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Basic information

Entry
Database: PDB / ID: 3soo
TitleCrystal structure of a LINE-1 type transposase domain-containing protein 1 (L1TD1) from HOMO SAPIENS at 2.73 A resolution
ComponentsLINE-1 type transposase domain-containing protein 1
KeywordsRNA BINDING PROTEIN / Alpha/beta protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / Partnership for Stem Cell Biology / STEMCELL
Function / homology
Function and homology information


retrotransposition / single-stranded RNA binding / ribonucleoprotein complex / intracellular membrane-bounded organelle
Similarity search - Function
L1 transposable element, C-terminal 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
LINE-1 type transposase domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.73 Å
AuthorsJoint Center for Structural Genomics (JCSG) / Partnership for Stem Cell Biology (STEMCELL)
CitationJournal: To be published
Title: Crystal structure of a LINE-1 type transposase domain-containing protein 1 (L1TD1) from HOMO SAPIENS at 2.73 A resolution
Authors: Joint Center for Structural Genomics (JCSG) / Partnership for Stem Cell Biology (STEMCELL)
History
DepositionJun 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Structure summary
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 1, 2023Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LINE-1 type transposase domain-containing protein 1
B: LINE-1 type transposase domain-containing protein 1
C: LINE-1 type transposase domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,63112
Polymers30,8273
Non-polymers8049
Water0
1
A: LINE-1 type transposase domain-containing protein 1
hetero molecules

A: LINE-1 type transposase domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,51212
Polymers20,5512
Non-polymers96110
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Buried area6250 Å2
ΔGint-127 kcal/mol
Surface area11270 Å2
MethodPISA
2
B: LINE-1 type transposase domain-containing protein 1
C: LINE-1 type transposase domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8756
Polymers20,5512
Non-polymers3244
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5730 Å2
ΔGint-95 kcal/mol
Surface area10960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.140, 69.140, 292.270
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-866-

SO4

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Components

#1: Protein LINE-1 type transposase domain-containing protein 1 / ES cell-associated protein 11


Mass: 10275.656 Da / Num. of mol.: 3 / Fragment: residues 235-321
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BC111559, ECAT11, L1TD1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5T7N2
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
Sequence details1. THE CONSTRUCT (RESIDUES 235-321) WAS EXPRESSED WITH A N-TERMINAL PURIFICATION TAG ...1. THE CONSTRUCT (RESIDUES 235-321) WAS EXPRESSED WITH A N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. 2. THE PROTEIN WAS REDUCTIVELY METHYLATED PRIOR TO CRYSTALLIZATION.

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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: 3.27 Å3/Da / Density % sol: 62.39 %
Description: While data were scaled with XSCALE, the final statistics reported in the REMARK 200 section have been calculated with SCALA with fixed scales and no sd correction.
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2M potassium sodium tartrate, 2.0M ammonium sulfate, 0.1M sodium citrate pH 5.6, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162,0.97932,0.97907
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 21, 2011 / Details: double crystal monochromator
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979321
30.979071
ReflectionResolution: 2.73→48.712 Å / Num. all: 11913 / Num. obs: 11913 / % possible obs: 99.8 % / Redundancy: 6.7 % / Rsym value: 0.063 / Net I/σ(I): 15.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.73-2.8870.5981.31172116790.59899.9
2.88-3.0570.352.21094415700.3599.9
3.05-3.266.90.2033.81050115110.203100
3.26-3.526.80.1156.2963614150.11599.9
3.52-3.866.80.0838.2892813100.083100
3.86-4.326.60.05310798712040.05399.9
4.32-4.986.50.03914.2699110730.039100
4.98-6.16.30.03915.358549270.039100
6.1-8.635.90.03616.245107660.036100
8.63-48.7124.80.02822.521824580.02896.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEdata scaling
BUSTER-TNT2.8.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.73→48.712 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.9186 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. SULFATE, CHLORIDE MODELED ARE PRESENT IN PROTEIN/CRYSTALLIZATION/ CRYO CONDITIONS. 4. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). 5. THE PROTEIN WAS SUBJECTED TO REDUCTIVE METHYLATION PRIOR TO CRYSTALLIZATION AND LYSINES HAVE BEEN MODELED AS N-DIMETHYL-LYSINE (MLY). HOWEVER, METHYL GROUPS ON LYSINES WERE NOT MODELED DUE TO POOR SIDE-CHAIN DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2593 575 4.86 %RANDOM
Rwork0.2259 ---
obs0.2275 11828 --
Displacement parametersBiso max: 224.81 Å2 / Biso mean: 118.5537 Å2 / Biso min: 66.96 Å2
Baniso -1Baniso -2Baniso -3
1--11.8937 Å20 Å20 Å2
2---11.8937 Å20 Å2
3---23.7873 Å2
Refinement stepCycle: LAST / Resolution: 2.73→48.712 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1977 0 41 0 2018
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d956SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes55HARMONIC2
X-RAY DIFFRACTIONt_gen_planes284HARMONIC5
X-RAY DIFFRACTIONt_it2036HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion270SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2143SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2036HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2754HARMONIC21.16
X-RAY DIFFRACTIONt_omega_torsion2.8
X-RAY DIFFRACTIONt_other_torsion3.01
LS refinement shellResolution: 2.73→2.99 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.309 133 4.88 %
Rwork0.2625 2595 -
all0.2646 2728 -
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)
11.1307-0.41780.39992.6231-0.20811.18920.2021-0.3050.05920.0740.0959-0.0059-0.380.5456-0.29790.1375-0.08570.01560.2831-0.1105-0.286-31.887921.177929.3758
22.09251.0502-2.46693.6694-0.6273.18930.5477-0.3140.71020.4334-0.09910.9469-0.8674-0.2324-0.44860.4208-0.02420.17910.0323-0.0954-0.4103-30.850541.688620.5772
33.75431.305-1.10463.2076-0.20032.72650.5497-0.39550.3164-0.0374-0.31270.4038-0.5589-0.0611-0.2370.3422-0.03290.02390.276-0.056-0.3496-20.896839.73717.634
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|0 - 320 }A0 - 320
2X-RAY DIFFRACTION2{ B|0 - 320 }B0 - 320
3X-RAY DIFFRACTION3{ C|235 - 320 }C235 - 320

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