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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
TitleStructure of the native full-length HIV-1 capsid protein in complex with Cyclophilin A from helical assembly (-13,10)
Map data
Sample
  • Complex: In vitro assembled HIV-1 capsid in tubular assembly
    • Complex: HIV-1 capsid
      • Protein or peptide: Gag protein
    • Complex: Cyclophilin A
      • Protein or peptide: Peptidyl-prolyl cis-trans isomerase A
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 / negative regulation of viral life cycle / lipid droplet organization / 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 / negative regulation of viral life cycle / 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 / Early Phase of HIV Life Cycle / Vpr-mediated nuclear import of PICs / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / viral release from host cell / protein peptidyl-prolyl isomerization / Calcineurin activates NFAT / Binding and entry of HIV virion / viral process / positive regulation of viral genome replication / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / : / Membrane binding and targetting of GAG proteins / 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 / positive regulation of protein secretion / peptidyl-prolyl cis-trans isomerase activity / negative regulation of protein kinase activity / Assembly Of The HIV Virion / Budding and maturation of HIV virion / neuron differentiation / host multivesicular body / platelet activation / platelet aggregation / SARS-CoV-1 activates/modulates innate immune responses / unfolded protein binding / integrin binding / protein folding / Platelet degranulation / viral capsid / 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 / viral translational frameshifting / 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
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 / Retroviral matrix protein / Retrovirus capsid, C-terminal / 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 / Peptidyl-prolyl cis-trans isomerase A / Gag protein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.8 Å
AuthorsNi T / Gerard S / Zhao G / Ning J / Zhang P
Funding support United Kingdom, United States, 2 items
OrganizationGrant numberCountry
Wellcome Trust206422/Z/17/Z United Kingdom
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P50AI150481 United States
CitationJournal: 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
DepositionJun 14, 2020-
Header (metadata) releaseAug 19, 2020-
Map releaseAug 19, 2020-
UpdateFeb 10, 2021-
Current statusFeb 10, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0089
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.0089
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6zdj
  • Surface level: 0.0089
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6zdj
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11176.png

Downloads & links

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Map

FileDownload / File: emd_11176.map.gz / Format: CCP4 / Size: 11.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 144 pix.
= 152.64 Å		1.06 Å/pix.
x 144 pix.
= 152.64 Å		1.06 Å/pix.
x 144 pix.
= 152.64 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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0089 / Movie #1: 0.0089
Minimum - Maximum-0.0078100595 - 0.031247204
Average (Standard dev.)0.0019731796 (±0.0039173006)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions144144144
Spacing144144144
CellA=B=C: 152.63998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z144144144
origin x/y/z0.0000.0000.000
length x/y/z152.640152.640152.640
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ280280280
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS144144144
D min/max/mean-0.0080.0310.002

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Supplemental data

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Half map: #1

Fileemd_11176_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_11176_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : In vitro assembled HIV-1 capsid in tubular assembly

EntireName: In vitro assembled HIV-1 capsid in tubular assembly
Components
  • Complex: In vitro assembled HIV-1 capsid in tubular assembly
    • Complex: HIV-1 capsid
      • Protein or peptide: Gag protein
    • Complex: Cyclophilin A
      • Protein or peptide: Peptidyl-prolyl cis-trans isomerase A

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Supramolecule #1: In vitro assembled HIV-1 capsid in tubular assembly

SupramoleculeName: 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

SupramoleculeName: HIV-1 capsid / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #3: Cyclophilin A

SupramoleculeName: Cyclophilin A / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: Gag protein

MacromoleculeName: Gag protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 24.531094 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #2: Peptidyl-prolyl cis-trans isomerase A

MacromoleculeName: Peptidyl-prolyl cis-trans isomerase A / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: peptidylprolyl isomerase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.905307 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
VNPTVFFDIA VDGEPLGRVS FELFADKVPK TAENFRALST GEKGFGYKGS CFHRIIPGFM CQGGDFTRHN GTGGKSIYGE KFEDENFIL KHTGPGILSM ANAGPNTNGS QFFICTAKTE WLDGKHVVFG KVKEGMNIVE AMERFGSRNG KTSKKITIAD C GQLE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statehelical array

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Sample preparation

Concentration2 mg/mL
BufferpH: 8
GridModel: Quantifoil R2/1 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE
DetailsPurified capsid protein were assembled in the presence of Cyclophilin A.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 6500 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: RELION (ver. 2.0; 3.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0; 3.0) / Number images used: 32305
Initial angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 2.0; 3.0)
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 2.0; 3.0)
Final 3D classificationNumber classes: 10 / Software - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4xfx


Chain - Chain ID: A
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient
Output model

PDB-6zdj:
Structure of the native full-length HIV-1 capsid protein in complex with Cyclophilin A from helical assembly (-13,10)

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