[English] 日本語
Yorodumi
- EMDB-3076: Cyclophilin A Stabilize HIV-1 Capsid through a Novel Non-canonica... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 3076
TitleCyclophilin A Stabilize HIV-1 Capsid through a Novel Non-canonical Binding Site
Map dataReconstruction by aligning both CA and Cypa
SampleHelical assembly of HIV-1 capsid protein and host cell factor Cyclophilin A
  • Human immunodeficiency virus 1Subtypes of HIV
Function / homologyIntegration of provirus / Plus-strand DNA synthesis / Retroviral matrix protein / Zinc knuckle / Zinc finger, CCHC-type superfamily / Binding and entry of HIV virion / 2-LTR circle formation / Early Phase of HIV Life Cycle / Cyclophilin-like domain superfamily / Cyclophilin-type peptidyl-prolyl cis-trans isomerase ...Integration of provirus / Plus-strand DNA synthesis / Retroviral matrix protein / Zinc knuckle / Zinc finger, CCHC-type superfamily / Binding and entry of HIV virion / 2-LTR circle formation / Early Phase of HIV Life Cycle / Cyclophilin-like domain superfamily / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Minus-strand DNA synthesis / gag gene protein p17 (matrix protein) / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Gag protein p6 / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Immunodeficiency lentiviral matrix, N-terminal / Retroviral nucleocapsid protein Gag / Zinc finger, CCHC-type / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Retrovirus capsid, C-terminal / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Membrane binding and targetting of GAG proteins / Synthesis And Processing Of GAG, GAGPOL Polyproteins / gag gene protein p24 (core nucleocapsid protein) / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / Budding and maturation of HIV virion / Neutrophil degranulation / Basigin interactions / Calcineurin activates NFAT / Vpr-mediated nuclear import of PICs / APOBEC3G mediated resistance to HIV-1 infection / Autointegration results in viral DNA circles / Uncoating of the HIV Virion / Integration of viral DNA into host genomic DNA / Retrovirus capsid, N-terminal / Platelet degranulation / Assembly Of The HIV Virion / Zinc finger CCHC-type profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Gag protein p6 / lipid particle organization / regulation of viral genome replication / virion binding / cyclosporin A binding / nuclear transport / viral budding via host ESCRT complex / protein peptidyl-prolyl isomerization / RNA-dependent DNA biosynthetic process / positive regulation of viral genome replication / uncoating of virus / positive regulation of protein secretion / entry into host cell / intracellular transport of virus / peptidylprolyl isomerase / interleukin-12-mediated signaling pathway / peptidyl-prolyl cis-trans isomerase activity / viral protein processing / viral release from host cell / viral life cycle / virion assembly / host multivesicular body / protein folding / unfolded protein binding / leukocyte migration / fusion of virus membrane with host plasma membrane / establishment of integrated proviral latency / vesicle / secretory granule lumen / viral nucleocapsid / ficolin-1-rich granule lumen / host cell nucleus / host cell plasma membrane / virion membrane / focal adhesion / structural molecule activity / neutrophil degranulation / protein-containing complex / RNA binding / zinc ion binding / membrane / extracellular space / extracellular exosome / extracellular region / nucleus / cytosol / Gag polyprotein / Gag polyprotein / Peptidyl-prolyl cis-trans isomerase A
Function and homology information
SourceHuman immunodeficiency virus 1
Methodhelical reconstruction / cryo EM / 8 Å resolution
AuthorsLiu 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 / Peter E Prevelige / Itay Rousso / Christopher Aiken / Tatyana Polenova / Klaus Schulten / Peijun Zhang
Validation ReportPDB-ID: 5fjb

SummaryFull reportAbout validation report
DateDeposition: Jul 5, 2015 / Header (metadata) release: Jul 29, 2015 / Map release: Mar 16, 2016 / Last update: Apr 6, 2016

-
Structure visualization

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

Downloads & links

-
Map

Fileemd_3076.map.gz (map file in CCP4 format, 193068 KB)
Projections & slices

Image control

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

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density
Contour Level:20 (by author), 15 (movie #1):
Minimum - Maximum-44.91537476 - 57.38076782
Average (Standard dev.)0.24355465 (11.38533211)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions436436260
Origin000
Limit435435259
Spacing436436260
CellA: 462.15997 Å / B: 462.15997 Å / C: 275.59998 Å
α=β=γ: 90 deg.

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
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS436436260
D min/max/mean-44.91557.3810.244

-
Supplemental data

-
Sample components

-
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
Number of components: 1 / Oligomeric State: hexamer
MassTheoretical: 42 kDa / Experimental: 42 kDa

-
Component #1: protein, Human immunodeficiency virus 1

ProteinName: Human immunodeficiency virus 1Subtypes of HIV / a.k.a: HIV-1 capsid protein with CypA / Oligomeric Details: Hexamer / Recombinant expression: Yes
MassTheoretical: 42 kDa / Experimental: 42 kDa
SourceSpecies: Human immunodeficiency virus 1
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: helical array / Method: cryo EM
Helical parametersAxial symmetry: C1 (asymmetric) / Hand: LEFT HANDED / Delta z: 7.393 Å / Delta phi: 138.133 deg.
Sample solutionSpecimen conc.: 2 mg/ml / Buffer solution: 1m NaCl,50mM Tris-Hcl / pH: 8
Support filmGlow discharged perforated Quantifoil R2/1 grid
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 120 K / Humidity: 100 %
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.

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20 / Date: Jun 20, 2013
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 15 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 59000 X (nominal) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 3500 nm
Specimen HolderHolder: side entry / Model: GATAN LIQUID NITROGEN
CameraDetector: KODAK SO-163 FILM

-
Image acquisition

Image acquisitionNumber of digital images: 19 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 6.349 microns / Bit depth: 32

-
Image processing

ProcessingMethod: helical reconstruction / Details: The particles were aligned using IHRSR
3D reconstructionSoftware: SPIDER, IHRSR / CTF correction: Each particle / Resolution: 8 Å / Resolution method: FSC 0.5, gold-standard

-
Atomic model buiding

Modeling #1Software: Chimera / Refinement protocol: rigid body / Refinement space: REAL
Input PDB model: 3J4F
Modeling #2Software: Chimera / Refinement protocol: rigid body / Refinement space: REAL
Input PDB model: 1AK4
Output model

+
About Yorodumi

-
News

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more