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- PDB-5en1: Crystal structure of hnRNPA2B1 in complex with RNA -

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Basic information

Entry
Database: PDB / ID: 5en1
TitleCrystal structure of hnRNPA2B1 in complex with RNA
Components
  • Heterogeneous nuclear ribonucleoproteins A2/B1
  • RNA (5'-R(*AP*GP*GP*AP*CP*UP*G)-3')
KeywordsRNA BINDING PROTEIN/RNA / HNRNP / RRM / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


positive regulation of telomerase RNA reverse transcriptase activity / miRNA transport / positive regulation of telomere maintenance via telomere lengthening / RNA transport / G-quadruplex DNA unwinding / primary miRNA processing / single-stranded telomeric DNA binding / N6-methyladenosine-containing RNA reader activity / G-rich strand telomeric DNA binding / miRNA binding ...positive regulation of telomerase RNA reverse transcriptase activity / miRNA transport / positive regulation of telomere maintenance via telomere lengthening / RNA transport / G-quadruplex DNA unwinding / primary miRNA processing / single-stranded telomeric DNA binding / N6-methyladenosine-containing RNA reader activity / G-rich strand telomeric DNA binding / miRNA binding / negative regulation of mRNA splicing, via spliceosome / Processing of Capped Intron-Containing Pre-mRNA / mRNA transport / Cajal body / mRNA export from nucleus / pre-mRNA intronic binding / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / catalytic step 2 spliceosome / molecular condensate scaffold activity / mRNA Splicing - Major Pathway / mRNA 3'-UTR binding / spliceosomal complex / mRNA processing / mRNA splicing, via spliceosome / nuclear matrix / chromosome, telomeric region / ribonucleoprotein complex / negative regulation of transcription by RNA polymerase II / RNA binding / extracellular exosome / nucleoplasm / membrane / identical protein binding / nucleus / cytoplasm
Similarity search - Function
hnRNP A2/B1, RNA recognition motif 1 / Heterogeneous nuclear ribonucleoprotein A1/A2, C-terminal / Heterogeneous nuclear ribonucleoprotein A1, LC domain / RRM (RNA recognition motif) domain / 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 ...hnRNP A2/B1, RNA recognition motif 1 / Heterogeneous nuclear ribonucleoprotein A1/A2, C-terminal / Heterogeneous nuclear ribonucleoprotein A1, LC domain / RRM (RNA recognition motif) domain / 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 / Heterogeneous nuclear ribonucleoproteins A2/B1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsWu, B.X. / Su, S.C. / Ma, J.B.
CitationJournal: Nat Commun / Year: 2018
Title: Molecular basis for the specific and multivariant recognitions of RNA substrates by human hnRNP A2/B1
Authors: Wu, B.X. / Su, S.C. / Patil, D.P. / Liu, H.H. / Gan, J.H. / Jaffrey, S.R. / Ma, J.B.
History
DepositionNov 9, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2018Group: Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 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

Downloads & links

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Assembly

Deposited unit
A: Heterogeneous nuclear ribonucleoproteins A2/B1
B: RNA (5'-R(*AP*GP*GP*AP*CP*UP*G)-3')


Theoretical massNumber of molelcules
Total (without water)23,4672
Polymers23,4672
Non-polymers00
Water19811
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-2 kcal/mol
Surface area12210 Å2
Unit cell
Length a, b, c (Å)122.623, 46.380, 37.516
Angle α, β, γ (deg.)90.00, 96.02, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Heterogeneous nuclear ribonucleoproteins A2/B1 / hnRNP A2/B1


Mass: 21206.969 Da / Num. of mol.: 1 / Fragment: UNP residues 12-195
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HNRNPA2B1, HNRPA2B1 / Production host: Escherichia coli (E. coli) / References: UniProt: P22626
#2: RNA chain RNA (5'-R(*AP*GP*GP*AP*CP*UP*G)-3')


Mass: 2260.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 25% PEG3350, 0.1M Tris pH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å
DetectorType: RIGAKU / Detector: CCD / Date: Oct 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.58→28.81 Å / Num. obs: 6187 / % possible obs: 91.89 % / Redundancy: 2.5 % / Net I/σ(I): 7.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
DENZOdata reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U1Q

1u1q


Resolution: 2.58→28.81 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.925 / SU B: 14.648 / SU ML: 0.298 / Cross valid method: THROUGHOUT / ESU R Free: 0.338 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23624 299 4.8 %RANDOM
Rwork0.19162 ---
obs0.19387 5889 91.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.201 Å2
Baniso -1Baniso -2Baniso -3
1-1.6 Å20 Å2-1.09 Å2
2--1.28 Å20 Å2
3----2.59 Å2
Refinement stepCycle: 1 / Resolution: 2.58→28.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1491 150 0 11 1652
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0181688
X-RAY DIFFRACTIONr_bond_other_d0.0020.021522
X-RAY DIFFRACTIONr_angle_refined_deg1.6151.8642295
X-RAY DIFFRACTIONr_angle_other_deg1.41733512
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4895183
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.1832380
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.34715286
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2271516
X-RAY DIFFRACTIONr_chiral_restr0.0950.2238
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021799
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02406
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7714.157735
X-RAY DIFFRACTIONr_mcbond_other2.7544.154734
X-RAY DIFFRACTIONr_mcangle_it4.4756.219917
X-RAY DIFFRACTIONr_mcangle_other4.4766.225918
X-RAY DIFFRACTIONr_scbond_it3.2024.835953
X-RAY DIFFRACTIONr_scbond_other3.1854.826952
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3687.131379
X-RAY DIFFRACTIONr_long_range_B_refined7.09935.2441838
X-RAY DIFFRACTIONr_long_range_B_other7.135.2931839
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.581→2.648 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 18 -
Rwork0.293 300 -
obs--64.9 %

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