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- PDB-4cop: HIV-1 capsid C-terminal domain mutant (Y169S) -

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Basic information

Entry
Database: PDB / ID: 4cop
TitleHIV-1 capsid C-terminal domain mutant (Y169S)
ComponentsCAPSID PROTEIN P24
KeywordsSTRUCTURAL PROTEIN / HUMAN IMMUNODEFICIENCY VIRUS / VIRUS ASSEMBLY / HELICAL RECONSTRUCTION / CAPSID
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / telomerase activity / viral penetration into host nucleus / RNA stem-loop binding / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / symbiont entry into host cell / viral translational frameshifting / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA 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. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / 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. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H 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: 1.85 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 29, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2014Group: Database references
Revision 1.2Aug 27, 2014Group: Other
Revision 1.3Nov 13, 2019Group: Data collection / Database references / Other / Category: pdbx_database_related / pdbx_database_status
Item: _pdbx_database_related.content_type / _pdbx_database_status.status_code_sf
Revision 1.4Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CAPSID PROTEIN P24
B: CAPSID PROTEIN P24


Theoretical massNumber of molelcules
Total (without water)18,9102
Polymers18,9102
Non-polymers00
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-8.5 kcal/mol
Surface area9480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.560, 72.390, 35.700
Angle α, β, γ (deg.)90.00, 109.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CAPSID PROTEIN P24 / PR160GAG-POL / GAG POLYPROTEIN


Mass: 9454.824 Da / Num. of mol.: 2 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.09 Å3/Da / Density % sol: 41.15 % / Description: NONE
Crystal growpH: 10.5
Details: 1.2 M NAH2PO4, 0.8 M K2HPO4, 0.1 M CAPS PH 10.5 AND 0.2 M LISO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / 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: 1.85→36.2 Å / Num. obs: 12273 / % possible obs: 91.4 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 29.67 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 26.1
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.8 / % possible all: 61.2

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BUO

2buo


Resolution: 1.85→10.21 Å / Cor.coef. Fo:Fc: 0.9183 / Cor.coef. Fo:Fc free: 0.9079 / SU R Cruickshank DPI: 0.199 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.207 / SU Rfree Blow DPI: 0.158 / SU Rfree Cruickshank DPI: 0.156
RfactorNum. reflection% reflectionSelection details
Rfree0.2468 594 4.93 %RANDOM
Rwork0.2356 ---
obs0.2361 12050 90.57 %-
Displacement parametersBiso mean: 32.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.6561 Å20 Å23.9669 Å2
2--4.4649 Å20 Å2
3----3.8088 Å2
Refine analyzeLuzzati coordinate error obs: 0.319 Å
Refinement stepCycle: LAST / Resolution: 1.85→10.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1186 0 0 124 1310
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081221HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.91648HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d449SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes36HARMONIC2
X-RAY DIFFRACTIONt_gen_planes172HARMONIC5
X-RAY DIFFRACTIONt_it1221HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.74
X-RAY DIFFRACTIONt_other_torsion15.41
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion164SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1515SEMIHARMONIC4
LS refinement shellResolution: 1.85→2.03 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.363 120 5.13 %
Rwork0.3376 2220 -
all0.3391 2340 -
obs--90.57 %

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