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- EMDB-8582: Structure of the HIV-1 Capsid Protein and spacer peptide 1 by Cryo-EM -

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Basic information

Entry
Database: EMDB / ID: EMD-8582
TitleStructure of the HIV-1 Capsid Protein and spacer peptide 1 by Cryo-EM
Map dataCryoEM structure of HIV-1 capsid protein and spacer peptide-1 (CA-SP1)
Sample
  • Complex: HIV-1 CA-SP1
    • Protein or peptide: HIV-1 Capsid Protein and spacer peptide 1
Function / homology
Function and homology information


viral process / viral nucleocapsid / host cell cytoplasm / structural molecule activity / virion membrane / RNA binding / zinc ion binding / cytoplasm
Similarity search - Function
gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / Zinc knuckle ...gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus 1
Methodhelical reconstruction / cryo EM / Resolution: 9.0 Å
AuthorsZhang P / Randall S
CitationJournal: Nat Commun / Year: 2017
Title: Quenching protein dynamics interferes with HIV capsid maturation.
Authors: Mingzhang Wang / Caitlin M Quinn / Juan R Perilla / Huilan Zhang / Randall Shirra / Guangjin Hou / In-Ja Byeon / Christopher L Suiter / Sherimay Ablan / Emiko Urano / Theodore J Nitz / ...Authors: Mingzhang Wang / Caitlin M Quinn / Juan R Perilla / Huilan Zhang / Randall Shirra / Guangjin Hou / In-Ja Byeon / Christopher L Suiter / Sherimay Ablan / Emiko Urano / Theodore J Nitz / Christopher Aiken / Eric O Freed / Peijun Zhang / Klaus Schulten / Angela M Gronenborn / Tatyana Polenova /
Abstract: Maturation of HIV-1 particles encompasses a complex morphological transformation of Gag via an orchestrated series of proteolytic cleavage events. A longstanding question concerns the structure of ...Maturation of HIV-1 particles encompasses a complex morphological transformation of Gag via an orchestrated series of proteolytic cleavage events. A longstanding question concerns the structure of the C-terminal region of CA and the peptide SP1 (CA-SP1), which represents an intermediate during maturation of the HIV-1 virus. By integrating NMR, cryo-EM, and molecular dynamics simulations, we show that in CA-SP1 tubes assembled in vitro, which represent the features of an intermediate assembly state during maturation, the SP1 peptide exists in a dynamic helix-coil equilibrium, and that the addition of the maturation inhibitors Bevirimat and DFH-055 causes stabilization of a helical form of SP1. Moreover, the maturation-arresting SP1 mutation T8I also induces helical structure in SP1 and further global dynamical and conformational changes in CA. Overall, our results show that dynamics of CA and SP1 are critical for orderly HIV-1 maturation and that small molecules can inhibit maturation by perturbing molecular motions.
History
DepositionFeb 1, 2017-
Header (metadata) releaseJul 12, 2017-
Map releaseDec 6, 2017-
UpdateDec 13, 2017-
Current statusDec 13, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.027
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.027
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5up4
  • Surface level: 0.027
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5up4
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8582.png

Downloads & links

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Map

FileDownload / File: emd_8582.map.gz / Format: CCP4 / Size: 465.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM structure of HIV-1 capsid protein and spacer peptide-1 (CA-SP1)
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy EMDB: 0.027 / Movie #1: 0.027
Minimum - Maximum-0.005759892 - 0.046030093
Average (Standard dev.)0.0023228726 (±0.006946994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions496496496
Spacing496496496
CellA=B=C: 545.60004 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z496496496
origin x/y/z0.0000.0000.000
length x/y/z545.600545.600545.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS496496496
D min/max/mean-0.0060.0460.002

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Supplemental data

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Sample components

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Entire : HIV-1 CA-SP1

EntireName: HIV-1 CA-SP1
Components
  • Complex: HIV-1 CA-SP1
    • Protein or peptide: HIV-1 Capsid Protein and spacer peptide 1

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Supramolecule #1: HIV-1 CA-SP1

SupramoleculeName: HIV-1 CA-SP1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: HIV-1 Capsid Protein and spacer peptide 1

MacromoleculeName: HIV-1 Capsid Protein and spacer peptide 1 / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 24.654268 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: PIVQNLQGQM VHQAISPRTL NAWVKVVEEK AFSPEVIPMF SALSEGATPQ DLNTMLNTVG GHQAAMQMLK ETINEEAAEW DRLHPVHAG PIAPGQMREP RGSDIAGTTS TLQEQIGWMT HNPPIPVGEI YKRWIILGLN KIVRMYSPTS ILDIRQGPKE P FRDYVDRF ...String:
PIVQNLQGQM VHQAISPRTL NAWVKVVEEK AFSPEVIPMF SALSEGATPQ DLNTMLNTVG GHQAAMQMLK ETINEEAAEW DRLHPVHAG PIAPGQMREP RGSDIAGTTS TLQEQIGWMT HNPPIPVGEI YKRWIILGLN KIVRMYSPTS ILDIRQGPKE P FRDYVDRF YKTLRAEQAS QEVKNWMTET LLVQNANPDC KTILKALGPG ATLEEMMTAC QGV

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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

Concentration2.2 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
1.0 MNaClSodium chloridesodium chloride
50.0 mMTRIS2-Amino-2-(hydroxymethyl)propane-1,3-diol
GridModel: Quantifoil / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 59000
Image recordingFilm or detector model: KODAK SO-163 FILM / Number real images: 200 / Average electron dose: 23.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 3)
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 13.46 Å
Applied symmetry - Helical parameters - Δ&Phi: 128.88 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN / Number images used: 14000
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

3j34

chain_id: A, residue_range: 1-220

2kod

chain_id: A, residue_range: 221-231

3j34

chain_id: B, residue_range: 1-220

3j34

chain_id: C, residue_range: 1-220

3j34

chain_id: D, residue_range: 1-220

3j34

chain_id: E, residue_range: 1-220

3j34

chain_id: F, residue_range: 1-220
Output model

PDB-5up4:
Structure of the HIV-1 Capsid Protein and spacer peptide 1 by Cryo-EM

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