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- EMDB-3075: Cyclophilin A Stabilizes HIV-1 Capsid through a Novel Non-canonic... -

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Basic information

Entry
Database: EMDB / ID: EMD-3075
TitleCyclophilin A Stabilizes HIV-1 Capsid through a Novel Non-canonical Binding Site
Map dataReconstruction of HIV-1 capsid with Cypa
Sample
  • Sample: Helical assembly of HIV-1 capsid protein and host cell factor Cyclophilin A
  • Protein or peptide: Human immunodeficiency virus 1
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 releaseAug 24, 2016-
UpdateSep 28, 2016-
Current statusSep 28, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 18
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 18
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 18
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMDB_3075.png

Downloads & links

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Map

FileDownload / File: emd_3075.map.gz / Format: CCP4 / Size: 184.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of HIV-1 capsid with 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: 18.0 / Movie #1: 18
Minimum - Maximum-38.070182799999998 - 44.688278199999999
Average (Standard dev.)0.33252865 (±9.44302177)
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
start NX/NY/NZ-147-147-146
NX/NY/NZ294294294
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS436436260
D min/max/mean-38.07044.6880.333

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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, 50 mM 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 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

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Atomic model buiding 2

Initial modelPDB ID:

1ak4

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

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