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Yorodumi- EMDB-29489: Dimeric form of HIV-1 Vif in complex with human CBF-beta, ELOB, E... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29489 | |||||||||
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Title | Dimeric form of HIV-1 Vif in complex with human CBF-beta, ELOB, ELOC, and CUL5 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | virus-host protein complex / VIRAL PROTEIN | |||||||||
Function / homology | Function and homology information RUNX3 regulates RUNX1-mediated transcription / RUNX1 regulates transcription of genes involved in BCR signaling / RUNX1 regulates transcription of genes involved in interleukin signaling / RUNX2 regulates bone development / core-binding factor complex / RUNX1 regulates expression of components of tight junctions / positive regulation of CD8-positive, alpha-beta T cell differentiation / RUNX2 regulates chondrocyte maturation / negative regulation of CD4-positive, alpha-beta T cell differentiation / lymphocyte differentiation ...RUNX3 regulates RUNX1-mediated transcription / RUNX1 regulates transcription of genes involved in BCR signaling / RUNX1 regulates transcription of genes involved in interleukin signaling / RUNX2 regulates bone development / core-binding factor complex / RUNX1 regulates expression of components of tight junctions / positive regulation of CD8-positive, alpha-beta T cell differentiation / RUNX2 regulates chondrocyte maturation / negative regulation of CD4-positive, alpha-beta T cell differentiation / lymphocyte differentiation / ERBB2 signaling pathway / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / RUNX2 regulates genes involved in cell migration / RUNX2 regulates genes involved in differentiation of myeloid cells / Transcriptional regulation by RUNX2 / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / myeloid cell differentiation / target-directed miRNA degradation / elongin complex / RUNX3 Regulates Immune Response and Cell Migration / VCB complex / definitive hemopoiesis / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / Regulation of RUNX1 Expression and Activity / Cul5-RING ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul2-RING ubiquitin ligase complex / SCF ubiquitin ligase complex / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / RUNX2 regulates osteoblast differentiation / site of DNA damage / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / RUNX3 regulates p14-ARF / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / cell maturation / viral life cycle / RNA Polymerase II Pre-transcription Events / intrinsic apoptotic signaling pathway / transcription corepressor binding / virion component / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / TP53 Regulates Transcription of DNA Repair Genes / Vif-mediated degradation of APOBEC3G / Regulation of RUNX3 expression and activity / G1/S transition of mitotic cell cycle / calcium channel activity / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Inactivation of CSF3 (G-CSF) signaling / Downregulation of ERBB2 signaling / osteoblast differentiation / Regulation of expression of SLITs and ROBOs / protein polyubiquitination / Transcriptional regulation of granulopoiesis / ubiquitin-protein transferase activity / Regulation of RUNX2 expression and activity / protein-macromolecule adaptor activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / signaling receptor activity / Neddylation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / ubiquitin-dependent protein catabolic process / protein-containing complex assembly / Estrogen-dependent gene expression / host cell cytoplasm / sequence-specific DNA binding / transcription by RNA polymerase II / transcription coactivator activity / protein ubiquitination / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / host cell plasma membrane / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / membrane / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Human immunodeficiency virus 1 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.54 Å | |||||||||
Authors | Ito F / Alvarez-Cabrera AL / Zhou ZH / Chen XS | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structural basis of HIV-1 Vif-mediated E3 ligase targeting of host APOBEC3H Authors: Ito F / Alvarez-Cabrera AL / Kim K / Zhou ZH / Chen XS | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_29489.map.gz | 1.3 GB | EMDB map data format | |
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Header (meta data) | emd-29489-v30.xml emd-29489.xml | 20.6 KB 20.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_29489_fsc.xml | 24 KB | Display | FSC data file |
Images | emd_29489.png | 98.4 KB | ||
Others | emd_29489_half_map_1.map.gz emd_29489_half_map_2.map.gz | 1.3 GB 1.3 GB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29489 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29489 | HTTPS FTP |
-Related structure data
Related structure data | 8fvjMC 8fviC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_29489.map.gz / Format: CCP4 / Size: 1.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.51 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_29489_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_29489_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Dimeric form of HIV-1 Vif in complex with human CBF-beta, ELOB, E...
Entire | Name: Dimeric form of HIV-1 Vif in complex with human CBF-beta, ELOB, ELOC, and CUL5 |
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Components |
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-Supramolecule #1: Dimeric form of HIV-1 Vif in complex with human CBF-beta, ELOB, E...
Supramolecule | Name: Dimeric form of HIV-1 Vif in complex with human CBF-beta, ELOB, ELOC, and CUL5 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 198 KDa |
-Macromolecule #1: Core-binding factor subunit beta
Macromolecule | Name: Core-binding factor subunit beta / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 18.643814 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MPRVVPDQRS KFENEEFFRK LSRECEIKYT GFRDRPHEER QARFQNACRD GRSEIAFVAT GTNLSLQFFP ASWQGEQRQT PSREYVDLE REAGKVYLKA PMILNGVCVI WKGWIDLQRL DGMGCLEFDE ERAQQEDALA QQAFEEARRR TREFEDRD UniProtKB: Core-binding factor subunit beta |
-Macromolecule #2: Virion infectivity factor
Macromolecule | Name: Virion infectivity factor / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Human immunodeficiency virus 1 / Strain: pNL4-3 |
Molecular weight | Theoretical: 21.160451 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GPMENRWQVM IVWQVDRMRI NTWKRLVKHH MYISRKAKDW FYRHHYESTH PKISSEVHIP LGDAKLVITT YWGLHTGERD WHLGQGVSI EWRKKRYSTQ VDPDLADQLI HLHYFDCFSE SAIRNTILGR IVSPRCEYQA GHNKVGSLQY LALAALIKPK Q IKPPLPSV RKLTEDRWNK UniProtKB: Virion infectivity factor |
-Macromolecule #3: Elongin-B
Macromolecule | Name: Elongin-B / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 11.48803 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MDVFLMIRRH KTTIFTDAKE SSTVFELKRI VEGILKRPPD EQRLYKDDQL LDDGKTLGEC GFTSQTARPQ APATVGLAFR ADDTFEALC IEPFSSPPEL PDV UniProtKB: Elongin-B |
-Macromolecule #4: Elongin-C
Macromolecule | Name: Elongin-C / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 10.84342 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MYVKLISSDG HEFIVKREHA LTSGTIKAML SGPGQFAENE TNEVNFREIP SHVLSKVCMY FTYKVRYTNS STEIPEFPIA PEIALELLM AANFLDC UniProtKB: Elongin-C |
-Macromolecule #5: Cullin-5
Macromolecule | Name: Cullin-5 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 36.61398 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GPAGSSLQFE DKWDFMRPIV LKLLRQESVT KQQWFDLFSD VHAVCLWDDK GPAKIHQALK EDILEFIKQA QARVLSHQDD TALLKAYIV EWRKFFTQCD ILPKPFCQLE ITLMGKQGSN KKSNVEDSIV RKLMLDTWNE SIFSNIKNRL QDSAMKLVHA E RLGEAFDS ...String: GPAGSSLQFE DKWDFMRPIV LKLLRQESVT KQQWFDLFSD VHAVCLWDDK GPAKIHQALK EDILEFIKQA QARVLSHQDD TALLKAYIV EWRKFFTQCD ILPKPFCQLE ITLMGKQGSN KKSNVEDSIV RKLMLDTWNE SIFSNIKNRL QDSAMKLVHA E RLGEAFDS QLVIGVRESY VNLCSNPEDK LQIYRDNFEK AYLDSTERFY RTQAPSYLQQ NGVQNYMKYA DAKLKEEEKR AL RYLETRR ECNSVEALME CCVNALVTSF KETILAECQG MIKRNETEKL HLMFSLMDKV PNGIEPMLKD LEEHIIS UniProtKB: Cullin-5 |
-Macromolecule #6: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.15 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 165000 |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 14725 / Average exposure time: 3.5 sec. / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |