TO 336.
RfactorNum. reflection% reflection
Rfree0.2639 2013 5 %
Rwork0.2081 --
obs0.2109 40085 97.27 %
Solvent computationShrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.663 Å2 / ksol: 0.445 e/Å3
Displacement parametersBiso mean: 52.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.767 Å20 Å20 Å2
2--0.8396 Å20 Å2
3----1.6066 Å2
Refinement stepCycle: LAST / Resolution: 2.1→36.824 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4951 0 2 190 5143
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125089
X-RAY DIFFRACTIONf_angle_d1.2736828
X-RAY DIFFRACTIONf_dihedral_angle_d14.5222087
X-RAY DIFFRACTIONf_chiral_restr0.073755
X-RAY DIFFRACTIONf_plane_restr0.006888
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.15250.34631210.26592709X-RAY DIFFRACTION98
2.1525-2.21070.2891580.24382667X-RAY DIFFRACTION98
2.2107-2.27580.27061610.22412708X-RAY DIFFRACTION98
2.2758-2.34920.26411390.21132718X-RAY DIFFRACTION98
2.3492-2.43310.29341390.22172734X-RAY DIFFRACTION99
2.4331-2.53050.28571590.22282684X-RAY DIFFRACTION99
2.5305-2.64570.3051490.23372729X-RAY DIFFRACTION99
2.6457-2.78510.29641500.22132763X-RAY DIFFRACTION99
2.7851-2.95960.32951200.2142764X-RAY DIFFRACTION98
2.9596-3.18790.25271440.21852749X-RAY DIFFRACTION98
3.1879-3.50850.26821480.19572750X-RAY DIFFRACTION98
3.5085-4.01570.22731350.18412727X-RAY DIFFRACTION97
4.0157-5.05730.21871380.16822735X-RAY DIFFRACTION96
5.0573-36.82970.26531520.23492635X-RAY DIFFRACTION89
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)
12.2579-2.5998-0.53786.691.0251.0289-0.0727-0.012-0.24410.03960.0926-0.33320.33440.17970.00070.21320.02980.0070.2708-0.02350.238360.535582.346719.7769
24.01230.19521.14854.7888-0.44422.98780.17960.26650.2136-0.1919-0.0050.2091-0.3085-0.27740.00020.28850.05650.00370.38540.07990.343542.0097117.01845.6544
34.8985-0.995-0.40493.0876-1.06622.87580.1687-0.1470.60340.3068-0.09860.5379-0.15170.05540.00130.25950.00020.09040.2639-0.05060.421430.1592106.332632.2318
44.6737-1.05560.48484.32330.76822.7715-0.306-0.11990.38760.19010.119-0.0537-0.2739-0.1769-0.00410.3035-0.0186-0.01350.1828-0.03450.281856.6678122.832731.3748
50.0310.0868-0.1020.4316-0.55460.708-0.35960.22480.8471-0.35610.1407-0.07140.43150.3617-0.03060.33060.05-0.04190.2974-0.03480.372343.656595.61235.4894
60.16740.0096-0.0766-0.0032-0.04020.277-0.10240.0581-0.0765-0.1282-0.121-0.07850.8102-0.1121-0.00010.4618-0.02350.03680.3099-0.05710.266144.309792.189637.2413
70.21830.2415-0.30111.0064-0.38730.42860.2656-0.5689-0.16891.0559-0.2601-0.3566-0.05711.20930.01640.33830.0421-0.01090.55040.00970.415768.3027106.342223.5099
82.36250.6209-0.61891.8371-0.40482.5051-0.1671-0.1585-0.149-0.09240.11490.22461.5188-0.7642-0.00610.7618-0.1867-0.06290.5933-0.00450.310430.088588.14723.8069
91.0351-0.09710.8631.5738-0.2252.9365-0.1641-0.6415-0.06931.07040.0486-0.3858-0.94360.47630.02630.68580.0250.10210.42930.12450.289848.43593.910152.0651
102.2813-1.6838-1.21423.0724-0.7442.1370.6411-0.31990.4030.0892-0.2878-1.0947-0.30040.79610.00450.4477-0.07890.06920.6002-0.00470.643977.0458111.417612.2761
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND (RESSEQ 110:156)) OR (CHAIN B AND (RESSEQ 114:156)) OR (CHAIN C AND (RESSEQ 113:156))
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 157:189 OR RESSEQ 193:203 OR RESSEQ 211:252)
3X-RAY DIFFRACTION3CHAIN B AND (RESSEQ 157:166 OR RESSEQ 172:189 OR RESSEQ 195:203 OR RESSEQ 211:252)
4X-RAY DIFFRACTION4CHAIN C AND (RESSEQ 157:203 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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