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- PDB-6b2i: E45A mutant of the HIV-1 capsid protein -

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Basic information

Entry
Database: PDB / ID: 6b2i
TitleE45A mutant of the HIV-1 capsid protein
ComponentsHIV-1 capsid protein
KeywordsVIRAL PROTEIN / HIV-1 capsid protein / hexamer / E45A mutant
Function / homology
Function and homology information


viral budding via host ESCRT complex / viral process / ISG15 antiviral mechanism / host multivesicular body / viral nucleocapsid / host cell cytoplasm / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity ...viral budding via host ESCRT complex / viral process / ISG15 antiviral mechanism / host multivesicular body / viral nucleocapsid / host cell cytoplasm / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding / zinc ion binding / membrane / cytoplasm
Similarity search - Function
Retrovirus capsid C-terminal domain / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Gag protein p6 / Gag protein p6 / 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) / 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 / Gag protein p6 / Gag protein p6 / 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) / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / 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. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
IODIDE ION / Gag polyprotein / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsGres, A.T. / Kirby, K.A. / Sarafianos, S.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI120860 United States
CitationJournal: Nat Commun / Year: 2023
Title: Multidisciplinary studies with mutated HIV-1 capsid proteins reveal structural mechanisms of lattice stabilization.
Authors: Gres, A.T. / Kirby, K.A. / McFadden, W.M. / Du, H. / Liu, D. / Xu, C. / Bryer, A.J. / Perilla, J.R. / Shi, J. / Aiken, C. / Fu, X. / Zhang, P. / Francis, A.C. / Melikyan, G.B. / Sarafianos, S.G.
History
DepositionSep 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Aug 17, 2022Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / database_2 / diffrn / entity / entity_src_gen / pdbx_contact_author / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_struct_assembly_prop / pdbx_struct_special_symmetry / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / software / struct_mon_prot_cis / struct_site / struct_site_gen
Item: _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] ..._atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn.pdbx_serial_crystal_experiment / _entity.pdbx_number_of_molecules / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _pdbx_contact_author.email / _pdbx_contact_author.id / _pdbx_contact_author.identifier_ORCID / _pdbx_contact_author.name_salutation / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_struct_assembly_prop.value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.d_res_high / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_ls_restr.dev_ideal / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_free / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.number_reflns_all / _refine_ls_shell.pdbx_total_number_of_bins_used / _reflns.d_resolution_high / _reflns.pdbx_number_measured_all / _struct_mon_prot_cis.pdbx_omega_angle
Description: Model completeness / Provider: author / Type: Coordinate replacement
Revision 2.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / pdbx_initial_refinement_model
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIV-1 capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,37916
Polymers25,5721
Non-polymers80615
Water1,11762
1
A: HIV-1 capsid protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)158,27196
Polymers153,4346
Non-polymers4,83790
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
Buried area27860 Å2
ΔGint-795 kcal/mol
Surface area63940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.608, 87.608, 56.474
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-412-

HOH

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Components

#1: Protein HIV-1 capsid protein


Mass: 25572.391 Da / Num. of mol.: 1 / Fragment: UNP residues 133-363 / Mutation: E45A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: NL4-3 / Gene: gag / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B6DRA0, UniProt: P12493*PLUS
#2: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.45 Å3/Da / Density % sol: 49.72 % / Mosaicity: 0.23 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG3350, NaI, Sodium cacodylate, Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.5→37.94 Å / Num. obs: 8647 / % possible obs: 99.3 % / Redundancy: 4.8 % / Biso Wilson estimate: 49.61 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.073 / Rrim(I) all: 0.162 / Net I/σ(I): 9.1 / Num. measured all: 41810
Reflection shell

Diffraction-ID: 1 / Redundancy: 4.4 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.5-2.60.80741399420.6430.4280.916295.9
9.01-37.940.0438701970.9980.0230.04925.797.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.84 Å34.61 Å
Translation5.84 Å34.61 Å

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Processing

Software
NameVersionClassification
PHENIX1.10.1refinement
Aimless0.5.27data scaling
Blu-Icedata collection
PDB_EXTRACT3.22data extraction
PHASER2.6.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XFX

4xfx


Resolution: 2.5→34.612 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2497 422 4.89 %
Rwork0.2022 8204 -
obs0.2047 8626 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 156.42 Å2 / Biso mean: 71.9187 Å2 / Biso min: 29.3 Å2
Refinement stepCycle: final / Resolution: 2.5→34.612 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1721 0 15 62 1798
Biso mean--83.36 63.26 -
Num. residues----221
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021765
X-RAY DIFFRACTIONf_angle_d0.4432402
X-RAY DIFFRACTIONf_chiral_restr0.038269
X-RAY DIFFRACTIONf_plane_restr0.004313
X-RAY DIFFRACTIONf_dihedral_angle_d15.3891086
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5-2.86160.4351440.2965269699
2.8616-3.60480.30351450.22982720100
3.6048-34.610.18871330.17012788100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.1661-0.41890.45763.12522.10792.4048-0.4208-1.2690.73162.3513-0.55150.41372.0010.06830.7071.4130.08590.12530.8384-0.10210.7271-5.3144-12.360621.6833
25.0127-2.3178-3.29273.76633.25745.17450.30860.43050.2498-0.3153-0.5727-0.0724-0.4179-0.51680.25450.4326-0.01720.03220.5088-0.01170.4911.6487-16.7471-0.3908
30.7187-1.24591.48841.7524-0.39466.56350.09490.0464-0.1275-0.0569-0.18460.4580.0493-0.25880.05950.3381-0.0472-0.01920.4866-0.04880.3791-6.1036-26.66771.9939
45.1159-1.01655.32547.6972-0.27478.9406-0.7952-0.1121-0.59280.6645-0.0303-0.02081.89570.7160.64860.67720.02030.14560.4791-0.00180.5425-1.6071-40.801713.8194
54.2826-1.8209-2.82421.83663.36758.7039-1.1746-0.1474-1.010.57090.36650.04712.12670.01560.69151.180.05570.20871.06260.02490.6195-11.4257-35.375627.4743
63.8817-0.3839-1.07277.34720.81555.6210.341-0.71320.19361.2414-0.2050.26580.44990.1626-0.12050.5824-0.06680.03570.6355-0.02650.3977-6.0973-27.579719.6071
74.91520.1623-2.88433.15720.33872.7574-0.26720.13670.0931-0.11750.2481-0.34620.06350.71120.030.33070.0133-0.01030.46510.02740.43544.0151-30.45710.5209
89.57092.6121-3.50359.0953-2.71493.1474-0.17360.2717-0.1873-1.4355-0.12760.45070.01130.22380.18940.4963-0.0161-0.02660.3877-0.05090.386422.5812-25.845-16.5813
92.38342.4653-0.96375.9295-2.62594.6405-0.3740.0034-0.4669-0.45320.0196-0.61410.73910.47970.34790.44610.02930.06460.4181-0.0410.569927.3995-31.1492-10.7296
108.74150.1715-2.89247.1633.95359.9901-0.2304-0.00120.4352-0.17870.12010.52-0.96350.97020.16790.5311-0.02510.01770.5639-0.0190.67534.4123-22.4043-10.5879
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:15)A1 - 15
2X-RAY DIFFRACTION2(chain A and resid 16:46)A16 - 46
3X-RAY DIFFRACTION3(chain A and resid 47:74)A47 - 74
4X-RAY DIFFRACTION4(chain A and resid 75:85)A75 - 85
5X-RAY DIFFRACTION5(chain A and resid 86:98)A86 - 98
6X-RAY DIFFRACTION6(chain A and resid 99:127)A99 - 127
7X-RAY DIFFRACTION7(chain A and resid 128:148)A128 - 148
8X-RAY DIFFRACTION8(chain A and resid 149:171)A149 - 171
9X-RAY DIFFRACTION9(chain A and resid 172:206)A172 - 206
10X-RAY DIFFRACTION10(chain A and resid 207:221)A207 - 221

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