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- PDB-5ho4: Crystal structure of hnRNPA2B1 in complex with 10-mer RNA -

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Basic information

Entry
Database: PDB / ID: 5ho4
TitleCrystal structure of hnRNPA2B1 in complex with 10-mer RNA
Components
  • Heterogeneous nuclear ribonucleoproteins A2/B1
  • RNA (5'-R(*AP*AP*GP*GP*AP*CP*UP*AP*GP*C)-3')
KeywordsRNA BINDING PROTEIN/RNA / hnRNPA2B1 / RRMs / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


miRNA transport / RNA transport / positive regulation of telomere maintenance via telomere lengthening / DNA geometric change / primary miRNA processing / N6-methyladenosine-containing RNA reader activity / single-stranded telomeric DNA binding / G-rich strand telomeric DNA binding / miRNA binding / Processing of Capped Intron-Containing Pre-mRNA ...miRNA transport / RNA transport / positive regulation of telomere maintenance via telomere lengthening / DNA geometric change / primary miRNA processing / N6-methyladenosine-containing RNA reader activity / single-stranded telomeric DNA binding / G-rich strand telomeric DNA binding / miRNA binding / Processing of Capped Intron-Containing Pre-mRNA / mRNA transport / mRNA export from nucleus / Cajal body / DNA polymerase binding / catalytic step 2 spliceosome / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / mRNA Splicing - Major Pathway / mRNA 3'-UTR binding / spliceosomal complex / molecular condensate scaffold activity / mRNA splicing, via spliceosome / nuclear matrix / mRNA processing / chromosome, telomeric region / ribonucleoprotein complex / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / membrane / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.85 Å
AuthorsWu, B.X. / Su, S.C. / Gan, J.H. / 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. / Gan, J.H. / Jaffrey, S.R. / Ma, J.B.
History
DepositionJan 19, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Structure summary
Revision 1.2Feb 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3May 22, 2019Group: Data collection / Database references / Structure summary
Category: citation / citation_author / struct
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _struct.title
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
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Assembly

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


Theoretical massNumber of molelcules
Total (without water)23,7582
Polymers23,7582
Non-polymers00
Water2,378132
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint1 kcal/mol
Surface area11710 Å2
Unit cell
Length a, b, c (Å)109.604, 38.959, 70.442
Angle α, β, γ (deg.)90.00, 116.26, 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: 20534.172 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 15-193 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P22626
#2: RNA chain RNA (5'-R(*AP*AP*GP*GP*AP*CP*UP*AP*GP*C)-3')


Mass: 3224.012 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.84 Å3/Da / Density % sol: 56.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M Tri-Sodium citrate, 20% (w/v) polyethylene glycol 3,350

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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: Dec 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.85→63.17 Å / Num. obs: 21311 / % possible obs: 92.43 % / Redundancy: 2.9 % / Net I/σ(I): 18.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-3000data processing
d*TREKdata reduction
PHASERphasing
RefinementResolution: 1.85→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.117 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.127 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22005 1103 5.2 %RANDOM
Rwork0.18294 ---
obs0.18493 20208 92.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.571 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å2-0.06 Å2
2---0.22 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1444 193 0 132 1769
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0181716
X-RAY DIFFRACTIONr_bond_other_d0.0020.021517
X-RAY DIFFRACTIONr_angle_refined_deg1.9611.8472345
X-RAY DIFFRACTIONr_angle_other_deg1.49133507
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.265183
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.69622.82178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.07315281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4221516
X-RAY DIFFRACTIONr_chiral_restr0.1360.2242
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021797
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02409
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_it2.1892.001727
X-RAY DIFFRACTIONr_mcbond_other2.1761.997726
X-RAY DIFFRACTIONr_mcangle_it3.2382.98910
X-RAY DIFFRACTIONr_mcangle_other3.242.985911
X-RAY DIFFRACTIONr_scbond_it3.1512.55989
X-RAY DIFFRACTIONr_scbond_other3.1512.55989
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9023.691435
X-RAY DIFFRACTIONr_long_range_B_refined7.27918.7692055
X-RAY DIFFRACTIONr_long_range_B_other7.10818.3692004
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.851→1.899 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 40 -
Rwork0.247 845 -
obs--52.12 %

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