[English] 日本語
Yorodumi
- EMDB-42494: Cryo-EM structure of the HIV-1 nuclear export complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-42494
TitleCryo-EM structure of the HIV-1 nuclear export complex
Map data
Sample
  • Complex: HIV-1 Nuclear Export complex
    • Complex: Crm1
      • Protein or peptide: Exportin-1
    • Complex: Ran Q69L 1-180
      • Protein or peptide: GTP-binding nuclear protein Ran
    • Complex: HIV-1 Rev/RRE RNP
      • Protein or peptide: Rev HIV-1
      • Protein or peptide: Rev HIV-1
  • RNA: HIV-1 RRE
KeywordsHIV Karyopherin Rev Crm1 / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


cellular response to triglyceride / cellular response to salt / 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 / nuclear export signal receptor activity / regulation of centrosome duplication ...cellular response to triglyceride / cellular response to salt / 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 / nuclear export signal receptor activity / regulation of centrosome duplication / manchette / cellular response to mineralocorticoid stimulus / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / regulation of protein export from nucleus / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / protein localization to nucleolus / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / GTP metabolic process / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / MicroRNA (miRNA) biogenesis / DNA metabolic process / Maturation of hRSV A proteins / dynein intermediate chain binding / mitotic sister chromatid segregation / ribosomal large subunit export from nucleus / spermatid development / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / protein localization to nucleus / viral process / positive regulation of protein binding / sperm flagellum / nuclear pore / mRNA export from nucleus / Cajal body / Cyclin A/B1/B2 associated events during G2/M transition / ribosomal subunit export from nucleus / ribosomal small subunit export from nucleus / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / NPAS4 regulates expression of target genes / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Transcriptional and post-translational regulation of MITF-M expression and activity / centriole / protein export from nucleus / Resolution of Sister Chromatid Cohesion / Downregulation of TGF-beta receptor signaling / mitotic spindle organization / male germ cell nucleus / hippocampus development / Deactivation of the beta-catenin transactivating complex / RHO GTPases Activate Formins / Heme signaling / Transcriptional regulation by small RNAs / MAPK6/MAPK4 signaling / recycling endosome / kinetochore / positive regulation of protein import into nucleus / small GTPase binding / protein import into nucleus / Separation of Sister Chromatids / GDP binding / nuclear envelope / melanosome / mitotic cell cycle / ribosome biogenesis / G protein activity / actin cytoskeleton organization / midbody / nuclear membrane / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / DNA-binding transcription factor binding / cadherin binding / response to xenobiotic stimulus / ribonucleoprotein complex / protein heterodimerization activity / protein domain specific binding / cell division / intracellular membrane-bounded organelle / GTPase activity / chromatin binding / chromatin / GTP binding / protein-containing complex binding / nucleolus / magnesium ion binding / negative regulation of transcription by RNA polymerase II / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
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 / CRM1 C terminal / Exportin-1/5 ...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 / CRM1 C terminal / Exportin-1/5 / Exportin-1/Importin-beta-like / Exportin 1-like protein / Ran GTPase / Small GTPase Ran-type domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta N-terminal domain profile. / 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 / Ras family / Rab subfamily of small GTPases / Armadillo-like helical / Small GTP-binding protein domain / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Exportin-1 / GTP-binding nuclear protein Ran
Similarity search - Component
Biological speciesHomo sapiens (human) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 4.25 Å
AuthorsSmith AM / Cheng Y / Frankel AD
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI170792 United States
National Institutes of Health/Office of the DirectorOD020054 United States
National Institutes of Health/Office of the DirectorOD021741 United States
National Institutes of Health/Office of the DirectorOD026881 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To Be Published
Title: Structure of the HIV-1 RNA Nuclear Export Complex Reveals Crm1 Versatility
Authors: Smith AM / Cheng Y / Frankel AD / Li Y / Velarde A
History
DepositionOct 26, 2023-
Header (metadata) releaseApr 30, 2025-
Map releaseApr 30, 2025-
UpdateApr 30, 2025-
Current statusApr 30, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_42494.png

Downloads & links

-
Map

FileDownload / File: emd_42494.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.67 Å/pix.
x 220 pix.
= 367.4 Å		1.67 Å/pix.
x 220 pix.
= 367.4 Å		1.67 Å/pix.
x 220 pix.
= 367.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.67 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.018
Minimum - Maximum-0.029989928 - 0.091458306
Average (Standard dev.)0.00006619032 (±0.0027936222)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 367.4 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_42494_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_42494_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_42494_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : HIV-1 Nuclear Export complex

EntireName: HIV-1 Nuclear Export complex
Components
  • Complex: HIV-1 Nuclear Export complex
    • Complex: Crm1
      • Protein or peptide: Exportin-1
    • Complex: Ran Q69L 1-180
      • Protein or peptide: GTP-binding nuclear protein Ran
    • Complex: HIV-1 Rev/RRE RNP
      • Protein or peptide: Rev HIV-1
      • Protein or peptide: Rev HIV-1
  • RNA: HIV-1 RRE

-
Supramolecule #1: HIV-1 Nuclear Export complex

SupramoleculeName: HIV-1 Nuclear Export complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Molecular weightTheoretical: 445 KDa

-
Supramolecule #2: Crm1

SupramoleculeName: Crm1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 / Details: Crm1 forms a dimer
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 123 KDa

-
Supramolecule #3: Ran Q69L 1-180

SupramoleculeName: Ran Q69L 1-180 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3 / Details: Each Crm1 subunit binds a Ran molecule
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.75 KDa

-
Supramolecule #4: HIV-1 Rev/RRE RNP

SupramoleculeName: HIV-1 Rev/RRE RNP / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #2, #4
Details: RRE was generated from T7 polymerase on a linearized plasmid
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 158 KDa

-
Macromolecule #1: Exportin-1

MacromoleculeName: Exportin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 122.267984 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GAMGSGMPAI MTMLADHAAR QLLDFSQKLD INLLDNVVNC LYHGEGAQQR MAQEVLTHLK EHPDAWTRVD TILEFSQNMN TKYYGLQIL ENVIKTRWKI LPRNQCEGIK KYVVGLIIKT SSDPTCVEKE KVYIGKLNMI LVQILKQEWP KHWPTFISDI V GASRTSES ...String:
GAMGSGMPAI MTMLADHAAR QLLDFSQKLD INLLDNVVNC LYHGEGAQQR MAQEVLTHLK EHPDAWTRVD TILEFSQNMN TKYYGLQIL ENVIKTRWKI LPRNQCEGIK KYVVGLIIKT SSDPTCVEKE KVYIGKLNMI LVQILKQEWP KHWPTFISDI V GASRTSES LCQNNMVILK LLSEEVFDFS SGQITQVKSK HLKDSMCNEF SQIFQLCQFV MENSQNAPLV HATLETLLRF LN WIPLGYI FETKLISTLI YKFLNVPMFR NVSLKCLTEI AGVSVSQYEE QFVTLFTLTM MQLKQMLPLN TNIRLAYSNG KDD EQNFIQ NLSLFLCTFL KEHDQLIEKR LNLRETLMEA LHYMLLVSEV EETEIFKICL EYWNHLAAEL YRESPFSTSA SPLL SGSQH FDVPPRRQLY LPMLFKVRLL MVSRMAKPEE VLVVENDQGE VVREFMKDTD SINLYKNMRE TLVYLTHLDY VDTER IMTE KLHNQVNGTE WSWKNLNTLC WAIGSISGAM HEEDEKRFLV TVIKDLLGLC EQKRGKDNKA IIASNIMYIV GQYPRF LRA HWKFLKTVVN KLFEFMHETH DGVQDMACDT FIKIAQKCRR HFVQVQVGEV MPFIDEILNN INTIICDLQP QQVHTFY EA VGYMIGAQTD QTVQEHLIEK YMLLPNQVWD SIIQQATKNV DILKDPETVK QLGSILKTNV RACKAVGHPF VIQLGRIY L DMLNVYKCLS ENISAAIQAN GEMVTKQPLI RSMRTVKRET LKLISGWVSR SNDPQMVAEN FVPPLLDAVL IDYQRNVPA AREPEVLSTM AIIVNKLGGH ITAEIPQIFD AVFECTLNMI NKDFEEYPEH RTNFFLLLQA VNSHCFPAFL AIPPTQFKLV LDSIIWAFK HTMRNVADTG LQILFTLLQN VAQEEAAAQS FYQTYFCDIL QHIFSVVTDT SHTAGLTMHA SILAYMFNLV E EGKISTSL NPGNPVNNQI FLQEYVANLL KSAFPHLQDA QVKLFVTGLF SLNQDIPAFK EHLRDFLVQI KEFAGEDTSD LF LEEREIA LRQADEEKHK RQMSV

UniProtKB: Exportin-1

-
Macromolecule #2: Rev HIV-1

MacromoleculeName: Rev HIV-1 / type: protein_or_peptide / ID: 2
Details: Native NES was exchanged with NS2Val NES Native NES: LPPLERLTL Ns2Val NES: TVDEMTKKFGTLTI
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: HXB3
Molecular weightTheoretical: 10.687159 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
AMAGRSGDSD EDLLKAVRLI KFLYQSNPPP NPEGTRQARR NRRRRWRARQ RQIHSISERI RSTYLGRSAE PVPLQTVDEM TKKFGTLTI DCN

-
Macromolecule #3: GTP-binding nuclear protein Ran

MacromoleculeName: GTP-binding nuclear protein Ran / type: protein_or_peptide / ID: 3 / Details: Q69L 1-180 / Number of copies: 2 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.722076 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
GHMTAQGEPQ VQFKLVLVGD GGTGKTTFVK RHLTGEFEKK YVATLGVEVH PLVFHTNRGP IKFNVWDTAG LEKFGGLRDG YYIQAQCAI IMFDVTSRVT YKNVPNWHRD LVRVCENIPI VLCGNKVDIK DRKVKAKSIV FHRKKNLQYY DISAKSNYNF E KPFLWLAR KLIGDPNLEF VAM

UniProtKB: GTP-binding nuclear protein Ran

-
Macromolecule #4: Rev HIV-1

MacromoleculeName: Rev HIV-1 / type: protein_or_peptide / ID: 4
Details: Native NES was exchanged with NS2Val NES Native NES: LPPLERLTL Ns2Val NES: TVDEMTKKFGTLTI
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: HXB3
Molecular weightTheoretical: 10.644108 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
GAMAGRSGDS DEDLLKAVRL IKFLYQSNPP PNPEGTRQAR RNRRRRWRER QRQIHSISER ILSTYLGRSA EPVPLQTVDE MTKKFGTLT IDC

-
Macromolecule #5: HIV-1 RRE

MacromoleculeName: HIV-1 RRE / type: rna / ID: 5 / Number of copies: 1
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 114.996102 KDa
SequenceString: UGAACCAUUA GGAAUAGCAC CCACCAAGGC AAAGAGAAGA GUGGUGCAGA GAGAAAAAAG AGCAGUGGGA AUAGUAGGAG CUAUGUUCC UUGGGUUCUU GGGAGCAGCA GGAAGCACUA UGGGCGCAGU GUCAUUGACG CUGACGGUAC AGGCCAGACA A UUAUUGUC ...String:
UGAACCAUUA GGAAUAGCAC CCACCAAGGC AAAGAGAAGA GUGGUGCAGA GAGAAAAAAG AGCAGUGGGA AUAGUAGGAG CUAUGUUCC UUGGGUUCUU GGGAGCAGCA GGAAGCACUA UGGGCGCAGU GUCAUUGACG CUGACGGUAC AGGCCAGACA A UUAUUGUC UGGUAUAGUG CAACAGCAGA ACAAUUUGCU GAGGGCUAUU GAGGCGCAAC AACAUCUGUU GCAACUCACA GU CUGGGGC AUCAAGCAGC UCCAAGCAAG AAUCCUGGCU GUGGAAAGAU ACCUAAGGGA UCAACAGCUC CUAGGGGAAU UCG GUUGCU CUGGAAAACU CAUUUGCACC ACUGCUGUG

GENBANK: GENBANK: K02007.1

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.7 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMC8H18N2O4SHEPES
50.0 mMKClPotassium Chloride
2.0 mMHOCH2CH2SHbeta-mercaptoethanol
2.0 % (v/v)C3H8O3glycerol
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298.15 K / Instrument: FEI VITROBOT MARK IV
Details: Washed grid 2x outside of vitrobot; with the second drop of buffer I loaded the tweezers; moved the grid into the chamber and then I blotted..

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / #0 - Number grids imaged: 6 / #0 - Number real images: 24447 / #0 - Average electron dose: 66.0 e/Å2
#0 - Details: graphene oxide grids treated with single stranded DNA oligos; tilt angles 0 and 25 degrees
#1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / #1 - Number grids imaged: 3 / #1 - Number real images: 22762 / #1 - Average electron dose: 68.0 e/Å2
#1 - Details: Graphene oxide grids treated with polyamine; tilt angles 0, 15 and 30 degrees
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated magnification: 59880 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Image recording ID1
Particle selectionNumber selected: 11176625
Startup modelType of model: OTHER / Details: ab initio reconstruction from cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.25 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 260885
Initial angle assignmentType: RANDOM ASSIGNMENT / Software: (Name: RELION, cryoSPARC)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChainDetails

5dis

chain_id: A, source_name: PDB, initial_model_type: experimental modelCrm1

5dis

chain_id: B, source_name: PDB, initial_model_type: experimental modelRan Q69L 1-180

4pmi

chain_id: A, source_name: PDB, initial_model_type: experimental modelRRE stem IIB mimic

4pmi

chain_id: B, source_name: PDB, initial_model_type: experimental modelRev

4pmi

chain_id: C, source_name: PDB, initial_model_type: experimental modelRev
RefinementProtocol: RIGID BODY FIT / Overall B value: 325
Output model

PDB-8urj:
Cryo-EM structure of the HIV-1 nuclear export complex

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more