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

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Basic information

Entry
Database: PDB / ID: 5wwf
TitleCrystal structure of hnRNPA2B1 in complex with RNA
Components
  • Heterogeneous nuclear ribonucleoproteins A2/B1
  • RNA
KeywordsRNA BINDING PROTEIN/RNA / HNRNP / RRM / 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 / mRNA Splicing - Major Pathway / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / 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 / MOLECULAR REPLACEMENT / Resolution: 2.15 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. / Su, S. / Patil, D.P. / Liu, H. / Gan, J. / Jaffrey, S.R. / Ma, J.
History
DepositionJan 1, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 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 1.2Feb 14, 2018Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Nov 22, 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
C: Heterogeneous nuclear ribonucleoproteins A2/B1
D: RNA


Theoretical massNumber of molelcules
Total (without water)48,9404
Polymers48,9404
Non-polymers00
Water1,08160
1
A: Heterogeneous nuclear ribonucleoproteins A2/B1
B: RNA


Theoretical massNumber of molelcules
Total (without water)24,4702
Polymers24,4702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Heterogeneous nuclear ribonucleoproteins A2/B1
D: RNA


Theoretical massNumber of molelcules
Total (without water)24,4702
Polymers24,4702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.351, 38.301, 107.931
Angle α, β, γ (deg.)90.00, 92.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 21206.969 Da / Num. of mol.: 2 / Fragment: RRMs (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


Mass: 3263.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.13 Å3/Da / Density % sol: 42.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M Lithium sulfate monohydrate, 0.1 M BIS-TRIS pH 6.5, 25% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97776 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. obs: 21583 / % possible obs: 96.8 % / Redundancy: 4.7 % / Net I/σ(I): 2.25
Reflection shellResolution: 2.15→2.23 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
DENZOdata reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EN1

5en1


Resolution: 2.15→30 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.89 / SU B: 7.455 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 0.34 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25772 1081 5.2 %RANDOM
Rwork0.20255 ---
obs0.20549 19662 92.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.476 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å2-0.52 Å2
2---0.49 Å20 Å2
3---0.2 Å2
Refinement stepCycle: 1 / Resolution: 2.15→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2849 426 0 60 3335
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0183457
X-RAY DIFFRACTIONr_bond_other_d0.0020.023023
X-RAY DIFFRACTIONr_angle_refined_deg1.7571.8294740
X-RAY DIFFRACTIONr_angle_other_deg1.13936988
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0085364
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.91722.987154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.08615552
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4021530
X-RAY DIFFRACTIONr_chiral_restr0.1150.2491
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023626
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02840
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_it2.2572.771443
X-RAY DIFFRACTIONr_mcbond_other2.2452.7681442
X-RAY DIFFRACTIONr_mcangle_it3.5944.1361808
X-RAY DIFFRACTIONr_mcangle_other3.5954.1391809
X-RAY DIFFRACTIONr_scbond_it2.483.0682014
X-RAY DIFFRACTIONr_scbond_other2.4793.0692013
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9944.4922930
X-RAY DIFFRACTIONr_long_range_B_refined6.04522.7023926
X-RAY DIFFRACTIONr_long_range_B_other6.03822.7053924
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.151→2.207 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 55 -
Rwork0.285 985 -
obs--65 %

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