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- PDB-4yvd: Crytsal structure of human Pleiotropic Regulator 1 (PRL1) -

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Basic information

Entry
Database: PDB / ID: 4yvd
TitleCrytsal structure of human Pleiotropic Regulator 1 (PRL1)
ComponentsPleiotropic regulator 1
KeywordsRNA BINDING PROTEIN / WD40 repeat / mRNA processing / mRNA splicing / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


Prp19 complex / U2-type catalytic step 2 spliceosome / protein localization to nucleus / positive regulation of G1/S transition of mitotic cell cycle / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / fibrillar center / nuclear membrane ...Prp19 complex / U2-type catalytic step 2 spliceosome / protein localization to nucleus / positive regulation of G1/S transition of mitotic cell cycle / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / fibrillar center / nuclear membrane / nuclear speck / nucleoplasm / nucleus
Similarity search - Function
WD repeat Prp46/PLRG1-like / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat ...WD repeat Prp46/PLRG1-like / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Pleiotropic regulator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsDong, A. / Zeng, H. / Xu, C. / Tempel, W. / Li, Y. / He, H. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. ...Dong, A. / Zeng, H. / Xu, C. / Tempel, W. / Li, Y. / He, H. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Min, J. / Wu, H. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crytsal structure of human Pleiotropic Regulator 1 (PRL1).
Authors: Zeng, H. / Dong, A. / Xu, C. / Tempel, W. / Li, Y. / He, H. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Min, J. / Wu, H. / Structural Genomics Consortium (SGC)
History
DepositionMar 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pleiotropic regulator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,87419
Polymers41,6741
Non-polymers20018
Water2,630146
1
A: Pleiotropic regulator 1
hetero molecules

A: Pleiotropic regulator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,74938
Polymers83,3482
Non-polymers40136
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area2820 Å2
ΔGint-127 kcal/mol
Surface area22080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.330, 34.185, 48.818
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-611-

UNX

DetailsAUTHORS STATE THAT THE BIOLOGICAL ASSEMBLY IS UNKNOWN.

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Components

#1: Protein Pleiotropic regulator 1


Mass: 41674.148 Da / Num. of mol.: 1 / Fragment: UNP residues 141-514
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLRG1 / Plasmid: pFBOH-MHL
Production host: Insect cell expression vector pTIE1 (others)
Strain (production host): Sf9 / References: UniProt: O43660
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 12 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2 M CaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97957 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jan 29, 2015
RadiationMonochromator: CCEL/BRUKER double crystal monochromator (DCM)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 29598 / % possible obs: 97.1 % / Redundancy: 7.8 % / Biso Wilson estimate: 22.93 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 11.7
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.874 / Mean I/σ(I) obs: 2.2 / % possible all: 81.5

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2GNQ

2gnq


Resolution: 1.7→41.55 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.935 / SU R Cruickshank DPI: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.117 / SU Rfree Blow DPI: 0.111 / SU Rfree Cruickshank DPI: 0.109
RfactorNum. reflection% reflectionSelection details
Rfree0.22 908 3.07 %RANDOM
Rwork0.187 ---
obs0.188 29532 96.3 %-
Displacement parametersBiso mean: 35.34 Å2
Baniso -1Baniso -2Baniso -3
1-5.6936 Å20 Å20 Å2
2--2.931 Å20 Å2
3----8.6247 Å2
Refine analyzeLuzzati coordinate error obs: 0.291 Å
Refinement stepCycle: LAST / Resolution: 1.7→41.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2286 0 6 146 2438
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082412HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.073300HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d808SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes43HARMONIC2
X-RAY DIFFRACTIONt_gen_planes367HARMONIC5
X-RAY DIFFRACTIONt_it2412HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.64
X-RAY DIFFRACTIONt_other_torsion17.35
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion325SEMIHARMONIC5
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_contact2820SEMIHARMONIC4
LS refinement shellResolution: 1.7→1.75 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2193 58 2.52 %
Rwork0.2349 2243 -
all0.2345 2301 -
obs--96.32 %
Refinement TLS params.Method: refined / Origin x: 22.8843 Å / Origin y: 7.0762 Å / Origin z: 14.0994 Å
111213212223313233
T-0.1361 Å20.056 Å2-0.0025 Å2--0.076 Å2-0.0254 Å2---0.0677 Å2
L4.3082 °2-1.7831 °2-1.0435 °2-1.4128 °20.3263 °2--0.7447 °2
S0.3285 Å °0.7256 Å °-0.0516 Å °-0.1398 Å °-0.3131 Å °0.0851 Å °-0.1309 Å °-0.2393 Å °-0.0154 Å °
Refinement TLS groupSelection details: { A|190 - A|492 }

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