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- PDB-7p3a: N-terminal domain of CGI-99 -

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Basic information

Entry
Database: PDB / ID: 7p3a
TitleN-terminal domain of CGI-99
ComponentsRNA transcription, translation and transport factor protein
KeywordsUNKNOWN FUNCTION / calponin homology domain / hCLE / RTRAF / c14orf166
Function / homology
Function and homology information


tRNA-splicing ligase complex / RNA transport / tRNA splicing, via endonucleolytic cleavage and ligation / tRNA processing in the nucleus / RNA polymerase II complex binding / negative regulation of protein kinase activity / mitotic spindle / centrosome / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II ...tRNA-splicing ligase complex / RNA transport / tRNA splicing, via endonucleolytic cleavage and ligation / tRNA processing in the nucleus / RNA polymerase II complex binding / negative regulation of protein kinase activity / mitotic spindle / centrosome / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
RNA transcription, translation and transport factor protein / RNA transcription, translation and transport factor protein
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / RNA transcription, translation and transport factor protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsKroupova, A. / Jinek, M.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
University of ZurichFK-18-033 Switzerland
Swiss National Science FoundationNational Competence Center for Research (NCCR) RNA & Disease Switzerland
CitationJournal: Elife / Year: 2021
Title: Molecular architecture of the human tRNA ligase complex.
Authors: Kroupova, A. / Ackle, F. / Asanovic, I. / Weitzer, S. / Boneberg, F.M. / Faini, M. / Leitner, A. / Chui, A. / Aebersold, R. / Martinez, J. / Jinek, M.
History
DepositionJul 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA transcription, translation and transport factor protein
B: RNA transcription, translation and transport factor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,68012
Polymers25,0122
Non-polymers66810
Water2,306128
1
A: RNA transcription, translation and transport factor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8406
Polymers12,5061
Non-polymers3345
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA transcription, translation and transport factor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8406
Polymers12,5061
Non-polymers3345
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.714, 91.714, 52.942
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid 0 through 76 or (resid 77...A0 - 94
121(chain 'A' and (resid 0 through 76 or (resid 77...A210
231(chain 'B' and (resid 0 through 94 or resid 201 through 221))B0 - 94
241(chain 'B' and (resid 0 through 94 or resid 201 through 221))B210

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Components

#1: Protein RNA transcription, translation and transport factor protein / CLE7 homolog / CLE / hCLE


Mass: 12506.033 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: SNA is the affinity tag cleavage scar / Source: (gene. exp.) Homo sapiens (human) / Gene: RTRAF, C14orf166, CGI-99 / Plasmid: pET His6 TEV LIC cloning vector (1B) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y224
#2: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.57 Å3/Da / Density % sol: 52.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES pH 7.5, 200 mM magnesium chloride, 20% isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.0084 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0084 Å / Relative weight: 1
ReflectionResolution: 2→45.86 Å / Num. obs: 17246 / % possible obs: 99.9 % / Redundancy: 20.2 % / Biso Wilson estimate: 30.79 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.032 / Net I/σ(I): 18.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 19.3 % / Rmerge(I) obs: 1.53 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3450 / CC1/2: 0.74 / Rpim(I) all: 0.354 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XSCALEdata scaling
PHENIX1.16_3549phasing
RefinementMethod to determine structure: SAD / Resolution: 2→45.86 Å / SU ML: 0.251 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.5107
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2242 864 5 %
Rwork0.1965 31837 -
obs0.1979 17235 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.91 Å2
Refinement stepCycle: LAST / Resolution: 2→45.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1688 0 42 128 1858
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01231765
X-RAY DIFFRACTIONf_angle_d1.10552374
X-RAY DIFFRACTIONf_chiral_restr0.0714231
X-RAY DIFFRACTIONf_plane_restr0.0063308
X-RAY DIFFRACTIONf_dihedral_angle_d22.5302652
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.060.32471380.29992662X-RAY DIFFRACTION99.82
2.06-2.130.32841290.26692635X-RAY DIFFRACTION99.93
2.13-2.20.26851540.25152720X-RAY DIFFRACTION99.93
2.2-2.290.25931360.24112600X-RAY DIFFRACTION99.64
2.29-2.40.27531420.22852634X-RAY DIFFRACTION99.78
2.4-2.520.25041370.21352676X-RAY DIFFRACTION100
2.52-2.680.29871360.21592617X-RAY DIFFRACTION100
2.68-2.890.21741430.2072693X-RAY DIFFRACTION99.93
2.89-3.180.21211400.20092629X-RAY DIFFRACTION99.89
3.18-3.640.20481400.17132673X-RAY DIFFRACTION100
3.64-4.580.1921350.14552643X-RAY DIFFRACTION100

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