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Yorodumi- EMDB-10739: Structure of the native full-length HIV-1 capsid protein in compl... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10739 | |||||||||
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Title | Structure of the native full-length HIV-1 capsid protein in complex with Cyclophilin A from helical assembly (-13,8) | |||||||||
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Sample |
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Function / homology | Function and homology information host cellular component / Synthesis And Processing Of GAG, GAGPOL Polyproteins / host cell nuclear membrane / negative regulation of protein K48-linked ubiquitination / negative regulation of viral life cycle / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication ...host cellular component / Synthesis And Processing Of GAG, GAGPOL Polyproteins / host cell nuclear membrane / negative regulation of protein K48-linked ubiquitination / negative regulation of viral life cycle / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication / leukocyte chemotaxis / negative regulation of stress-activated MAPK cascade / endothelial cell activation / virion binding / Basigin interactions / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / cyclosporin A binding / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / viral budding via host ESCRT complex / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Calcineurin activates NFAT / viral release from host cell / positive regulation of viral genome replication / Binding and entry of HIV virion / protein peptidyl-prolyl isomerization / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of protein dephosphorylation / Membrane binding and targetting of GAG proteins / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / activation of protein kinase B activity / neutrophil chemotaxis / negative regulation of protein phosphorylation / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / positive regulation of protein secretion / Assembly Of The HIV Virion / negative regulation of protein kinase activity / HIV-1 retropepsin / : / Budding and maturation of HIV virion / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / neuron differentiation / platelet aggregation / platelet activation / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / SARS-CoV-1 activates/modulates innate immune responses / RNA-directed DNA polymerase activity / unfolded protein binding / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / integrin binding / protein folding / Platelet degranulation / cellular response to oxidative stress / positive regulation of NF-kappaB transcription factor activity / viral nucleocapsid / secretory granule lumen / DNA recombination / vesicle / ficolin-1-rich granule lumen / positive regulation of MAPK cascade / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / positive regulation of protein phosphorylation / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / focal adhesion / lipid binding / apoptotic process / host cell nucleus / Neutrophil degranulation / structural molecule activity / host cell plasma membrane / virion membrane / protein-containing complex / proteolysis / DNA binding / extracellular space / RNA binding / extracellular exosome / zinc ion binding / extracellular region / membrane Similarity search - Function | |||||||||
Biological species | Human immunodeficiency virus 1 / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||
Authors | Ni T / Gerard S / Zhao G / Ning J / Zhang P | |||||||||
Funding support | United Kingdom, United States, 2 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2020 Title: Intrinsic curvature of the HIV-1 CA hexamer underlies capsid topology and interaction with cyclophilin A. Authors: Tao Ni / Samuel Gerard / Gongpu Zhao / Kyle Dent / Jiying Ning / Jing Zhou / Jiong Shi / Jordan Anderson-Daniels / Wen Li / Sooin Jang / Alan N Engelman / Christopher Aiken / Peijun Zhang / Abstract: The mature retrovirus capsid consists of a variably curved lattice of capsid protein (CA) hexamers and pentamers. High-resolution structures of the curved assembly, or in complex with host factors, ...The mature retrovirus capsid consists of a variably curved lattice of capsid protein (CA) hexamers and pentamers. High-resolution structures of the curved assembly, or in complex with host factors, have not been available. By devising cryo-EM methodologies for exceedingly flexible and pleomorphic assemblies, we have determined cryo-EM structures of apo-CA hexamers and in complex with cyclophilin A (CypA) at near-atomic resolutions. The CA hexamers are intrinsically curved, flexible and asymmetric, revealing the capsomere and not the previously touted dimer or trimer interfaces as the key contributor to capsid curvature. CypA recognizes specific geometries of the curved lattice, simultaneously interacting with three CA protomers from adjacent hexamers via two noncanonical interfaces, thus stabilizing the capsid. By determining multiple structures from various helical symmetries, we further revealed the essential plasticity of the CA molecule, which allows formation of continuously curved conical capsids and the mechanism of capsid pattern sensing by CypA. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10739.map.gz | 3.9 MB | EMDB map data format | |
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Header (meta data) | emd-10739-v30.xml emd-10739.xml | 19.3 KB 19.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10739_fsc.xml | 5.2 KB | Display | FSC data file |
Images | emd_10739.png | 70.1 KB | ||
Masks | emd_10739_msk_1.map | 11.4 MB | Mask map | |
Others | emd_10739_half_map_1.map.gz emd_10739_half_map_2.map.gz | 9.9 MB 9.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10739 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10739 | HTTPS FTP |
-Related structure data
Related structure data | 6y9wMC 6skkC 6skmC 6sknC 6slqC 6sluC 6smuC 6y9vC 6y9xC 6y9yC 6y9zC 6yj5C 6zdjC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_10739.map.gz / Format: CCP4 / Size: 11.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_10739_msk_1.map | ||||||||||||
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Density Histograms |
-Half map: #1
File | emd_10739_half_map_1.map | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_10739_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : In vitro assembled HIV-1 capsid in tubular assembly
Entire | Name: In vitro assembled HIV-1 capsid in tubular assembly |
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Components |
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-Supramolecule #1: In vitro assembled HIV-1 capsid in tubular assembly
Supramolecule | Name: In vitro assembled HIV-1 capsid in tubular assembly / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #2: HIV-1 capsid
Supramolecule | Name: HIV-1 capsid / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Human immunodeficiency virus 1 |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Supramolecule #3: Cyclophilin A
Supramolecule | Name: Cyclophilin A / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: Gag-Pol polyprotein
Macromolecule | Name: Gag-Pol polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO / EC number: HIV-1 retropepsin |
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Source (natural) | Organism: Human immunodeficiency virus 1 |
Molecular weight | Theoretical: 24.531094 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: PIVQNIQGQM VHQAISPRTL NAWVKVVEEK AFSPEVIPMF SALSEGATPQ DLNTMLNTVG GHQAAMQMLK ETINEEAAEW DRVHPVHAG PIAPGQMREP RGSDIAGTTS TLQEQIGWMT NNPPIPVGEI YKRWIILGLN KIVRMYSPTS ILDIRQGPKE P FRDYVDRF ...String: PIVQNIQGQM VHQAISPRTL NAWVKVVEEK AFSPEVIPMF SALSEGATPQ DLNTMLNTVG GHQAAMQMLK ETINEEAAEW DRVHPVHAG PIAPGQMREP RGSDIAGTTS TLQEQIGWMT NNPPIPVGEI YKRWIILGLN KIVRMYSPTS ILDIRQGPKE P FRDYVDRF YKTLRAEQAS QEVKNWMTET LLVQNANPDC KTILKALGPA ATLEEMMTAC QG |
-Macromolecule #2: Peptidyl-prolyl cis-trans isomerase A
Macromolecule | Name: Peptidyl-prolyl cis-trans isomerase A / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: peptidylprolyl isomerase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 17.905307 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: VNPTVFFDIA VDGEPLGRVS FELFADKVPK TAENFRALST GEKGFGYKGS CFHRIIPGFM CQGGDFTRHN GTGGKSIYGE KFEDENFIL KHTGPGILSM ANAGPNTNGS QFFICTAKTE WLDGKHVVFG KVKEGMNIVE AMERFGSRNG KTSKKITIAD C GQLE |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | helical array |
-Sample preparation
Concentration | 2 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Quantifoil R2/1 / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE |
Details | Purified capsid protein were assembled in the presence of Cyclophilin A. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 6500 / Average electron dose: 40.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |