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- PDB-3j34: Structure of HIV-1 Capsid Protein by Cryo-EM -

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Basic information

Entry
Database: PDB / ID: 3j34
TitleStructure of HIV-1 Capsid Protein by Cryo-EM
Componentscapsid protein
KeywordsVIRAL PROTEIN / HIV-1 capsid / core / all-atom model / MDFF / tubular assembly / hexamer
Function / homology
Function and homology information


viral budding via host ESCRT complex / viral nucleocapsid / host cell cytoplasm / viral translational frameshifting / host cell nucleus / structural molecule activity / virion membrane / RNA binding / zinc ion binding / identical protein binding / cytoplasm
Similarity search - Function
Gag protein p6 / Gag protein p6 / : / 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 ...Gag protein p6 / Gag protein p6 / : / 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 finger / 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: 8.6 Å
AuthorsZhao, G. / Perilla, J.R. / Yufenyuy, E. / Meng, X. / Chen, B. / Ning, J. / Ahn, J. / Gronenborn, A.M. / Schulten, K. / Aiken, C. / Zhang, P.
CitationJournal: Nature / Year: 2013
Title: Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics.
Authors: Gongpu Zhao / Juan R Perilla / Ernest L Yufenyuy / Xin Meng / Bo Chen / Jiying Ning / Jinwoo Ahn / Angela M Gronenborn / Klaus Schulten / Christopher Aiken / Peijun Zhang /
Abstract: Retroviral capsid proteins are conserved structurally but assemble into different morphologies. The mature human immunodeficiency virus-1 (HIV-1) capsid is best described by a 'fullerene cone' model, ...Retroviral capsid proteins are conserved structurally but assemble into different morphologies. The mature human immunodeficiency virus-1 (HIV-1) capsid is best described by a 'fullerene cone' model, in which hexamers of the capsid protein are linked to form a hexagonal surface lattice that is closed by incorporating 12 capsid-protein pentamers. HIV-1 capsid protein contains an amino-terminal domain (NTD) comprising seven α-helices and a β-hairpin, a carboxy-terminal domain (CTD) comprising four α-helices, and a flexible linker with a 310-helix connecting the two structural domains. Structures of the capsid-protein assembly units have been determined by X-ray crystallography; however, structural information regarding the assembled capsid and the contacts between the assembly units is incomplete. Here we report the cryo-electron microscopy structure of a tubular HIV-1 capsid-protein assembly at 8 Å resolution and the three-dimensional structure of a native HIV-1 core by cryo-electron tomography. The structure of the tubular assembly shows, at the three-fold interface, a three-helix bundle with critical hydrophobic interactions. Mutagenesis studies confirm that hydrophobic residues in the centre of the three-helix bundle are crucial for capsid assembly and stability, and for viral infectivity. The cryo-electron-microscopy structures enable modelling by large-scale molecular dynamics simulation, resulting in all-atom models for the hexamer-of-hexamer and pentamer-of-hexamer elements as well as for the entire capsid. Incorporation of pentamers results in closer trimer contacts and induces acute surface curvature. The complete atomic HIV-1 capsid model provides a platform for further studies of capsid function and for targeted pharmacological intervention.
History
DepositionFeb 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Database references
Revision 1.2Jun 19, 2013Group: Refinement description
Revision 1.3Jul 18, 2018Group: Author supporting evidence / Data collection / Category: em_single_particle_entity / em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.4Oct 30, 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 / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: capsid protein
B: capsid protein
C: capsid protein
D: capsid protein
E: capsid protein
F: capsid protein
G: capsid protein
H: capsid protein
I: capsid protein
J: capsid protein
K: capsid protein
L: capsid protein
M: capsid protein
N: capsid protein
O: capsid protein
P: capsid protein
Q: capsid protein
R: capsid protein
S: capsid protein
T: capsid protein
U: capsid protein
V: capsid protein
W: capsid protein
X: capsid protein
Y: capsid protein
Z: capsid protein
5: capsid protein
a: capsid protein
b: capsid protein
c: capsid protein
6: capsid protein
i: capsid protein
j: capsid protein
k: capsid protein
l: capsid protein
m: capsid protein
7: capsid protein
d: capsid protein
e: capsid protein
f: capsid protein
g: capsid protein
h: capsid protein


Theoretical massNumber of molelcules
Total (without water)1,079,50542
Polymers1,079,50542
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
capsid protein


Mass: 25702.490 Da / Num. of mol.: 42 / Fragment: UNP residues 133-363 / Mutation: A92E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: Q79791
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 capsid protein / Type: COMPLEX / Details: hexamer
Molecular weightValue: 0.025 MDa / Experimental value: NO
Buffer solutionName: 1 M NaCl, 50 mM Tris-HCl / pH: 8 / Details: 1 M NaCl, 50 mM Tris-HCl
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 200 mesh quantifoil R2/1 copper grid
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temp: 110 K / Humidity: 80 %
Details: 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 and plunge into liquid ethane with a 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 imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300 / Date: Dec 11, 2010
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 59000 X / Calibrated magnification: 58257 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm / Cs: 2 mm / Camera length: 0 mm
Specimen holderSpecimen holder model: OTHER / Specimen holder type: Polara cartridge / Temperature: 82 K / Temperature (max): 85 K / Temperature (min): 80 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 27

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Processing

EM software
IDNameCategory
1MDFFmodel fitting
2FREALIGN3D reconstruction
CTF correctionDetails: each filament
Helical symmertyAngular rotation/subunit: 31.13 ° / Axial rise/subunit: 7.247 Å / Axial symmetry: C1
3D reconstructionMethod: real space helical reconstruction / Resolution: 8.6 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 3210 / Actual pixel size: 1.09 Å
Details: (Helical Details: The segments were aligned and reconstructed using Frealign. Twofold symmetry was imposed using IHRSR++.)
Symmetry type: HELICAL
Atomic model building
IDProtocolSpaceDetails
1FLEXIBLE FITREALMETHOD--The MDFF-derived HOH structure was equilibrated in 1 M NaCl FOR 425 ns using MD without applying restraints. PDB entries 3H47 AND 2KOD were the starting structures. REFINEMENT PROTOCOL--flexible
2FLEXIBLE FITREALMETHOD--The MDFF-derived HOH structure was equilibrated in 1 M NaCl FOR 425 ns using MD without applying restraints. PDB entries 3H47 AND 2KOD were the starting structures. REFINEMENT PROTOCOL--flexible
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
13H47

3h47

13H471PDBexperimental model
22KOD

2kod

22KOD2PDBexperimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms75600 0 0 0 75600

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