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- PDB-3iab: Crystal structure of RNase P /RNase MRP proteins Pop6, Pop7 in a ... -

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Basic information

Entry
Database: PDB / ID: 3iab
TitleCrystal structure of RNase P /RNase MRP proteins Pop6, Pop7 in a complex with the P3 domain of RNase MRP RNA
Components
  • P3 domain of the RNA component of RNase MRP
  • Ribonucleases P/MRP protein subunit POP6
  • Ribonucleases P/MRP protein subunit POP7
KeywordsHYDROLASE/RNA / RNase P / RNase MRP / Ribonuclease P / Ribonuclease MRP / Pop6 / Pop6p / Pop7 / Pop7p / P3 / NME1 / yeast / tRNA / pre-tRNA / rRNA / Ribozyme / PROTEIN-RNA COMPLEX / ALBA / heterodimer / Coiled coil / Hydrolase / Nucleus / rRNA processing / tRNA processing / Phosphoprotein / HYDROLASE-RNA COMPLEX
Function / homology
Function and homology information


nuclear-transcribed mRNA catabolic process, RNase MRP-dependent / intronic box C/D snoRNA processing / nucleolar ribonuclease P complex / ribonuclease MRP complex / ribonuclease P / rRNA primary transcript binding / ribonuclease P activity / tRNA 5'-leader removal / telomerase holoenzyme complex / tRNA processing ...nuclear-transcribed mRNA catabolic process, RNase MRP-dependent / intronic box C/D snoRNA processing / nucleolar ribonuclease P complex / ribonuclease MRP complex / ribonuclease P / rRNA primary transcript binding / ribonuclease P activity / tRNA 5'-leader removal / telomerase holoenzyme complex / tRNA processing / maturation of 5.8S rRNA / rRNA processing / RNA binding / nucleus / cytosol
Similarity search - Function
Ribonuclease P/MRP subunit Pop7, fungi / Ribonucleases P/MRP protein subunit Rpp20/Pop7 / Rpp20 subunit of nuclear RNase MRP and P / Alba-like domain / DNA/RNA-binding protein Alba-like / Alba / Alba-like domain superfamily / Translation Initiation Factor IF3 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Ribonucleases P/MRP protein subunit POP7 / Ribonucleases P/MRP protein subunit POP6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsPerederina, A. / Esakova, O.A. / Quan, C. / Khanova, E. / Krasilnikov, A.S.
CitationJournal: Embo J. / Year: 2010
Title: Eukaryotic ribonucleases P/MRP: the crystal structure of the P3 domain
Authors: Perederina, A. / Esakova, O. / Quan, C. / Khanova, E. / Krasilnikov, A.S.
History
DepositionJul 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonucleases P/MRP protein subunit POP6
B: Ribonucleases P/MRP protein subunit POP7
R: P3 domain of the RNA component of RNase MRP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4516
Polymers49,2543
Non-polymers1963
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7190 Å2
ΔGint-107 kcal/mol
Surface area19030 Å2
MethodPISA
2
A: Ribonucleases P/MRP protein subunit POP6
B: Ribonucleases P/MRP protein subunit POP7
R: P3 domain of the RNA component of RNase MRP
hetero molecules

A: Ribonucleases P/MRP protein subunit POP6
B: Ribonucleases P/MRP protein subunit POP7
R: P3 domain of the RNA component of RNase MRP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,90112
Polymers98,5096
Non-polymers3926
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+3/21
Buried area17150 Å2
ΔGint-283 kcal/mol
Surface area35380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.514, 126.514, 76.766
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number93
Space group name H-MP4222
Components on special symmetry positions
IDModelComponents
11B-141-

ZN

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Components

#1: Protein Ribonucleases P/MRP protein subunit POP6 / RNA-processing protein POP6 / RNases P/MRP 18.2 kDa subunit


Mass: 18440.576 Da / Num. of mol.: 1 / Fragment: Pop6 / Mutation: L141M
Source method: isolated from a genetically manipulated source
Details: Co-expression with Pop7
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: POP6, YGR030C / Plasmid: 762 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 / References: UniProt: P53218, ribonuclease P
#2: Protein Ribonucleases P/MRP protein subunit POP7 / RNA-processing protein POP7 / RNases P/MRP 15.8 kDa subunit


Mass: 15984.972 Da / Num. of mol.: 1 / Fragment: Pop7 / Mutation: none
Source method: isolated from a genetically manipulated source
Details: Co-expression with Pop6
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: POP7, RPP2, YBR1219, YBR167C / Plasmid: 762 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 / References: UniProt: P38291, ribonuclease P
#3: RNA chain P3 domain of the RNA component of RNase MRP


Mass: 14828.875 Da / Num. of mol.: 1 / Fragment: P3 domain
Mutation: circular permutation; A49C, A50C, U59G, U60G (yeast sequence numbering). See important note regarging nucleotide numbering in the model.
Source method: obtained synthetically
Details: In vitro transcription; circular permutation of naturally occurring sequence.
References: ribonuclease P
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE MODEL INCLUDES NUCLEOTIDES 29-50 AND 59-79 OF THE ORIGINAL YEAST P3 DOMAIN. THE CRYSTALLIZED ...THE MODEL INCLUDES NUCLEOTIDES 29-50 AND 59-79 OF THE ORIGINAL YEAST P3 DOMAIN. THE CRYSTALLIZED CONSTRUCT CONTAINS A GAAA LINKER CONNECTING G78 AND C29 (YEAST NUMBERING). IN THE MODEL, THE NUMBERING OF NUCLEOTIDES 59 TO 78 MATCHES THAT IN YEAST; THE MODEL NUCLEOTIDES 79-82 ARE THE LINKER; THE NUMBERING OF NUCLEOTIDES 83-104 IS SHIFTED RELATIVE TO THAT IN YEAST BY 54 (YEAST NUCLEOTIDE 29 IS CALLED 83 IN THE MODEL, ETC).

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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: 3.12 Å3/Da / Density % sol: 60.55 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 2M Ammonium Sulfate, 200 mM Potassium Chloride, 2% PEG 400, 5% D-trehalose, 2 mM Zinc Chloride, 5 mM Magnesium Chloride, 100 mM HEPES-Na, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 28, 2009 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 17601 / Num. obs: 16350 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 82.1 Å2 / Rmerge(I) obs: 0.057
Reflection shellResolution: 2.7→2.76 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 2 / Num. unique all: 934 / % possible all: 93.3

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Processing

Software
NameClassification
HKL-2000data collection
SHARPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD
Starting model: none

Resolution: 2.7→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Residues 1-3, 122-128 in Pop6 (chain A) and residues 1-13, 105-124 in Pop7 (chain B) are disordered
RfactorNum. reflection% reflectionSelection details
Rfree0.265 821 -RANDOM
Rwork0.25 ---
all0.25 17659 --
obs0.25 16346 92.6 %-
Displacement parametersBiso mean: 89.9 Å2
Baniso -1Baniso -2Baniso -3
1--10.219 Å20 Å20 Å2
2---10.219 Å20 Å2
3---20.437 Å2
Refine analyzeLuzzati coordinate error obs: 0.68 Å
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 985 3 50 3087
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.054
X-RAY DIFFRACTIONc_angle_deg1.14
LS refinement shellResolution: 2.7→2.774 Å
RfactorNum. reflection% reflection
Rfree0.333 44 -
Rwork0.355 --
obs-970 92.7 %

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