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- PDB-6r8c: HIV capsid hexamer with IP5 ligand -

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Basic information

Entry
Database: PDB / ID: 6r8c
TitleHIV capsid hexamer with IP5 ligand
ComponentsGag polyprotein
KeywordsVIRAL PROTEIN / HIV
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
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 / 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 ...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 / 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. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
MYO-INOSITOL-(1,3,4,5,6)-PENTAKISPHOSPHATE / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsJames, L.C.
CitationJournal: to be published
Title: HIV hexamer
Authors: James, L.C.
History
DepositionApr 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gag polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5542
Polymers22,9731
Non-polymers5801
Water3,531196
1
A: Gag polyprotein
hetero molecules

A: Gag polyprotein
hetero molecules

A: Gag polyprotein
hetero molecules

A: Gag polyprotein
hetero molecules

A: Gag polyprotein
hetero molecules

A: Gag polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,32112
Polymers137,8416
Non-polymers3,4806
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.663, 90.663, 56.997
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-536-

HOH

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Components

#1: Protein Gag polyprotein


Mass: 22973.498 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: myo-IP5 / Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag / Production host: Escherichia coli (E. coli) / References: UniProt: B6DRA0
#2: Chemical ChemComp-5MY / MYO-INOSITOL-(1,3,4,5,6)-PENTAKISPHOSPHATE


Mass: 580.055 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H17O21P5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.94 Å3/Da / Density % sol: 58.21 %
Crystal growTemperature: 270 K / Method: batch mode / Details: PEG 6K, 1M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.978 Å
DetectorType: OXFORD SAPPHIRE CCD / Detector: CCD / Date: Mar 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.913→78.52 Å / Num. obs: 20758 / % possible obs: 99.3 % / Redundancy: 6.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.056 / Net I/σ(I): 17.7
Reflection shellResolution: 1.93→1.98 Å / Redundancy: 6 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1240 / CC1/2: 0.883 / % possible all: 90

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ES8

6es8


Resolution: 1.92→29.69 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.317 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.141 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23426 972 4.7 %RANDOM
Rwork0.19111 ---
obs0.19308 19575 98.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.456 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å2-0 Å2
2---0.04 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.92→29.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1580 0 32 196 1808
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131684
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171550
X-RAY DIFFRACTIONr_angle_refined_deg1.6521.6642305
X-RAY DIFFRACTIONr_angle_other_deg1.4091.5683611
X-RAY DIFFRACTIONr_dihedral_angle_1_deg23.4085.43221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.22622.93375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.55615281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0911511
X-RAY DIFFRACTIONr_chiral_restr0.0920.2232
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022100
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02317
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_it3.2753.505833
X-RAY DIFFRACTIONr_mcbond_other3.273.503832
X-RAY DIFFRACTIONr_mcangle_it4.3935.2341041
X-RAY DIFFRACTIONr_mcangle_other4.3925.2361042
X-RAY DIFFRACTIONr_scbond_it3.7884.08850
X-RAY DIFFRACTIONr_scbond_other3.7944.055847
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5336.0091259
X-RAY DIFFRACTIONr_long_range_B_refined7.2442.9071988
X-RAY DIFFRACTIONr_long_range_B_other7.17942.3141937
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.913→1.963 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 65 -
Rwork0.28 1304 -
obs--90.18 %

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