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- PDB-9ejy: Human hnRNPR extended eRRM1 domain -

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Basic information

Entry
Database: PDB / ID: 9ejy
TitleHuman hnRNPR extended eRRM1 domain
ComponentsHeterogeneous nuclear ribonucleoprotein R
KeywordsRNA BINDING PROTEIN / RRM / extended RRM / RNA binding
Function / homology
Function and homology information


Processing of Capped Intron-Containing Pre-mRNA / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / mRNA processing / ribonucleoprotein complex / mRNA binding / endoplasmic reticulum / RNA binding ...Processing of Capped Intron-Containing Pre-mRNA / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / mRNA processing / ribonucleoprotein complex / mRNA binding / endoplasmic reticulum / RNA binding / nucleoplasm / nucleus
Similarity search - Function
: / Heterogeneous nuclear ribonucleoprotein R, RNA recognition motif 2 / Heterogeneous nuclear ribonucleoprotein Q acidic domain / Heterogeneous nuclear ribonucleoprotein Q acidic domain / HnRNP R/Q splicing factor / 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
Heterogeneous nuclear ribonucleoprotein R
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsEichhorn, C.D. / Atsrim, E.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM143030 United States
CitationJournal: Protein Sci. / Year: 2025
Title: An evolutionarily conserved tryptophan cage promotes folding of the extended RNA recognition motif in the hnRNPR-like protein family.
Authors: Atsrim, E.S. / Eichhorn, C.D.
History
DepositionNov 29, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heterogeneous nuclear ribonucleoprotein R


Theoretical massNumber of molelcules
Total (without water)15,8261
Polymers15,8261
Non-polymers00
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.023, 77.023, 52.893
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein Heterogeneous nuclear ribonucleoprotein R / hnRNP R


Mass: 15825.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HNRNPR, HNRPR / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): NiCo21(DE3) / References: UniProt: O43390
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.86 Å3/Da / Density % sol: 57.02 %
Description: rod-like morphology. Crystals grew to 300-500 um within 48 hours.
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.04 M potassium phosphate, monobasic; 20% v/v glycerol; 8% w/v PEG 8,000; 1:1 drop ratio; 16 mg/mL protein

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.72929 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 21, 2024
Details: Mirror: Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M2 Monochromator: Liquid nitrogen-cooled double crystal Si(111)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.72929 Å / Relative weight: 1
ReflectionResolution: 1.9→31.13 Å / Num. obs: 14604 / % possible obs: 100 % / Redundancy: 20.9 % / Biso Wilson estimate: 49.62 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.011 / Rrim(I) all: 0.035 / Net I/σ(I): 40.7
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 21 % / Rmerge(I) obs: 2.174 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1445 / CC1/2: 0.626 / Rpim(I) all: 0.686 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
Aimlessdata scaling
PHENIX1.21.2-5419phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→31.13 Å / SU ML: 0.2186 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.0266
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2218 1456 9.98 %
Rwork0.1942 13126 -
obs0.197 14582 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.51 Å2
Refinement stepCycle: LAST / Resolution: 1.9→31.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms972 0 0 65 1037
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007994
X-RAY DIFFRACTIONf_angle_d0.95291347
X-RAY DIFFRACTIONf_chiral_restr0.058145
X-RAY DIFFRACTIONf_plane_restr0.0078178
X-RAY DIFFRACTIONf_dihedral_angle_d13.7755375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.970.32341460.30051299X-RAY DIFFRACTION99.86
1.97-2.050.28261380.24991298X-RAY DIFFRACTION100
2.05-2.140.28521410.25941288X-RAY DIFFRACTION100
2.14-2.250.21961450.23061304X-RAY DIFFRACTION100
2.25-2.390.27751410.21181311X-RAY DIFFRACTION100
2.39-2.580.24921460.24181287X-RAY DIFFRACTION100
2.58-2.840.25891420.25211324X-RAY DIFFRACTION100
2.84-3.250.25291480.23151295X-RAY DIFFRACTION100
3.25-4.090.23081500.18531340X-RAY DIFFRACTION100
4.09-31.130.18041590.15371380X-RAY DIFFRACTION99.94
Refinement TLS params.Method: refined / Origin x: 2.78772646449 Å / Origin y: 29.6517193405 Å / Origin z: 19.0315361078 Å
111213212223313233
T0.436641393638 Å20.037066663382 Å2-0.0247263453338 Å2-0.419331283667 Å2-0.0210090318895 Å2--0.448015359033 Å2
L6.02791692761 °2-1.17689505789 °22.4113734819 °2-5.51421688507 °2-1.49515505488 °2--4.41100948737 °2
S0.310317887728 Å °-0.0119575161887 Å °-0.469948827664 Å °-0.311755667892 Å °-0.00278084181463 Å °0.412374644106 Å °0.360128107863 Å °-0.174139211841 Å °-0.270088279783 Å °
Refinement TLS groupSelection details: all

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