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Open data
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Basic information
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Title | Cryo-EM structure of Karyopherin-beta2 bound to HNRNPH2 PY-NLS | |||||||||||||||
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![]() | RNA-binding protein TNPO1 Cryo-EM KapB2 HNRNP / TRANSPORT PROTEIN | |||||||||||||||
Function / homology | ![]() Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Intraflagellar transport / Postmitotic nuclear pore complex (NPC) reformation / nuclear import signal receptor activity / nuclear localization sequence binding / regulation of RNA splicing / Processing of Capped Intron-Containing Pre-mRNA / mRNA Splicing - Major Pathway / small GTPase binding / cilium ...Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Intraflagellar transport / Postmitotic nuclear pore complex (NPC) reformation / nuclear import signal receptor activity / nuclear localization sequence binding / regulation of RNA splicing / Processing of Capped Intron-Containing Pre-mRNA / mRNA Splicing - Major Pathway / small GTPase binding / cilium / protein import into nucleus / postsynaptic density / ribonucleoprotein complex / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.17 Å | |||||||||||||||
![]() | Gonzalez A / Fung HYJ / Chook YM | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: A new Karyopherin-β2 binding PY-NLS epitope of HNRNPH2 linked to neurodevelopmental disorders. Authors: Abner Gonzalez / Hong Joo Kim / Brian D Freibaum / Ho Yee Joyce Fung / Chad A Brautigam / J Paul Taylor / Yuh Min Chook / ![]() Abstract: The HNRNPH2 proline-tyrosine nuclear localization signal (PY-NLS) is mutated in HNRNPH2-related X-linked neurodevelopmental disorder, causing the normally nuclear HNRNPH2 to accumulate in the ...The HNRNPH2 proline-tyrosine nuclear localization signal (PY-NLS) is mutated in HNRNPH2-related X-linked neurodevelopmental disorder, causing the normally nuclear HNRNPH2 to accumulate in the cytoplasm. We solved the cryoelectron microscopy (cryo-EM) structure of Karyopherin-β2/Transportin-1 bound to the HNRNPH2 PY-NLS to understand importin-NLS recognition and disruption in disease. HNRNPH2 RPGPY is a typical R-X-P-Y motif comprising PY-NLS epitopes 2 and 3, followed by an additional Karyopherin-β2-binding epitope, we term epitope 4, at residues DRP; no density is present for PY-NLS epitope 1. Disease variant mutations at epitopes 2-4 impair Karyopherin-β2 binding and cause aberrant cytoplasmic accumulation in cells, emphasizing the role of nuclear import defect in disease. Sequence/structure analysis suggests that strong PY-NLS epitopes 4 are rare and thus far limited to close paralogs of HNRNPH2, HNRNPH1, and HNRNPF. Epitope 4-binidng hotspot Karyopherin-β2 W373 corresponds to close paralog Karyopherin-β2b/Transportin-2 W370, a pathological variant site in neurodevelopmental abnormalities, suggesting that Karyopherin-β2b/Transportin-2-HNRNPH2/H1/F interactions may be compromised in the abnormalities. | |||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 403.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.2 KB 18.2 KB | Display Display | ![]() |
Images | ![]() | 53 KB | ||
Others | ![]() ![]() | 764 MB 764 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 967.2 KB | Display | ![]() |
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Full document | ![]() | 966.8 KB | Display | |
Data in XML | ![]() | 20.6 KB | Display | |
Data in CIF | ![]() | 24.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8sghMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.415 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_40455_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_40455_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Karyopherin-beta2 bound to hnRNP H2 PY-NLS
Entire | Name: Karyopherin-beta2 bound to hnRNP H2 PY-NLS |
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Components |
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-Supramolecule #1: Karyopherin-beta2 bound to hnRNP H2 PY-NLS
Supramolecule | Name: Karyopherin-beta2 bound to hnRNP H2 PY-NLS / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Transportin-1
Macromolecule | Name: Transportin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 101.738812 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GGSKMEYEWK PDEQGLQQIL QLLKESQSPD TTIQRTVQQK LEQLNQYPDF NNYLIFVLTK LKSEDEPTRS LSGLILKNNV KAHFQNFPN GVTDFIKSEC LNNIGDSSPL IRATVGILIT TIASKGELQN WPDLLPKLCS LLDSEDYNTC EGAFGALQKI C EDSAEILD ...String: GGSKMEYEWK PDEQGLQQIL QLLKESQSPD TTIQRTVQQK LEQLNQYPDF NNYLIFVLTK LKSEDEPTRS LSGLILKNNV KAHFQNFPN GVTDFIKSEC LNNIGDSSPL IRATVGILIT TIASKGELQN WPDLLPKLCS LLDSEDYNTC EGAFGALQKI C EDSAEILD SDVLDRPLNI MIPKFLQFFK HSSPKIRSHA VACVNQFIIS RTQALMLHID SFIENLFALA GDEEPEVRKN VC RALVMLL EVRMDRLLPH MHNIVEYMLQ RTQDQDENVA LEACEFWLTL AEQPICKDVL VRHLPKLIPV LVNGMKYSDI DII LLKGDV EEDETIPDSE QDIRPRFHRS RTVAQQHDED GIEEEDDDDD EIDDDDTISD WNLRKCSAAA LDVLANVYRD ELLP HILPL LKELLFHHEW VVKESGILVL GAIAEGCMQG MIPYLPELIP HLIQCLSDKK ALVRSITCWT LSRYAHWVVS QPPDT YLKP LMTELLKRIL DSNKRVQEAA CSAFATLEEE ACTELVPYLA YILDTLVFAF SKYQHKNLLI LYDAIGTLAD SVGHHL NKP EYIQMLMPPL IQKWNMLKDE DKDLFPLLEC LSSVATALQS GFLPYCEPVY QRCVNLVQKT LAQAMLNNAQ PDQYEAP DK DFMIVALDLL SGLAEGLGGN IEQLVARSNI LTLMYQCMQD KMPEVRQSSF ALLGDLTKAC FQHVKPCIAD FMPILGTN L NPEFISVCNN ATWAIGEISI QMGIEMQPYI PMVLHQLVEI INRPNTPKTL LENTAITIGR LGYVCPQEVA PMLQQFIRP WCTSLRNIRD NEEKDSAFRG ICTMISVNPS GVIQDFIFFC DAVASWINPK DDLRDMFCKI LHGFKNQVGD ENWRRFSDQF PLPLKERLA AFYGV UniProtKB: Transportin-1 |
-Macromolecule #2: Heterogeneous nuclear ribonucleoprotein H2, N-terminally processed
Macromolecule | Name: Heterogeneous nuclear ribonucleoprotein H2, N-terminally processed type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 13.993811 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GGSNSPDTAN DGFVRLRGLP FGCSKEEIVQ FFSGLEIVPN GMTLPVDFQG RSTGEAFVQF ASQEIAEKAL KKHKERIGHR YIEIFKSSR AEVRTHYDPP RKLMAMQRPG PYDRPGAGRG YNSIGRG UniProtKB: Heterogeneous nuclear ribonucleoprotein H2 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 2.7 mg/mL |
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Buffer | pH: 7.5 Details: 20 mM Tris-HCl pH 7.5, 150 nM NaCl, 2 mM BME, 0.003125% [w/v] NP-40 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Details | Initial docking performed using Chimera, then manual model building by Coot, ISOLDE in ChimerX and Phenix real-space refinement. |
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Output model | ![]() PDB-8sgh: |