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

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Basic information

Entry
Database: PDB / ID: 5up4
TitleStructure of the HIV-1 Capsid Protein and spacer peptide 1 by Cryo-EM
ComponentsHIV-1 Capsid Protein and spacer peptide 1
KeywordsVIRUS / HIV-1 / spacer peptide 1 / capsid protein / cryoEM / Helical assembly / reconstruction
Function / homology
Function and homology information


viral nucleocapsid / host cell cytoplasm / viral translational frameshifting / host cell nucleus / virion membrane / structural molecule activity / RNA binding / zinc ion binding / ATP binding
Similarity search - Function
: / 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 ...: / 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 knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus 1
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 9 Å
AuthorsPerilla, J.R. / Schirra, R. / Zhang, P. / Schulten, K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of HealthP50 GM082251 United States
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, 2017Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Refinement description / Category: em_3d_fitting_list
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
B: HIV-1 Capsid Protein and spacer peptide 1
K: HIV-1 Capsid Protein and spacer peptide 1
L: HIV-1 Capsid Protein and spacer peptide 1
M: HIV-1 Capsid Protein and spacer peptide 1
N: HIV-1 Capsid Protein and spacer peptide 1
O: HIV-1 Capsid Protein and spacer peptide 1
P: HIV-1 Capsid Protein and spacer peptide 1
Q: HIV-1 Capsid Protein and spacer peptide 1
R: HIV-1 Capsid Protein and spacer peptide 1
S: HIV-1 Capsid Protein and spacer peptide 1
C: HIV-1 Capsid Protein and spacer peptide 1
D: HIV-1 Capsid Protein and spacer peptide 1
E: HIV-1 Capsid Protein and spacer peptide 1
F: HIV-1 Capsid Protein and spacer peptide 1
G: HIV-1 Capsid Protein and spacer peptide 1
H: HIV-1 Capsid Protein and spacer peptide 1
I: HIV-1 Capsid Protein and spacer peptide 1
J: HIV-1 Capsid Protein and spacer peptide 1


Theoretical massNumber of molelcules
Total (without water)443,77718
Polymers443,77718
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area43710 Å2
ΔGint-293 kcal/mol
Surface area196060 Å2
MethodPISA

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Components

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


Mass: 24654.268 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag / Production host: Escherichia coli (E. coli) / References: UniProt: B6DRA0
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: HIV-1 CA-SP1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Human immunodeficiency virus 1
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
11 Msodium chlorideNaCl1
250 mM2-Amino-2-(hydroxymethyl)propane-1,3-diolTRIS1
SpecimenConc.: 2.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 59000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 23 e/Å2 / Film or detector model: KODAK SO-163 FILM / Num. of real images: 200

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Processing

EM software
IDNameVersionCategory
1EMANparticle selection
4CTFFIND3CTF correction
7MDFFmodel fitting
13FREALIGN3D reconstruction
14NAMDmodel fitting
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 128.88 ° / Axial rise/subunit: 13.46 Å / Axial symmetry: C1
3D reconstructionResolution: 9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14000 / Symmetry type: HELICAL
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeInitial refinement model-IDPdb chain residue range
13J34

3j34

A3J3411-220
22KOD

2kod

A2KOD2221-231
33J34

3j34

B3J3411-220
43J34

3j34

C3J3411-220
53J34

3j34

D3J3411-220
63J34

3j34

E3J3411-220
73J34

3j34

F3J3411-220

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