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- PDB-7dh6: Crystal structure of PLRG1 -

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Basic information

Entry
Database: PDB / ID: 7dh6
TitleCrystal structure of PLRG1
ComponentsPleiotropic regulator 1
KeywordsSPLICING / PLRG1 offers an interesting link between the control of pre-mRNA splicing and DNA metabolism.
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 / 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
Similarity search - Domain/homology
NICKEL (II) ION / Pleiotropic regulator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.584 Å
AuthorsWang, X. / Xu, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Crystal structure of the WD40 domain of human PLRG1.
Authors: Wang, X. / Li, Y. / Dai, H. / Xu, C.
History
DepositionNov 13, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pleiotropic regulator 1
B: Pleiotropic regulator 1
C: Pleiotropic regulator 1
D: Pleiotropic regulator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,65910
Polymers167,3254
Non-polymers3346
Water2,396133
1
A: Pleiotropic regulator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9863
Polymers41,8311
Non-polymers1552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11190 Å2
MethodPISA
2
B: Pleiotropic regulator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8712
Polymers41,8311
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-11 kcal/mol
Surface area11970 Å2
MethodPISA
3
C: Pleiotropic regulator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9303
Polymers41,8311
Non-polymers992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11580 Å2
MethodPISA
4
D: Pleiotropic regulator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8712
Polymers41,8311
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.005, 82.124, 99.388
Angle α, β, γ (deg.)90.000, 99.440, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Pleiotropic regulator 1


Mass: 41831.340 Da / Num. of mol.: 4 / Fragment: UNP residues 140-514
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLRG1
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: O43660
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.64 Å3/Da / Density % sol: 24.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2 Calcium chloride 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.58→50 Å / Num. obs: 33636 / % possible obs: 99.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 8.9
Reflection shellResolution: 2.58→2.65 Å / Rmerge(I) obs: 0.804 / Num. unique obs: 3125

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YVD

4yvd


Resolution: 2.584→38.156 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 29.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.276 1702 5.07 %
Rwork0.2262 31868 -
obs0.2287 33570 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.16 Å2 / Biso mean: 47.5529 Å2 / Biso min: 5.74 Å2
Refinement stepCycle: final / Resolution: 2.584→38.156 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8893 0 10 133 9036
Biso mean--61.37 34.98 -
Num. residues----1160
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.584-2.660.35571340.3157244792
2.66-2.74580.39771480.3075266199
2.7458-2.84390.35961470.29262649100
2.8439-2.95780.34321460.27162670100
2.9578-3.09230.3041310.25332668100
3.0923-3.25530.29041520.23642667100
3.2553-3.45910.26131500.2116264899
3.4591-3.7260.25551270.20362701100
3.726-4.10050.2451420.196267799
4.1005-4.6930.20631360.178265899
4.693-5.90910.2471370.2047271699
5.9091-38.10.28251520.2411270698
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)
12.95030.2928-2.4371.05080.24214.04130.3547-0.53770.5037-0.14250.03880.017-0.62741.1864-0.21570.2878-0.1120.10770.6174-0.11210.403926.754514.424236.7031
22.2010.37480.05420.970.26932.26010.0529-0.2729-0.1955-0.20830.15820.2033-0.3495-0.6982-0.16920.25680.1475-0.01010.44950.16420.406232.754-25.9412.5508
31.3313-0.1562-0.11150.86250.57453.38130.0544-0.04250.0364-0.0272-0.06220.07-0.17470.44180.01440.3031-0.0410.01030.19260.0040.2648-1.627-27.874112.0512
42.31410.3172-0.92641.22850.85743.9150.11930.43310.2456-0.0473-0.01240.1288-0.372-0.7237-0.02950.36650.13810.03070.34180.04810.263-6.734412.556337.0706
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 189 through 492)A189 - 492
2X-RAY DIFFRACTION2(chain 'B' and resid 190 through 491)B190 - 491
3X-RAY DIFFRACTION3(chain 'C' and resid 189 through 492)C189 - 492
4X-RAY DIFFRACTION4(chain 'D' and resid 189 through 492)D189 - 492

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