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- PDB-4coc: HIV-1 capsid C-terminal domain mutant (Y169L) -

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Basic information

Entry
Database: PDB / ID: 4coc
TitleHIV-1 capsid C-terminal domain mutant (Y169L)
ComponentsCAPSID PROTEIN P24
KeywordsVIRAL PROTEIN / VIRUS ASSEMBLY / HELICAL RECONSTRUCTION
Function / homology
Function and homology information


HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane
Similarity search - Function
Retrovirus capsid C-terminal domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain ...Retrovirus capsid C-terminal domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / 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. / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHUMAN IMMUNODEFICIENCY VIRUS 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsBharat, T.A.M. / Castillo-Menendez, L.R. / Hagen, W.J.H. / Lux, V. / Igonet, S. / Schorb, M. / Schur, F.K.M. / Krausslich, H.-G. / Briggs, J.A.G.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2014
Title: Cryo-electron microscopy of tubular arrays of HIV-1 Gag resolves structures essential for immature virus assembly.
Authors: Tanmay A M Bharat / Luis R Castillo Menendez / Wim J H Hagen / Vanda Lux / Sebastien Igonet / Martin Schorb / Florian K M Schur / Hans-Georg Kräusslich / John A G Briggs /
Abstract: The assembly of HIV-1 is mediated by oligomerization of the major structural polyprotein, Gag, into a hexameric protein lattice at the plasma membrane of the infected cell. This leads to budding and ...The assembly of HIV-1 is mediated by oligomerization of the major structural polyprotein, Gag, into a hexameric protein lattice at the plasma membrane of the infected cell. This leads to budding and release of progeny immature virus particles. Subsequent proteolytic cleavage of Gag triggers rearrangement of the particles to form mature infectious virions. Obtaining a structural model of the assembled lattice of Gag within immature virus particles is necessary to understand the interactions that mediate assembly of HIV-1 particles in the infected cell, and to describe the substrate that is subsequently cleaved by the viral protease. An 8-Å resolution structure of an immature virus-like tubular array assembled from a Gag-derived protein of the related retrovirus Mason-Pfizer monkey virus (M-PMV) has previously been reported, and a model for the arrangement of the HIV-1 capsid (CA) domains has been generated based on homology to this structure. Here we have assembled tubular arrays of a HIV-1 Gag-derived protein with an immature-like arrangement of the C-terminal CA domains and have solved their structure by using hybrid cryo-EM and tomography analysis. The structure reveals the arrangement of the C-terminal domain of CA within an immature-like HIV-1 Gag lattice, and provides, to our knowledge, the first high-resolution view of the region immediately downstream of CA, which is essential for assembly, and is significantly different from the respective region in M-PMV. Our results reveal a hollow column of density for this region in HIV-1 that is compatible with the presence of a six-helix bundle at this position.
History
DepositionJan 28, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CAPSID PROTEIN P24
B: CAPSID PROTEIN P24
C: CAPSID PROTEIN P24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6355
Polymers28,4433
Non-polymers1922
Water3,135174
1
A: CAPSID PROTEIN P24
hetero molecules

A: CAPSID PROTEIN P24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1544
Polymers18,9622
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1390 Å2
ΔGint-27.9 kcal/mol
Surface area8780 Å2
MethodPISA
2
B: CAPSID PROTEIN P24


Theoretical massNumber of molelcules
Total (without water)9,4811
Polymers9,4811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: CAPSID PROTEIN P24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5772
Polymers9,4811
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.480, 33.760, 77.730
Angle α, β, γ (deg.)90.00, 108.32, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CAPSID PROTEIN P24 / / GAG POLYPROTEIN


Mass: 9480.904 Da / Num. of mol.: 3 / Fragment: C-TERMINAL DOMAIN, RESIDUES 278-363 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS 1 / Strain: NL4-3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS-RIL / References: UniProt: P12497
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.28 % / Description: NONE
Crystal growpH: 8.5 / Details: 30% PEG 4000, 0.2 M LISO4, 0.1 M TRIS PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
Details: ONE PAIR OF (300X40X15) MM3 LONG PT COATED SI MIRROR, 260MM USABLE, IN A KIRKPATRICK-BAEZ GEOMETRY
RadiationMonochromator: HORIZONTALLY SIDE DIFFRACTING SILICON 111 CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.59→47.42 Å / Num. obs: 33062 / % possible obs: 97.9 % / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.1
Reflection shellResolution: 1.59→1.68 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2 / % possible all: 77.8

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Processing

Software
NameVersionClassification
REFMAC5.4.0073refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BUO

2buo


Resolution: 1.59→47.42 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.682 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES HAVE BEEN REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22323 1675 5.1 %RANDOM
Rwork0.18656 ---
obs0.1884 31387 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.288 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20 Å2-0.34 Å2
2---0.39 Å20 Å2
3---0.75 Å2
Refinement stepCycle: LAST / Resolution: 1.59→47.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1775 0 10 174 1959
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0330.0221826
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.6421.9892468
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg18.1015227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.5362580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.57715342
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4641514
X-RAY DIFFRACTIONr_chiral_restr0.1990.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0211346
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8661.51147
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.19621852
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.4253679
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.3074.5616
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.59→1.631 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 99 -
Rwork0.248 1833 -
obs--77.75 %

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