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- PDB-6es8: HIV capsid hexamer with IP6 ligand -

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Basic information

Entry
Database: PDB / ID: 6es8
TitleHIV capsid hexamer with IP6 ligand
ComponentsGag proteinHIV-1 protease
KeywordsVIRAL PROTEIN / HIV
Function / homology
Function and homology information


viral process / : / : / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase ...viral process / : / : / 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 / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / host cell cytoplasm / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane / cytoplasm
Similarity search - Function
Retroviral nucleocapsid Gag protein p24, N-terminal / Retrovirus capsid C-terminal domain / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / gag protein p24 N-terminal domain / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain ...Retroviral nucleocapsid Gag protein p24, N-terminal / Retrovirus capsid C-terminal domain / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / gag protein p24 N-terminal domain / 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. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Ribonuclease H superfamily / 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
INOSITOL HEXAKISPHOSPHATE / Capsid protein p24 / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJames, L.C.
CitationJournal: Elife / Year: 2018
Title: IP6 is an HIV pocket factor that prevents capsid collapse and promotes DNA synthesis.
Authors: Mallery, D.L. / Marquez, C.L. / McEwan, W.A. / Dickson, C.F. / Jacques, D.A. / Anandapadamanaban, M. / Bichel, K. / Towers, G.J. / Saiardi, A. / Bocking, T. / James, L.C.
History
DepositionOct 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Derived calculations / Structure summary / Category: chem_comp / struct_conn
Item: _chem_comp.pdbx_synonyms / _struct_conn.pdbx_dist_value ..._chem_comp.pdbx_synonyms / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.2Jan 17, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Gag protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1642
Polymers24,5041
Non-polymers6601
Water2,162120
1
A: Gag protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)150,98512
Polymers147,0256
Non-polymers3,9606
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_855-y+3,x-y,z1
crystal symmetry operation3_885-x+y+3,-x+3,z1
crystal symmetry operation4_975-x+4,-y+2,z1
crystal symmetry operation5_675y+1,-x+y+2,z1
crystal symmetry operation6_645x-y+1,x-1,z1
Buried area18440 Å2
ΔGint-228 kcal/mol
Surface area58880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.299, 91.299, 57.201
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

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Components

#1: Protein Gag protein / HIV-1 protease


Mass: 24504.178 Da / Num. of mol.: 1
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: B9V8I5, UniProt: P12497*PLUS
#2: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / Phytic acid


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.81 Å3/Da / Density % sol: 56.18 %
Crystal growTemperature: 277 K / Method: batch mode / Details: PEG4K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1 Å
DetectorType: OXFORD RUBY CCD / Detector: CCD / Date: Jan 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→79 Å / Num. obs: 21569 / % possible obs: 91.5 % / Redundancy: 4.6 % / Rrim(I) all: 0.084 / Net I/σ(I): 10.8
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 1.6 / CC1/2: 0.943 / Rrim(I) all: 0.878 / % possible all: 94.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HGP

5hgp


Resolution: 1.9→46.39 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.465 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22372 967 4.9 %RANDOM
Rwork0.18573 ---
obs0.18763 18790 91.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.23 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0.05 Å2-0 Å2
2---0.1 Å20 Å2
3---0.32 Å2
Refinement stepCycle: 1 / Resolution: 1.9→46.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1580 0 36 120 1736
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0141698
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171506
X-RAY DIFFRACTIONr_angle_refined_deg1.9311.7012324
X-RAY DIFFRACTIONr_angle_other_deg1.1721.6293551
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7125214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.8422.19582
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.73415288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4851512
X-RAY DIFFRACTIONr_chiral_restr0.480.2233
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021857
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02275
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_it3.1083.474835
X-RAY DIFFRACTIONr_mcbond_other3.1073.471834
X-RAY DIFFRACTIONr_mcangle_it4.2475.1791044
X-RAY DIFFRACTIONr_mcangle_other4.2455.1821045
X-RAY DIFFRACTIONr_scbond_it4.3343.944861
X-RAY DIFFRACTIONr_scbond_other4.3423.944857
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5215.7291271
X-RAY DIFFRACTIONr_long_range_B_refined8.08141.8351905
X-RAY DIFFRACTIONr_long_range_B_other8.03141.5061877
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 73 -
Rwork0.273 1427 -
obs--94.34 %

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