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- PDB-6ern: HIV Hexamer with ligand -

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Basic information

Entry
Database: PDB / ID: 6ern
TitleHIV Hexamer with 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
ADENOSINE-5'-TRIPHOSPHATE / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsJames, L.C.
CitationJournal: To Be Published
Title: HIV hexamer
Authors: James, L.C.
History
DepositionOct 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2Apr 1, 2020Group: Advisory / Derived calculations
Category: pdbx_validate_symm_contact / struct_conn / struct_conn_type
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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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)24,7132
Polymers24,2061
Non-polymers5071
Water1,47782
1
A: Gag polyprotein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)148,27812
Polymers145,2356
Non-polymers3,0436
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
crystal symmetry operation4_775-x+2,-y+2,z1
crystal symmetry operation5_565y,-x+y+1,z1
crystal symmetry operation6_655x-y+1,x,z1
Buried area18100 Å2
ΔGint-131 kcal/mol
Surface area57850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.846, 90.846, 56.747
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-301-

ATP

21A-301-

ATP

31A-301-

ATP

41A-301-

ATP

51A-301-

ATP

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Components

#1: Protein Gag polyprotein


Mass: 24205.844 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: B6DRA0
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.98 Å3/Da / Density % sol: 58.74 %
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: 2.359→78.68 Å / Num. obs: 11142 / % possible obs: 91.03 % / Redundancy: 4.9 % / Net I/σ(I): 15.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.36→78.67 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.909 / SU B: 6.632 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.338 / ESU R Free: 0.242 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23665 506 4.9 %RANDOM
Rwork0.18454 ---
obs0.18709 9738 91.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.873 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20.22 Å2-0 Å2
2--0.43 Å20 Å2
3----1.4 Å2
Refinement stepCycle: 1 / Resolution: 2.36→78.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1555 0 31 82 1668
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0191630
X-RAY DIFFRACTIONr_bond_other_d0.0020.021490
X-RAY DIFFRACTIONr_angle_refined_deg1.8251.9872225
X-RAY DIFFRACTIONr_angle_other_deg1.0953.0013468
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3235202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.3124.84866
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.69215270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.986159
X-RAY DIFFRACTIONr_chiral_restr0.0990.2253
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211757
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02295
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_it2.8973.512808
X-RAY DIFFRACTIONr_mcbond_other2.8853.51807
X-RAY DIFFRACTIONr_mcangle_it4.2735.2291004
X-RAY DIFFRACTIONr_mcangle_other4.2755.2311005
X-RAY DIFFRACTIONr_scbond_it3.8184.107821
X-RAY DIFFRACTIONr_scbond_other3.8164.11822
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9326.061220
X-RAY DIFFRACTIONr_long_range_B_refined7.41140.8281802
X-RAY DIFFRACTIONr_long_range_B_other7.40840.8321803
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.36→2.421 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.198 36 -
Rwork0.166 741 -
obs--93.61 %

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