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- PDB-7p3b: Human RNA ligase RTCB in complex with GMP and Co(II) -

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Basic information

Entry
Database: PDB / ID: 7p3b
TitleHuman RNA ligase RTCB in complex with GMP and Co(II)
ComponentsRNA-splicing ligase RtcB homolog
KeywordsLIGASE / tRNA splicing ligase / HSPC117 / 3'-phosphate/5'-hydroxy nucleic acid ligase
Function / homology
Function and homology information


tRNA-splicing ligase complex / 3'-phosphate/5'-hydroxy nucleic acid ligase / RNA ligase (GTP) activity / tRNA splicing, via endonucleolytic cleavage and ligation / vinculin binding / tRNA processing in the nucleus / placenta development / nuclear envelope / in utero embryonic development / intracellular membrane-bounded organelle ...tRNA-splicing ligase complex / 3'-phosphate/5'-hydroxy nucleic acid ligase / RNA ligase (GTP) activity / tRNA splicing, via endonucleolytic cleavage and ligation / vinculin binding / tRNA processing in the nucleus / placenta development / nuclear envelope / in utero embryonic development / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / GTP binding / RNA binding / nucleoplasm / metal ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
RNA-splicing ligase RtcB homologue, eukaryotic / Uncharacterized protein family UPF0027 signature. / RNA-splicing ligase, RtcB / tRNA-splicing ligase RtcB-like superfamily / tRNA-splicing ligase RtcB
Similarity search - Domain/homology
GUANOSINE-5'-MONOPHOSPHATE / ACETATE ION / : / FORMIC ACID / RNA-splicing ligase RtcB homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKroupova, A. / Ackle, F. / 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 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA-splicing ligase RtcB homolog
B: RNA-splicing ligase RtcB homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,20715
Polymers110,8512
Non-polymers1,35613
Water5,350297
1
A: RNA-splicing ligase RtcB homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9064
Polymers55,4251
Non-polymers4813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA-splicing ligase RtcB homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,30111
Polymers55,4251
Non-polymers87510
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.906, 96.906, 227.137
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-747-

HOH

21A-841-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGCYSCYS(chain 'A' and (resid 3 through 50 or (resid 51...AA3 - 545 - 56
12GLYGLYALAALA(chain 'A' and (resid 3 through 50 or (resid 51...AA60 - 43362 - 435
13ASPASPLYSLYS(chain 'A' and (resid 3 through 50 or (resid 51...AA444 - 504446 - 506
145GP5GP5GP5GP(chain 'A' and (resid 3 through 50 or (resid 51...AC601
25ARGARGCYSCYS(chain 'B' and (resid 3 through 16 or (resid 17...BB3 - 545 - 56
26GLYGLYALAALA(chain 'B' and (resid 3 through 16 or (resid 17...BB60 - 43362 - 435
27ASPASPLYSLYS(chain 'B' and (resid 3 through 16 or (resid 17...BB444 - 504446 - 506
285GP5GP5GP5GP(chain 'B' and (resid 3 through 16 or (resid 17...BF601

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein RNA-splicing ligase RtcB homolog / 3'-phosphate/5'-hydroxy nucleic acid ligase


Mass: 55425.254 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal SNA is the affinity tag cleavage scar / Source: (gene. exp.) Homo sapiens (human) / Gene: RTCB, C22orf28, HSPC117 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9Y3I0, 3'-phosphate/5'-hydroxy nucleic acid ligase

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Non-polymers , 6 types, 310 molecules

#2: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.42 Å3/Da / Density % sol: 49.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M sodium acetate pH 5.5, 0.6 M sodium formate, 14% (w/v) PEG 4000, 5 mM cobalt(II) chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→48.99 Å / Num. obs: 48937 / % possible obs: 99.9 % / Redundancy: 26.3 % / Biso Wilson estimate: 40.63 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.068 / Net I/σ(I): 11.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 25.9 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4769 / CC1/2: 0.548 / Rpim(I) all: 0.648 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
PHASERphasing
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1uc2

1uc2


Resolution: 2.3→48.99 Å / SU ML: 0.2908 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.9019
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2202 2447 5 %
Rwork0.1921 46465 -
obs0.1935 48912 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.09 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7487 0 78 297 7862
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02277702
X-RAY DIFFRACTIONf_angle_d1.676310418
X-RAY DIFFRACTIONf_chiral_restr0.24271155
X-RAY DIFFRACTIONf_plane_restr0.00961368
X-RAY DIFFRACTIONf_dihedral_angle_d19.70282810
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.350.35811390.31442653X-RAY DIFFRACTION98.9
2.35-2.40.32231420.28562688X-RAY DIFFRACTION100
2.4-2.450.27721410.28022674X-RAY DIFFRACTION100
2.45-2.520.28631410.26532678X-RAY DIFFRACTION99.86
2.52-2.580.25921420.24432699X-RAY DIFFRACTION99.96
2.58-2.660.2771420.23922697X-RAY DIFFRACTION100
2.66-2.750.24361430.22232716X-RAY DIFFRACTION100
2.75-2.840.26421420.21852696X-RAY DIFFRACTION99.89
2.84-2.960.25051420.22152707X-RAY DIFFRACTION99.93
2.96-3.090.2831430.21092704X-RAY DIFFRACTION100
3.09-3.250.20441430.18722727X-RAY DIFFRACTION99.9
3.25-3.460.18441440.17712735X-RAY DIFFRACTION99.97
3.46-3.730.20831450.16452740X-RAY DIFFRACTION100
3.73-4.10.18241450.14782754X-RAY DIFFRACTION100
4.1-4.690.16491460.13072781X-RAY DIFFRACTION99.97
4.69-5.910.16631490.16142823X-RAY DIFFRACTION100
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)
10.2698477193330.07669670184130.01652948296940.989222395995-0.3442115019250.79826112723-0.0200064535151-0.01356843132980.0459484417241-0.0904086524511-0.0526456168219-0.08027455305240.08235972833860.0513595213832-1.84529616199E-50.24927107957-0.01564684778110.01533849431980.2423750287510.01212409146370.25874539919715.458644175-40.88276530513.63914579893
20.6783449216910.2343198463640.001011539884781.080361391060.1365634386460.6350892355560.018906668184-0.01000078763650.01683409093650.0678674182823-0.057252677890.06005595779070.0374078723391-0.100738563901-1.42530725886E-100.21362285825-0.007131269656830.001621470939950.3070673114280.007298638448640.229744142441-15.9468187269-42.3510742356-24.5881648468
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 3 through 601)
2X-RAY DIFFRACTION2(chain 'B' and resid 3 through 601)

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