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- PDB-6j60: hnRNP A1 reversible amyloid core GFGGNDNFG (residues 209-217) -

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Basic information

Entry
Database: PDB / ID: 6j60
TitlehnRNP A1 reversible amyloid core GFGGNDNFG (residues 209-217)
Components9-mer peptide (GFGGNDNFG) from Heterogeneous nuclear ribonucleoprotein A1
KeywordsRNA BINDING PROTEIN / phase separation / reversibility / MicroED
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 / RNA export from nucleus / nuclear export / negative regulation of telomere maintenance via telomerase / miRNA binding ...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 / RNA export from nucleus / nuclear export / negative regulation of telomere maintenance via telomerase / miRNA binding / FGFR2 alternative splicing / regulation of alternative mRNA splicing, via spliceosome / intracellular non-membrane-bounded organelle / regulation of RNA splicing / SARS-CoV-1 modulates host translation machinery / Processing of Capped Intron-Containing Pre-mRNA / mRNA transport / localization / cellular response to glucose starvation / positive regulation of telomere maintenance via telomerase / catalytic step 2 spliceosome / molecular condensate scaffold activity / mRNA Splicing - Major Pathway / mRNA 3'-UTR binding / spliceosomal complex / mRNA splicing, via spliceosome / single-stranded DNA binding / amyloid fibril formation / single-stranded RNA binding / ribonucleoprotein complex / protein domain specific binding / DNA binding / RNA binding / extracellular exosome / nucleoplasm / membrane / identical protein binding / nucleus / 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
Heterogeneous nuclear ribonucleoprotein A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 0.96 Å
AuthorsLuo, F. / Zhou, H. / Gui, X. / Li, D. / Li, X. / Liu, C.
CitationJournal: Nat Commun / Year: 2019
Title: Structural basis for reversible amyloids of hnRNPA1 elucidates their role in stress granule assembly.
Authors: Xinrui Gui / Feng Luo / Yichen Li / Heng Zhou / Zhenheng Qin / Zhenying Liu / Jinge Gu / Muyun Xie / Kun Zhao / Bin Dai / Woo Shik Shin / Jianhua He / Lin He / Lin Jiang / Minglei Zhao / Bo ...Authors: Xinrui Gui / Feng Luo / Yichen Li / Heng Zhou / Zhenheng Qin / Zhenying Liu / Jinge Gu / Muyun Xie / Kun Zhao / Bin Dai / Woo Shik Shin / Jianhua He / Lin He / Lin Jiang / Minglei Zhao / Bo Sun / Xueming Li / Cong Liu / Dan Li /
Abstract: Subcellular membrane-less organelles consist of proteins with low complexity domains. Many of them, such as hnRNPA1, can assemble into both a polydisperse liquid phase and an ordered solid phase of ...Subcellular membrane-less organelles consist of proteins with low complexity domains. Many of them, such as hnRNPA1, can assemble into both a polydisperse liquid phase and an ordered solid phase of amyloid fibril. The former mirrors biological granule assembly, while the latter is usually associated with neurodegenerative disease. Here, we observe a reversible amyloid formation of hnRNPA1 that synchronizes with liquid-liquid phase separation, regulates the fluidity and mobility of the liquid-like droplets, and facilitates the recruitment of hnRNPA1 into stress granules. We identify the reversible amyloid-forming cores of hnRNPA1 (named hnRACs). The atomic structures of hnRACs reveal a distinct feature of stacking Asp residues, which contributes to fibril reversibility and explains the irreversible pathological fibril formation caused by the Asp mutations identified in familial ALS. Our work characterizes the structural diversity and heterogeneity of reversible amyloid fibrils and illuminates the biological function of reversible amyloid formation in protein phase separation.
History
DepositionJan 12, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 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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Assembly

Deposited unit
A: 9-mer peptide (GFGGNDNFG) from Heterogeneous nuclear ribonucleoprotein A1


Theoretical massNumber of molelcules
Total (without water)8841
Polymers8841
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy, EM
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1120 Å2
Unit cell
Length a, b, c (Å)5.010, 27.800, 36.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide 9-mer peptide (GFGGNDNFG) from Heterogeneous nuclear ribonucleoprotein A1


Mass: 883.863 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P09651*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: 9-mer peptide from Heterogeneous nuclear ribonucleoprotein A1
Type: COMPLEX / Entity ID: #1 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.88 kDa/nm / Experimental value: YES
EM crystal formationLipid protein ratio: 1 / Temperature: 289 K
Buffer solutionpH: 10.5 / Details: 2M NH4SO4, 0.1M CAPS PH 10.5, 0.2m LiSO4
SpecimenConc.: 20 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: powder
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 30 % / Chamber temperature: 293.15 K / Details: blot 2 times

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Data collection

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN
Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Image recordingAverage exposure time: 5.72 sec. / Electron dose: 0.05 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
EM imaging opticsPhase plate: no / Spherical aberration corrector: no
EM diffractionCamera length: 500 mm
EM diffraction shellResolution: 0.96→0.994 Å / Fourier space coverage: 82 % / Multiplicity: 3.5 / Num. of structure factors: 262 / Phase residual: 28.59 °
EM diffraction statsFourier space coverage: 82.9 % / High resolution: 0.96 Å / Num. of intensities measured: 14361 / Num. of structure factors: 2935 / Phase error: 30.87 ° / Phase residual: 1 ° / Phase error rejection criteria: 0 / Rmerge: 0.251 / Rsym: 0.282

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Processing

SoftwareName: PHENIX / Version: (1.10_2155: ???) / Classification: refinement
EM software
IDNameVersionCategoryDetails
6Coot0.8.2model fitting
8PHENIX1.13-2998-000molecular replacement
12SHELXD3D reconstructiondirect method
13PHENIX3D reconstructionrefine
14Coot3D reconstructionbuild model
15PHENIX1.13-2998-000model refinement
Image processingDetails: .mrc file was transfered to SMV .img format
EM 3D crystal entity∠α: 90 ° / ∠β: 90 ° / ∠γ: 90 ° / A: 5.01 Å / B: 27.8 Å / C: 36.45 Å / Space group name: P2(1)2(1)2(1) / Space group num: 19
CTF correctionType: NONE
3D reconstructionResolution: 0.96 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingProtocol: AB INITIO MODEL / Space: RECIPROCAL
Details: We have used the direct mehod of SHELXD to solve the structure
RefinementResolution: 0.96→3.967 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.52 / Details: phenix.refine
RfactorNum. reflection% reflection
Rfree0.2484 521 10.12 %
Rwork0.2332 --
obs0.2349 5150 86.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.01464
ELECTRON CRYSTALLOGRAPHYf_angle_d1.04484
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d10.98119
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.1225
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.00614

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