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- PDB-7pcv: Crystal structure of RBM5 RRM1-zinc finger -

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Basic information

Entry
Database: PDB / ID: 7pcv
TitleCrystal structure of RBM5 RRM1-zinc finger
ComponentsRNA-binding protein 5
KeywordsRNA BINDING PROTEIN / RRM domain / zinc finger domain
Function / homology
Function and homology information


spliceosomal complex assembly / regulation of alternative mRNA splicing, via spliceosome / RNA processing / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / positive regulation of apoptotic process / negative regulation of cell population proliferation / mRNA binding / apoptotic process ...spliceosomal complex assembly / regulation of alternative mRNA splicing, via spliceosome / RNA processing / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / positive regulation of apoptotic process / negative regulation of cell population proliferation / mRNA binding / apoptotic process / DNA binding / RNA binding / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
RNA-binding protein 5, RNA recognition motif 1 / RNA-binding protein 5, RNA recognition motif 2 / OCRE domain / OCRE domain / G-patch domain / G-patch domain profile. / G-patch domain / glycine rich nucleic binding domain / Zinc finger domain / Zn-finger in Ran binding protein and others ...RNA-binding protein 5, RNA recognition motif 1 / RNA-binding protein 5, RNA recognition motif 2 / OCRE domain / OCRE domain / G-patch domain / G-patch domain profile. / G-patch domain / glycine rich nucleic binding domain / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / Zinc finger C2H2 type domain profile. / Zinc finger C2H2-type / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
RNA-binding protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.42 Å
AuthorsSoni, K. / Jagtap, P.K.A. / Sattler, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Nat Commun / Year: 2023
Title: Structural basis for specific RNA recognition by the alternative splicing factor RBM5.
Authors: Soni, K. / Jagtap, P.K.A. / Martinez-Lumbreras, S. / Bonnal, S. / Geerlof, A. / Stehle, R. / Simon, B. / Valcarcel, J. / Sattler, M.
History
DepositionAug 4, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA-binding protein 5
B: RNA-binding protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0894
Polymers27,9592
Non-polymers1312
Water66737
1
A: RNA-binding protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0452
Polymers13,9791
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA-binding protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0452
Polymers13,9791
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.380, 39.880, 96.850
Angle α, β, γ (deg.)90.000, 96.030, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein RNA-binding protein 5 / Protein G15 / Putative tumor suppressor LUCA15 / RNA-binding motif protein 5 / Renal carcinoma ...Protein G15 / Putative tumor suppressor LUCA15 / RNA-binding motif protein 5 / Renal carcinoma antigen NY-REN-9


Mass: 13979.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBM5, H37, LUCA15 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P52756
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.07 Å3/Da / Density % sol: 40.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1M BICINE pH 8.5, 12% PEG 6000, 10% 1M cesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.42→33.22 Å / Num. obs: 8712 / % possible obs: 97.6 % / Redundancy: 3.067 % / Biso Wilson estimate: 52.36 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.148 / Rrim(I) all: 0.179 / Χ2: 0.872 / Net I/σ(I): 5.45 / Num. measured all: 26716
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.42-2.492.7331.1830.914626535350.2471.45881.9
2.49-2.552.9731.1431.0418616386260.3161.3998.1
2.55-2.632.9880.9351.3717966096010.4451.13998.7
2.63-2.712.9380.751.5717456015940.6030.91498.8
2.71-2.82.810.6251.8316616025910.6480.7798.2
2.8-2.92.9110.5092.1515435425300.7520.62397.8
2.9-3.013.1280.442.7217055505450.8030.53199.1
3.01-3.132.9610.3383.2415225235140.8610.41298.3
3.13-3.273.1670.2414.7216155165100.9230.29198.8
3.27-3.433.3710.1885.7615614634630.9690.223100
3.43-3.613.2950.1367.7316084914880.9770.16299.4
3.61-3.833.2410.1198.8113064054030.9790.14499.5
3.83-4.13.3280.1049.7314014254210.9880.12599.1
4.1-4.423.2650.08811.312803933920.9910.10599.7
4.42-4.853.1570.08412.2310643403370.9870.10199.1
4.85-5.422.8840.07811.289233243200.9890.09598.8
5.42-6.263.1340.08811.149152942920.9840.10699.3
6.26-7.663.1550.07212.137732462450.9880.08699.6
7.66-10.843.2950.06113.886361931930.9940.073100
10.84-33.223.0270.05114.933391171120.9990.06295.7

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.42→33.22 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 40.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3131 436 5.01 %
Rwork0.2584 8272 -
obs0.2613 8708 97.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.94 Å2 / Biso mean: 58.162 Å2 / Biso min: 23.83 Å2
Refinement stepCycle: final / Resolution: 2.42→33.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1850 0 2 37 1889
Biso mean--46.86 51.44 -
Num. residues----232
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.42-2.770.41821400.36372648278895
2.77-3.490.37451450.29632759290499
3.49-33.220.27081510.22242865301699

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