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- PDB-7csx: Crystal structure of the N-terminal tandem RRM domains of RBM45 -

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Basic information

Entry
Database: PDB / ID: 7csx
TitleCrystal structure of the N-terminal tandem RRM domains of RBM45
ComponentsRNA-binding protein 45
KeywordsRNA BINDING PROTEIN / RNA-binding / RRM / ALS / FTLD
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
RNA-binding protein 45
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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


Theoretical massNumber of molelcules
Total (without water)21,7501
Polymers21,7501
Non-polymers00
Water1,54986
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.485, 62.485, 52.023
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: 21749.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBM45, DRB1, DRBP1 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8IUH3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.33 Å3/Da / Density % sol: 47.32 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.2M Ammonium phosphate dibasic, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 7056 / % possible obs: 99.7 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.052 / Rrim(I) all: 0.169 / Χ2: 1.133 / Net I/σ(I): 5.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.599.20.956970.810.3311.0091.18299.3
2.59-2.6910.40.7576900.8760.2480.7981.11199
2.69-2.8211.50.6487040.8910.2050.6821.073100
2.82-2.9611.20.456940.9450.1450.4741.053100
2.96-3.1511.10.2917040.9810.0920.3061.037100
3.15-3.3911.40.1957090.9850.0620.2051.101100
3.39-3.7311.10.1276990.9920.0410.1341.17199.4
3.73-4.2711.10.0897100.9970.0290.0931.21599.9
4.27-5.38110.077140.9980.0220.0731.13599.9
5.38-5010.50.0637350.9980.0210.0671.26899.6

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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: 6JVX

6jvx


Resolution: 2.5→44.184 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2549 747 10.63 %
Rwork0.2008 6282 -
obs0.2067 7029 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.19 Å2 / Biso mean: 37.9601 Å2 / Biso min: 23.79 Å2
Refinement stepCycle: final / Resolution: 2.5→44.184 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1366 0 0 86 1452
Biso mean---37.29 -
Num. residues----169
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5-2.69160.31831480.2554124099
2.6916-2.96250.2991570.26451242100
2.9625-3.3910.27041330.21971274100
3.391-4.27180.26291290.17651277100
4.2718-44.180.20871800.1715124999

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