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- EMDB-3076: Cyclophilin A Stabilize HIV-1 Capsid through a Novel Non-canonica... -

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Basic information

Entry
Database: EMDB / ID: EMD-3076
TitleCyclophilin A Stabilize HIV-1 Capsid through a Novel Non-canonical Binding Site
Map dataReconstruction by aligning both CA and Cypa
Sample
  • Sample: Helical assembly of HIV-1 capsid protein and host cell factor Cyclophilin A
  • Protein or peptide: Human immunodeficiency virus 1
Function / homology
Function and homology information


Synthesis And Processing Of GAG, GAGPOL Polyproteins / host cellular component / host cell nuclear membrane / negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / negative regulation of viral life cycle / heparan sulfate binding / regulation of viral genome replication ...Synthesis And Processing Of GAG, GAGPOL Polyproteins / host cellular component / host cell nuclear membrane / negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / negative regulation of viral life cycle / heparan sulfate binding / regulation of viral genome replication / leukocyte chemotaxis / virion binding / negative regulation of stress-activated MAPK cascade / endothelial cell activation / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Basigin interactions / protein peptidyl-prolyl isomerization / 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 / negative regulation of protein phosphorylation / APOBEC3G mediated resistance to HIV-1 infection / viral release from host cell / Calcineurin activates NFAT / activation of protein kinase B activity / Binding and entry of HIV virion / positive regulation of viral genome replication / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of protein kinase activity / neutrophil chemotaxis / Membrane binding and targetting of GAG proteins / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / positive regulation of protein secretion / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / Assembly Of The HIV Virion / positive regulation of NF-kappaB transcription factor activity / Budding and maturation of HIV virion / platelet activation / host multivesicular body / platelet aggregation / integrin binding / positive regulation of protein phosphorylation / neuron differentiation / SARS-CoV-1 activates/modulates innate immune responses / unfolded protein binding / Platelet degranulation / protein folding / viral nucleocapsid / cellular response to oxidative stress / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / positive regulation of MAPK cascade / viral translational frameshifting / focal adhesion / apoptotic process / Neutrophil degranulation / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / protein-containing complex / extracellular space / RNA binding / extracellular exosome / extracellular region / zinc ion binding / identical protein binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Gag protein p6 / Gag protein p6 / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / : / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily ...Gag protein p6 / Gag protein p6 / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / : / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
Gag polyprotein / Gag polyprotein / Peptidyl-prolyl cis-trans isomerase A
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Methodhelical reconstruction / cryo EM / Resolution: 8.0 Å
AuthorsLiu C / Perilla JR / Ning J / Lu M / Hou G / Ramalhu R / Bedwell GJ / Ahn J / Shi J / Gronenborn AM ...Liu C / Perilla JR / Ning J / Lu M / Hou G / Ramalhu R / Bedwell GJ / Ahn J / Shi J / Gronenborn AM / Prevelige Jr PE / Rousso I / Aiken C / Polenova T / Schulten K / Zhang P
CitationJournal: Nat Commun / Year: 2016
Title: Cyclophilin A stabilizes the HIV-1 capsid through a novel non-canonical binding site.
Authors: Chuang Liu / Juan R Perilla / Jiying Ning / Manman Lu / Guangjin Hou / Ruben Ramalho / Benjamin A Himes / Gongpu Zhao / Gregory J Bedwell / In-Ja Byeon / Jinwoo Ahn / Angela M Gronenborn / ...Authors: Chuang Liu / Juan R Perilla / Jiying Ning / Manman Lu / Guangjin Hou / Ruben Ramalho / Benjamin A Himes / Gongpu Zhao / Gregory J Bedwell / In-Ja Byeon / Jinwoo Ahn / Angela M Gronenborn / Peter E Prevelige / Itay Rousso / Christopher Aiken / Tatyana Polenova / Klaus Schulten / Peijun Zhang /
Abstract: The host cell factor cyclophilin A (CypA) interacts directly with the HIV-1 capsid and regulates viral infectivity. Although the crystal structure of CypA in complex with the N-terminal domain of the ...The host cell factor cyclophilin A (CypA) interacts directly with the HIV-1 capsid and regulates viral infectivity. Although the crystal structure of CypA in complex with the N-terminal domain of the HIV-1 capsid protein (CA) has been known for nearly two decades, how CypA interacts with the viral capsid and modulates HIV-1 infectivity remains unclear. We determined the cryoEM structure of CypA in complex with the assembled HIV-1 capsid at 8-Å resolution. The structure exhibits a distinct CypA-binding pattern in which CypA selectively bridges the two CA hexamers along the direction of highest curvature. EM-guided all-atom molecular dynamics simulations and solid-state NMR further reveal that the CypA-binding pattern is achieved by single-CypA molecules simultaneously interacting with two CA subunits, in different hexamers, through a previously uncharacterized non-canonical interface. These results provide new insights into how CypA stabilizes the HIV-1 capsid and is recruited to facilitate HIV-1 infection.
History
DepositionJul 5, 2015-
Header (metadata) releaseJul 29, 2015-
Map releaseMar 16, 2016-
UpdateApr 6, 2016-
Current statusApr 6, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 15
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 15
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 15
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5fjb
  • Surface level: 15
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5fjb
  • Surface level: 15
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5fjb
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMDB_3076.png

Downloads & links

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Map

FileDownload / File: emd_3076.map.gz / Format: CCP4 / Size: 184.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction by aligning both CA and Cypa
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 260 pix.
= 275.6 Å		1.06 Å/pix.
x 436 pix.
= 462.16 Å		1.06 Å/pix.
x 436 pix.
= 462.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 20.0 / Movie #1: 15
Minimum - Maximum-44.915374759999999 - 57.380767820000003
Average (Standard dev.)0.24355465 (±11.38533211)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions436436260
Spacing436436260
CellA: 462.15997 Å / B: 462.15997 Å / C: 275.59998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z436436260
origin x/y/z0.0000.0000.000
length x/y/z462.160462.160275.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS436436260
D min/max/mean-44.91557.3810.244

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Supplemental data

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Sample components

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Entire : Helical assembly of HIV-1 capsid protein and host cell factor Cyc...

EntireName: Helical assembly of HIV-1 capsid protein and host cell factor Cyclophilin A
Components
  • Sample: Helical assembly of HIV-1 capsid protein and host cell factor Cyclophilin A
  • Protein or peptide: Human immunodeficiency virus 1

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Supramolecule #1000: Helical assembly of HIV-1 capsid protein and host cell factor Cyc...

SupramoleculeName: Helical assembly of HIV-1 capsid protein and host cell factor Cyclophilin A
type: sample / ID: 1000 / Oligomeric state: hexamer / Number unique components: 1
Molecular weightExperimental: 42 KDa / Theoretical: 42 KDa

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Macromolecule #1: Human immunodeficiency virus 1

MacromoleculeName: Human immunodeficiency virus 1 / type: protein_or_peptide / ID: 1 / Name.synonym: HIV-1 capsid protein with CypA / Oligomeric state: Hexamer / Recombinant expression: Yes
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightExperimental: 42 KDa / Theoretical: 42 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

Concentration2 mg/mL
BufferpH: 8 / Details: 1m NaCl,50mM Tris-Hcl
GridDetails: Glow discharged perforated Quantifoil R2/1 grid
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 120 K / Instrument: HOMEMADE PLUNGER
Method: With 2.5 uL sample on carbon side, add 3 uL dilution buffer (100 mM NaCl,50mM Tris,PH 8.0)to back side. Blot 3-5 seconds from back side.

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Electron microscopy

MicroscopeFEI TECNAI F20
DateJun 20, 2013
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.349 µm / Number real images: 19 / Average electron dose: 15 e/Å2 / Bits/pixel: 32
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 59000
Sample stageSpecimen holder: side entry / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

DetailsThe particles were aligned using IHRSR
Final reconstructionApplied symmetry - Helical parameters - Δz: 7.393 Å
Applied symmetry - Helical parameters - Δ&Phi: 138.133 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 8.0 Å / Resolution method: OTHER / Software - Name: SPIDER, IHRSR
CTF correctionDetails: Each particle

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Atomic model buiding 1

Initial modelPDB ID:

3j4f

SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-5fjb:
Cyclophilin A Stabilize HIV-1 Capsid through a Novel Non- canonical Binding Site

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Atomic model buiding 2

Initial modelPDB ID:

1ak4

SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-5fjb:
Cyclophilin A Stabilize HIV-1 Capsid through a Novel Non- canonical Binding Site

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