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- EMDB-6231: The export receptor Crm1 forms a dimer to promote nuclear export ... -

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Basic information

Entry
Database: EMDB / ID: EMD-6231
TitleThe export receptor Crm1 forms a dimer to promote nuclear export of HIV RNA
Map dataRandom conical tilt reconstruction from negative-stain electron micrographs of a human Crm1/RanGTP dimer bound to the HIV-1 Rev-RRE complex.
Sample
  • Sample: A dimer of human Crm1/RanGTP bound to the HIV Rev-RRE complex
  • Protein or peptide: Crm1
  • Protein or peptide: Ran
  • Protein or peptide: Rev
  • RNA: Rev Response Element
KeywordsRNA Nuclear Export / HIV-host interactions / Human Crm1 / Human Ran / HIV-1 Rev / HIV-1 Rev Response Element
Function / homology
Function and homology information


structural constituent of nuclear pore => GO:0017056 / small GTPase binding => GO:0031267 / protein binding / HuR (ELAVL1) binds and stabilizes mRNA / annulate lamellae / regulation of proteasomal ubiquitin-dependent protein catabolic process / pre-miRNA export from nucleus / RNA nuclear export complex / snRNA import into nucleus / regulation of centrosome duplication ...structural constituent of nuclear pore => GO:0017056 / small GTPase binding => GO:0031267 / protein binding / HuR (ELAVL1) binds and stabilizes mRNA / annulate lamellae / regulation of proteasomal ubiquitin-dependent protein catabolic process / pre-miRNA export from nucleus / RNA nuclear export complex / snRNA import into nucleus / regulation of centrosome duplication / nuclear export signal receptor activity / Regulation of cholesterol biosynthesis by SREBP (SREBF) / host cell nucleolus / regulation of protein export from nucleus / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / NEP/NS2 Interacts with the Cellular Export Machinery / GTP metabolic process / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / nucleocytoplasmic transport / MicroRNA (miRNA) biogenesis / DNA metabolic process / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / Maturation of hRSV A proteins / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / mitotic sister chromatid segregation / ribosomal large subunit export from nucleus / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / protein localization to nucleus / mRNA transport / Binding and entry of HIV virion / viral process / nuclear pore / ribosomal subunit export from nucleus / mRNA export from nucleus / Cajal body / Cyclin A/B1/B2 associated events during G2/M transition / ribosomal small subunit export from nucleus / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / viral life cycle / NPAS4 regulates expression of target genes / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / centriole / Transcriptional and post-translational regulation of MITF-M expression and activity / Resolution of Sister Chromatid Cohesion / protein export from nucleus / Downregulation of TGF-beta receptor signaling / mitotic spindle organization / Deactivation of the beta-catenin transactivating complex / Transcriptional regulation by small RNAs / RHO GTPases Activate Formins / Heme signaling / Assembly Of The HIV Virion / MAPK6/MAPK4 signaling / Budding and maturation of HIV virion / recycling endosome / small GTPase binding / kinetochore / positive regulation of protein import into nucleus / protein import into nucleus / GDP binding / Separation of Sister Chromatids / positive regulation of protein binding / nuclear envelope / melanosome / mitotic cell cycle / ribosome biogenesis / G protein activity / midbody / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / nuclear membrane / host cell cytoplasm / cadherin binding / protein heterodimerization activity / DNA-binding transcription factor activity / ribonucleoprotein complex / cell division / GTPase activity / intracellular membrane-bounded organelle / chromatin binding / GTP binding / chromatin / nucleolus / host cell nucleus / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm
Similarity search - Function
Anti-repression trans-activator protein, REV protein / Anti-repression trans-activator protein, REV protein / REV protein (anti-repression trans-activator protein) / Exportin-1, repeat 3 / Chromosome region maintenance repeat / Exportin-1, repeat 2 / Chromosome region maintenance or exportin repeat / CRM1 / Exportin repeat 2 / CRM1 / Exportin repeat 3 / CRM1 C terminal ...Anti-repression trans-activator protein, REV protein / Anti-repression trans-activator protein, REV protein / REV protein (anti-repression trans-activator protein) / Exportin-1, repeat 3 / Chromosome region maintenance repeat / Exportin-1, repeat 2 / Chromosome region maintenance or exportin repeat / CRM1 / Exportin repeat 2 / CRM1 / Exportin repeat 3 / CRM1 C terminal / Exportin-1, C-terminal / Exportin-1, C-terminal / CRM1 C terminal / Exportin-1/5 / Exportin-1/Importin-beta-like / Exportin-1/Importin-beta-like / Exportin 1-like protein / small GTPase Ran family profile. / Ran GTPase / Ran GTPase / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta N-terminal domain profile. / Importin-beta, N-terminal domain / Importin-beta, N-terminal domain / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Small GTPase / Ras family / Rab subfamily of small GTPases / Armadillo-like helical / Armadillo-like helical / Small GTP-binding protein domain / Small GTP-binding protein domain / Armadillo-type fold / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Exportin-1 / Protein Rev / GTP-binding nuclear protein Ran
Similarity search - Component
Biological speciesHomo sapiens (human) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / negative staining / Resolution: 25.0 Å
AuthorsBooth DS / Cheng Y / Frankel AD
CitationJournal: Elife / Year: 2014
Title: The export receptor Crm1 forms a dimer to promote nuclear export of HIV RNA.
Authors: David S Booth / Yifan Cheng / Alan D Frankel /
Abstract: The HIV Rev protein routes viral RNAs containing the Rev Response Element (RRE) through the Crm1 nuclear export pathway to the cytoplasm where viral proteins are expressed and genomic RNA is ...The HIV Rev protein routes viral RNAs containing the Rev Response Element (RRE) through the Crm1 nuclear export pathway to the cytoplasm where viral proteins are expressed and genomic RNA is delivered to assembling virions. The RRE assembles a Rev oligomer that displays nuclear export sequences (NESs) for recognition by the Crm1-Ran(GTP) nuclear receptor complex. Here we provide the first view of an assembled HIV-host nuclear export complex using single-particle electron microscopy. Unexpectedly, Crm1 forms a dimer with an extensive interface that enhances association with Rev-RRE and poises NES binding sites to interact with a Rev oligomer. The interface between Crm1 monomers explains differences between Crm1 orthologs that alter nuclear export and determine cellular tropism for viral replication. The arrangement of the export complex identifies a novel binding surface to possibly target an HIV inhibitor and may point to a broader role for Crm1 dimerization in regulating host gene expression.
History
DepositionJan 4, 2015-
Header (metadata) releaseJan 14, 2015-
Map releaseJan 14, 2015-
UpdateFeb 10, 2016-
Current statusFeb 10, 2016Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.31
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.31
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_6231.gif

Downloads & links

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Map

FileDownload / File: emd_6231.map.gz / Format: CCP4 / Size: 1.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRandom conical tilt reconstruction from negative-stain electron micrographs of a human Crm1/RanGTP dimer bound to the HIV-1 Rev-RRE complex.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.04 Å/pix.
x 80 pix.
= 323.2 Å		4.04 Å/pix.
x 80 pix.
= 323.2 Å		4.04 Å/pix.
x 80 pix.
= 323.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.31 / Movie #1: 0.31
Minimum - Maximum-0.20516232 - 1.0428586
Average (Standard dev.)-0.0182145 (±0.09284244)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-40-40-40
Dimensions808080
Spacing808080
CellA=B=C: 323.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.044.044.04
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z323.200323.200323.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-40-40-40
NC/NR/NS808080
D min/max/mean-0.2051.043-0.018

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Supplemental data

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Sample components

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Entire : A dimer of human Crm1/RanGTP bound to the HIV Rev-RRE complex

EntireName: A dimer of human Crm1/RanGTP bound to the HIV Rev-RRE complex
Components
  • Sample: A dimer of human Crm1/RanGTP bound to the HIV Rev-RRE complex
  • Protein or peptide: Crm1
  • Protein or peptide: Ran
  • Protein or peptide: Rev
  • RNA: Rev Response Element

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Supramolecule #1000: A dimer of human Crm1/RanGTP bound to the HIV Rev-RRE complex

SupramoleculeName: A dimer of human Crm1/RanGTP bound to the HIV Rev-RRE complex
type: sample / ID: 1000
Oligomeric state: Crm1/RanGTP dimer, HIV-1 Rev homohexamer, HIV-1 RRE monomer
Number unique components: 4
Molecular weightExperimental: 462 KDa / Theoretical: 457 KDa / Method: Multi-angle laser light scattering

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Macromolecule #1: Crm1

MacromoleculeName: Crm1 / type: protein_or_peptide / ID: 1 / Name.synonym: Xpo1 / Number of copies: 2 / Oligomeric state: Dimer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Organelle: Nucleus, cytoplasm
Molecular weightExperimental: 125 KDa / Theoretical: 124 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: BL21(DE3) / Recombinant plasmid: pET19b
SequenceUniProtKB: Exportin-1
GO: structural constituent of nuclear pore => GO:0017056, viral process, viral life cycle, small GTPase binding => GO:0031267
InterPro: Armadillo-type fold, Armadillo-like helical, Importin-beta, N-terminal domain, Exportin-1/Importin-beta-like, Exportin-1, C-terminal

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Macromolecule #2: Ran

MacromoleculeName: Ran / type: protein_or_peptide / ID: 2
Details: Mutation of Gln69Leu with guanosine tri-phosphate bound.
Number of copies: 2 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Organelle: Nucleus, cytoplasm
Molecular weightExperimental: 26 KDa / Theoretical: 25 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: BL21(DE3) / Recombinant plasmid: pET19b
SequenceUniProtKB: GTP-binding nuclear protein Ran
GO: GTP binding, structural constituent of nuclear pore => GO:0017056, viral process, viral life cycle
InterPro: P-loop containing nucleoside triphosphate hydrolase, Ran GTPase, Small GTP-binding protein domain, Small GTPase

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Macromolecule #3: Rev

MacromoleculeName: Rev / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Oligomeric state: Hexamer / Recombinant expression: Yes
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: HXB3 / synonym: HIV-1 / Organelle: Nucleus, cytoplasm of host human cells
Molecular weightTheoretical: 13 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: BL21(DE3) / Recombinant plasmid: pHGB1
SequenceUniProtKB: Protein Rev
GO: viral process, viral life cycle, mRNA transport, RNA binding, host cell nucleus, host cell cytoplasm, protein binding
InterPro: Anti-repression trans-activator protein, REV protein

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Macromolecule #4: Rev Response Element

MacromoleculeName: Rev Response Element / type: rna / ID: 4 / Name.synonym: RRE
Details: 245-nucleotide portion of the 351-nucleotide Rev Response Element from the HIV-1 genome
Classification: OTHER / Structure: SINGLE STRANDED / Synthetic?: Yes
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: SF-2 / synonym: HIV-1
Molecular weightTheoretical: 80 KDa
SequenceString: GGGCUAGUAG GAGCUAUGUU CCUUGGGUUC UUGGGAGCAG CAGGAAGCAC UAUGGGCGCA GUGUCAUUGA CGCUGACGGU ACAGGCCAGA CAAUUAUUGU CUGGUAUAGU GCAACAGCAG AACAAUUUGC UGAGGGCUAU UGAGGCGCAA CAACAUCUGU UGCAACUCAC ...String:
GGGCUAGUAG GAGCUAUGUU CCUUGGGUUC UUGGGAGCAG CAGGAAGCAC UAUGGGCGCA GUGUCAUUGA CGCUGACGGU ACAGGCCAGA CAAUUAUUGU CUGGUAUAGU GCAACAGCAG AACAAUUUGC UGAGGGCUAU UGAGGCGCAA CAACAUCUGU UGCAACUCAC AGUCUGGGGC AUCAAGCAGC UCCAGGCAAG AGUCCUGGCU GUGGAAAGAU ACCUAAGGGA UCAACAGCUC CUAGGGG

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.4
Details: 50 mM HEPES-KOH, 50 mM potassium chloride, 2 mM magnesium acetate, 2 mM 2-mercaptoethanol, 2% v/v glycerol
StainingType: NEGATIVE / Details: 0.75% w/v uranyl formate
GridDetails: 200 mesh copper grid with thin carbon support, glow discharged
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI 12
Alignment procedureLegacy - Electron beam tilt params: 0
DateDec 5, 2012
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 44 / Average electron dose: 40 e/Å2
Tilt angle min0
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 52000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC / Tilt angle max: 60

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Image processing

DetailsRandom conical tilt reconstructions were generated from samples tilted to 60 degrees using angular parameters from class averages of untilted particles. The structure was further refined by projection matching using both tilted and untilted particles.
CTF correctionDetails: Each particle
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: OTHER / Software - Name: FREALIGN, Spider / Number images used: 845
Final two d classificationNumber classes: 5

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Atomic model buiding 1

Initial modelPDB ID:

3gb8


Chain - Chain ID: A
SoftwareName: Chimera
DetailsA human Crm1 dimer was extracted from the unit cell of the crystal structure.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation

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