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- PDB-5zsy: RBM10-RRM2 domain and its lung cancer related mutant -

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Basic information

Entry
Database: PDB / ID: 5zsy
TitleRBM10-RRM2 domain and its lung cancer related mutant
ComponentsRNA-binding protein 10
KeywordsRNA BINDING PROTEIN / classical folding and binding mode
Function / homology
Function and homology information


vascular associated smooth muscle cell apoptotic process / vascular associated smooth muscle cell proliferation / miRNA binding / 3'-UTR-mediated mRNA stabilization / positive regulation of vascular associated smooth muscle cell apoptotic process / negative regulation of vascular associated smooth muscle cell proliferation / negative regulation of mRNA splicing, via spliceosome / Processing of Capped Intron-Containing Pre-mRNA / mRNA Splicing - Major Pathway / mRNA splicing, via spliceosome ...vascular associated smooth muscle cell apoptotic process / vascular associated smooth muscle cell proliferation / miRNA binding / 3'-UTR-mediated mRNA stabilization / positive regulation of vascular associated smooth muscle cell apoptotic process / negative regulation of vascular associated smooth muscle cell proliferation / negative regulation of mRNA splicing, via spliceosome / Processing of Capped Intron-Containing Pre-mRNA / mRNA Splicing - Major Pathway / mRNA splicing, via spliceosome / nuclear speck / negative regulation of transcription by RNA polymerase II / protein-containing complex / RNA binding / nucleoplasm / identical protein binding / metal ion binding / nucleus
Similarity search - Function
RNA-binding protein 10, RNA recognition motif 2 / RBM10, OCRE domain / 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 10, RNA recognition motif 2 / RBM10, OCRE domain / 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 / RRM (RNA recognition motif) domain / 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 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA-binding protein 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsQin, H.
CitationJournal: To be published
Title: Structural, dynamics, and RNA binding comparison between RBM10-RRM2 domain and its lung cancer related mutation.
Authors: Qin, H.
History
DepositionApr 30, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA-binding protein 10


Theoretical massNumber of molelcules
Total (without water)9,5771
Polymers9,5771
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5850 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 40structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein RNA-binding protein 10 / G patch domain-containing protein 9 / RNA-binding motif protein 10 / RNA-binding protein S1-1 / S1-1


Mass: 9577.053 Da / Num. of mol.: 1 / Fragment: RBM10 RRM2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBM10, DXS8237E, GPATC9, GPATCH9, KIAA0122 / Production host: Escherichia coli (E. coli) / References: UniProt: P98175
Sequence detailsSequence of the protein is based on isoform 4 of database P98175 (RBM10_HUMAN).

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic14D APSY-HACANH
121isotropic15D APSY-CBCA(CO)NH
131isotropic15D APSY-(HA)CA(CO)NH
141isotropic23D 1H-15N NOESY
151isotropic23D 1H-13C NOESY aliphatic
161isotropic23D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution
Contents: 1.0 mM [U-100% 13C; U-100% 15N] RBM10 RRM2[V354del], 90% H2O/10% D2O
Label: 15N_13C_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 1.0 mM / Component: RBM10 RRM2[V354del] / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsDetails: 20mM sodium Phosphate, 50mM sodium chloride
Ionic strength: 20mM sodium Phosphate, 50mM sodium chloride mM
Label: condition_1 / pH: 6.5 / Pressure: 1 Pa / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
UNIO-ASCANVolk, J.; Herrmann, T.; Fiorito, F.; Wuthrich, K.chemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
OPALLuginbuhl, Guntert, Billeter and Wuthrichrefinement
RefinementMethod: molecular dynamics / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 20

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