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- PDB-7csz: Crystal structure of the N-terminal tandem RRM domains of RBM45 i... -

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Basic information

Entry
Database: PDB / ID: 7csz
TitleCrystal structure of the N-terminal tandem RRM domains of RBM45 in complex with single-stranded DNA
Components
  • DNA (5'-D(*CP*GP*AP*CP*GP*GP*GP*AP*CP*GP*C)-3')
  • RNA-binding protein 45
KeywordsRNA BINDING PROTEIN/DNA / RNA-binding / RRM / ALS / FTLD / RNA BINDING PROTEIN / RNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


nervous system development / cell differentiation / ribonucleoprotein complex / RNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
RNA-binding protein 45 / RBM45, RNA recognition motif 1 / RBM45, RNA recognition motif 2 / RBM45, RNA recognition motif 3 / RBM45, RNA recognition motif 4 / 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
DNA / DNA (> 10) / RNA-binding protein 45
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChen, X. / Yang, Z. / Wang, W. / Wang, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31470719 China
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Structural basis for RNA recognition by the N-terminal tandem RRM domains of human RBM45.
Authors: Chen, X. / Yang, Z. / Wang, W. / Qian, K. / Liu, M. / Wang, J. / Wang, M.
History
DepositionAug 17, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 31, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 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

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Assembly

Deposited unit
A: RNA-binding protein 45
B: DNA (5'-D(*CP*GP*AP*CP*GP*GP*GP*AP*CP*GP*C)-3')
C: DNA (5'-D(*CP*GP*AP*CP*GP*GP*GP*AP*CP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)29,6183
Polymers29,6183
Non-polymers00
Water3,045169
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.546, 86.546, 27.374
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein RNA-binding protein 45 / Developmentally-regulated RNA-binding protein 1 / RB-1 / RNA-binding motif protein 45


Mass: 22849.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBM45, DRB1, DRBP1 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8IUH3
#2: DNA chain DNA (5'-D(*CP*GP*AP*CP*GP*GP*GP*AP*CP*GP*C)-3')


Mass: 3384.212 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / 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

CrystalDensity Matthews: 1.72 Å3/Da / Density % sol: 28.31 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.2M sodium formate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 19410 / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.036 / Rrim(I) all: 0.098 / Χ2: 0.983 / Net I/σ(I): 6.4 / Num. measured all: 141140
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.867.41.39119090.7640.5441.4960.916100
1.86-1.947.50.8919310.8710.3450.9550.937100
1.94-2.037.30.56118930.920.2230.6040.907100
2.03-2.137.10.37219300.9630.150.4010.966100
2.13-2.277.60.22819130.9830.0880.2450.978100
2.27-2.447.30.16619510.9880.0650.1791.034100
2.44-2.697.20.11919270.9920.0480.1281.027100
2.69-3.087.40.0919540.9940.0360.0971.065100
3.08-3.887.20.06619570.9960.0260.0711.064100
3.88-506.90.05820450.9970.0240.0630.93599.9

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CSX

7csx


Resolution: 1.8→21.637 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2335 1917 9.95 %
Rwork0.1851 17356 -
obs0.1899 19273 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 137.93 Å2 / Biso mean: 46.7838 Å2 / Biso min: 18.8 Å2
Refinement stepCycle: final / Resolution: 1.8→21.637 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1406 212 0 169 1787
Biso mean---50.14 -
Num. residues----185
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.8001-1.84510.37161410.33321222
1.8451-1.89490.3671540.29351194
1.8949-1.95070.32961500.25791213
1.9507-2.01360.25151200.24581234
2.0136-2.08550.32151450.22841221
2.0855-2.16890.24781310.2241235
2.1689-2.26750.29371240.19961256
2.2675-2.38690.24551400.19321204
2.3869-2.53630.26131500.19261232
2.5363-2.73170.24641270.20021266
2.7317-3.0060.29021250.20541245
3.006-3.43950.23231320.17961263
3.4395-4.32770.19261450.14681248
4.3277-21.630.17431330.15781323
Refinement TLS params.Method: refined / Origin x: 13.4578 Å / Origin y: -32.7604 Å / Origin z: 4.0807 Å
111213212223313233
T0.2172 Å2-0.0048 Å2-0.0112 Å2-0.2279 Å20.0242 Å2--0.2386 Å2
L3.3472 °2-3.5359 °20.1604 °2-5.0177 °20.0278 °2--0.3684 °2
S0.112 Å °-0.0736 Å °-0.4472 Å °-0.1927 Å °-0.0492 Å °0.4877 Å °0.1038 Å °0.0052 Å °-0.0693 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA20 - 194
2X-RAY DIFFRACTION1allB2 - 6
3X-RAY DIFFRACTION1allC6 - 10
4X-RAY DIFFRACTION1allS1 - 169

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