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- PDB-8x0n: The molecular mechanism of hnRNPA1 recognize TERRA RNA. -

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Basic information

Entry
Database: PDB / ID: 8x0n
TitleThe molecular mechanism of hnRNPA1 recognize TERRA RNA.
Components
  • Heterogeneous nuclear ribonucleoprotein A1
  • RNA (5'-R(*UP*UP*AP*GP*GP*GP*UP*UP*AP*GP*GP*G)-3')
KeywordsRNA BINDING PROTEIN/RNA / hnRNPA1 / UP1 / TERRA / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


cellular response to sodium arsenite / SARS-CoV-1-host interactions / import into nucleus / telomeric repeat-containing RNA binding / G-rich strand telomeric DNA binding / pre-mRNA binding / nuclear export / RNA export from nucleus / miRNA binding / FGFR2 alternative splicing ...cellular response to sodium arsenite / SARS-CoV-1-host interactions / import into nucleus / telomeric repeat-containing RNA binding / G-rich strand telomeric DNA binding / pre-mRNA binding / nuclear export / RNA export from nucleus / miRNA binding / FGFR2 alternative splicing / regulation of alternative mRNA splicing, via spliceosome / negative regulation of telomere maintenance via telomerase / regulation of RNA splicing / SARS-CoV-1 modulates host translation machinery / Processing of Capped Intron-Containing Pre-mRNA / mRNA transport / cellular response to glucose starvation / positive regulation of telomere maintenance via telomerase / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / single-stranded DNA binding / single-stranded RNA binding / ribonucleoprotein complex / protein domain specific binding / DNA binding / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
hnRNP A3, RNA recognition motif 2 / hnRNP A1, RNA recognition motif 1 / Heterogeneous nuclear ribonucleoprotein A1/A2, C-terminal / Heterogeneous nuclear ribonucleoprotein A1, LC 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
Similarity search - Domain/homology
RNA / RNA (> 10) / Heterogeneous nuclear ribonucleoprotein A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsXu, Z.Y. / Liu, Y. / Li, F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32090040 China
CitationJournal: J Mol Cell Biol / Year: 2025
Title: Phase separation of hnRNPA1 and TERRA regulates telomeric stability.
Authors: Xu, Z. / Liu, Y. / Li, F. / Yang, Y. / Zhang, H. / Meng, F. / Liu, X. / Xie, X. / Chen, X. / Shi, Y. / Zhang, L.
History
DepositionNov 5, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 7, 2025Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heterogeneous nuclear ribonucleoprotein A1
B: RNA (5'-R(*UP*UP*AP*GP*GP*GP*UP*UP*AP*GP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)27,0412
Polymers27,0412
Non-polymers00
Water00
1
A: Heterogeneous nuclear ribonucleoprotein A1
B: RNA (5'-R(*UP*UP*AP*GP*GP*GP*UP*UP*AP*GP*GP*G)-3')

A: Heterogeneous nuclear ribonucleoprotein A1
B: RNA (5'-R(*UP*UP*AP*GP*GP*GP*UP*UP*AP*GP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)54,0834
Polymers54,0834
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area7340 Å2
ΔGint-18 kcal/mol
Surface area20370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.298, 101.298, 55.339
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Heterogeneous nuclear ribonucleoprotein A1


Mass: 23131.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HNRNPA1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P09651
#2: RNA chain RNA (5'-R(*UP*UP*AP*GP*GP*GP*UP*UP*AP*GP*GP*G)-3')


Mass: 3909.352 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
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: 2.88 Å3/Da / Density % sol: 57.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5 / Details: 100mM HEPES, pH7.0, 10% PEG 4000, 10% 2-Propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 7512 / % possible obs: 99.9 % / Redundancy: 5.7 % / CC1/2: 0.976 / Rmerge(I) obs: 0.158 / Net I/σ(I): 9
Reflection shellResolution: 2.8→2.85 Å / Rmerge(I) obs: 0.523 / Num. unique obs: 350 / CC1/2: 0.735

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→28.824 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 26.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2897 548 7.75 %
Rwork0.2344 --
obs0.2385 7075 94.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→28.824 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1449 259 0 0 1708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021768
X-RAY DIFFRACTIONf_angle_d0.4582439
X-RAY DIFFRACTIONf_dihedral_angle_d8.1161033
X-RAY DIFFRACTIONf_chiral_restr0.039271
X-RAY DIFFRACTIONf_plane_restr0.003274
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8005-3.0820.35951260.31321464X-RAY DIFFRACTION87
3.082-3.52730.34231400.26171638X-RAY DIFFRACTION97
3.5273-4.44140.28131440.21671682X-RAY DIFFRACTION98
4.4414-28.820.24551380.21251743X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.7862.8460.88922.61130.3830.4272-0.0184-0.13510.0660.0427-0.07560.0663-0.12580.03590.07050.2812-0.0025-0.00440.3346-0.04680.2187-25.537926.574-0.0841
20.74270.2945-0.75890.5920.37723.65990.48720.0938-0.29170.13570.2139-0.37860.42470.8652-0.49310.52980.0479-0.15250.419-0.0030.447-8.713929.4333-6.7751
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 6 through 186)
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 12)

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