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- EMDB-11176: Structure of the native full-length HIV-1 capsid protein in compl... -
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Basic information
Entry | Database: EMDB / ID: EMD-11176 | |||||||||
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Title | Structure of the native full-length HIV-1 capsid protein in complex with Cyclophilin A from helical assembly (-13,10) | |||||||||
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Function / homology | ![]() 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 / virion binding / leukocyte chemotaxis / endothelial cell activation / negative regulation of stress-activated MAPK cascade / 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 / 2-LTR circle formation / Uncoating of the HIV Virion / viral budding via host ESCRT complex / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / protein peptidyl-prolyl isomerization / Calcineurin activates NFAT / viral release from host cell / Binding and entry of HIV virion / positive regulation of viral genome replication / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / : / Membrane binding and targetting of GAG proteins / viral process / neutrophil chemotaxis / activation of protein kinase B activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / negative regulation of protein phosphorylation / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / positive regulation of protein secretion / negative regulation of protein kinase activity / Assembly Of The HIV Virion / Budding and maturation of HIV virion / neuron differentiation / platelet activation / platelet aggregation / host multivesicular body / SARS-CoV-1 activates/modulates innate immune responses / viral capsid / unfolded protein binding / integrin binding / protein folding / Platelet degranulation / positive regulation of NF-kappaB transcription factor activity / cellular response to oxidative stress / viral nucleocapsid / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / positive regulation of MAPK cascade / positive regulation of protein phosphorylation / focal adhesion / Neutrophil degranulation / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / protein-containing complex / RNA binding / extracellular space / extracellular exosome / zinc ion binding / extracellular region / identical protein binding / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.8 Å | |||||||||
![]() | Ni T / Gerard S / Zhao G / Ning J / Zhang P | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.2 KB 19.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 5.2 KB | Display | ![]() |
Images | ![]() | 84.8 KB | ||
Others | ![]() ![]() | 9.9 MB 9.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6zdjMC ![]() 6skkC ![]() 6skmC ![]() 6sknC ![]() 6slqC ![]() 6sluC ![]() 6smuC ![]() 6y9vC ![]() 6y9wC ![]() 6y9xC ![]() 6y9yC ![]() 6y9zC ![]() 6yj5C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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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: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #1
File | emd_11176_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_11176_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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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: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Supramolecule #3: Cyclophilin A
Supramolecule | Name: Cyclophilin A / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Macromolecule #1: Gag protein
Macromolecule | Name: Gag protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 24.531094 KDa |
Recombinant expression | Organism: ![]() ![]() |
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: ![]() |
Molecular weight | Theoretical: 17.905307 KDa |
Recombinant expression | Organism: ![]() ![]() |
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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![]() | single particle reconstruction |
Aggregation state | helical array |
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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. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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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 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |