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- PDB-6b2g: P38A mutant of HIV-1 capsid protein -

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Basic information

Entry
Database: PDB / ID: 6b2g
TitleP38A mutant of HIV-1 capsid protein
ComponentsHIV-1 capsid protein
KeywordsVIRAL PROTEIN / HIV-1 capsid protein / hexamer / P38A mutant
Function / homology
Function and homology information


viral budding via host ESCRT complex / host multivesicular body / ISG15 antiviral mechanism / viral nucleocapsid / host cell cytoplasm / viral translational frameshifting / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity ...viral budding via host ESCRT complex / host multivesicular body / ISG15 antiviral mechanism / viral nucleocapsid / host cell cytoplasm / viral translational frameshifting / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding / zinc ion binding / ATP binding / membrane
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) ...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) / 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 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: 2.407 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 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / database_2 / 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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)26,79714
Polymers25,6041
Non-polymers1,19213
Water59433
1
A: HIV-1 capsid protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)160,78184
Polymers153,6266
Non-polymers7,15578
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 area28330 Å2
ΔGint-421 kcal/mol
Surface area61090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.139, 92.139, 57.481
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6

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Components

#1: Protein HIV-1 capsid protein


Mass: 25604.389 Da / Num. of mol.: 1 / Fragment: UNP residues 133-363 / Mutation: P38A
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 (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B6DRA0, UniProt: P12493*PLUS
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.75 Å3/Da / Density % sol: 55.29 % / Mosaicity: 0.14 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG3350, NaI, MIB, Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.407→46.64 Å / Num. obs: 10898 / % possible obs: 99.6 % / Redundancy: 10.1 % / Biso Wilson estimate: 69.59 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.022 / Rrim(I) all: 0.068 / Net I/σ(I): 19.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.41-2.59.61.03811160.7160.3441.09596.7
9-46.649.20.052280.9970.0180.05399.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.34 Å46.64 Å
Translation5.34 Å46.64 Å

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Processing

Software
NameVersionClassification
Aimless0.5.31data scaling
Blu-Icedata collection
PHENIX1.11.1-2575_1692refinement
PDB_EXTRACT3.22data extraction
Aimless0.5.31data reduction
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XFX

4xfx


Resolution: 2.407→46.64 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 33.55
RfactorNum. reflection% reflection
Rfree0.2578 631 5.79 %
Rwork0.238 --
obs0.2391 10894 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 177.35 Å2 / Biso mean: 93.4195 Å2 / Biso min: 55.83 Å2
Refinement stepCycle: final / Resolution: 2.407→46.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1696 0 13 33 1742
Biso mean--105.51 78.08 -
Num. residues----219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021742
X-RAY DIFFRACTIONf_angle_d0.4472371
X-RAY DIFFRACTIONf_chiral_restr0.037267
X-RAY DIFFRACTIONf_plane_restr0.004308
X-RAY DIFFRACTIONf_dihedral_angle_d12.061071
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4068-2.59260.37941150.35672013212899
2.5926-2.85350.38441250.340320382163100
2.8535-3.26630.32281330.308420392172100
3.2663-4.11480.23251220.247520652187100
4.1148-46.64860.22811360.194421082244100
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)
14.764-2.21161.7061.0158-0.860.59152.8395-0.1953-1.61510.90410.09490.1807-0.98280.53310.451.2548-0.23380.0111.02020.25940.815-0.5018-11.919216.3806
20.56510.95520.54322.00881.01331.0482-0.13310.66991.42280.14280.2056-1.0292-0.22650.0642-0.00670.5529-0.00930.11660.73850.31951.19262.7622-16.8195-3.4878
30.8517-2.46120.33853.98010.04183.1154-0.30540.2512-0.06820.3133-0.1615-0.14040.5395-0.0299-0.00010.6054-0.06330.17210.51840.08280.6738-3.2112-29.18443.7228
40.21860.0879-0.40920.1361-0.03950.29090.03280.2596-0.4698-1.0374-0.21280.3174-0.3634-0.2348-0.00021.3825-0.12670.17860.90810.060.6685-7.5231-33.792822.8462
5-0.00330.3049-0.21441.3144-0.62160.5703-0.3396-1.3704-0.56420.91010.68470.1914-0.2558-0.22670.00011.34270.04280.20880.8977-0.03140.8595-4.8006-24.487319.2592
61.3281-0.9727-0.05171.4944-0.96890.99050.05090.2786-0.28770.6556-0.4905-0.49360.2132-0.28950.00030.6018-0.05020.11750.7360.18270.75183.7819-29.9221.9215
70.031-0.1613-0.35030.33790.64861.04260.20320.99550.3364-0.98310.18230.2035-0.02850.0243-0.00020.94160.1720.05870.8680.16760.587121.8512-29.26-19.587
80.58810.59380.26670.5904-0.0660.32770.6191.44811.8968-0.587-0.13210.74340.2469-0.4907-0.08270.66360.18710.14590.79660.42030.843122.0886-24.4941-13.0389
90.31310.67270.0983.0209-0.44510.34570.26680.67990.83920.81590.1391-0.11510.9179-0.0765-0.01080.6340.12660.00140.63240.13990.65224.3605-34.5085-6.4965
100.96-0.3399-0.21651.23080.06510.9902-0.61360.8725-0.0032-0.24410.175-0.62780.48571.8565-0.00520.66250.2630.06641.42370.05920.838635.7323-25.452-14.6094
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 16 )A1 - 16
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 43 )A17 - 43
3X-RAY DIFFRACTION3chain 'A' and (resid 44 through 83 )A44 - 83
4X-RAY DIFFRACTION4chain 'A' and (resid 84 through 104 )A84 - 104
5X-RAY DIFFRACTION5chain 'A' and (resid 105 through 125 )A105 - 125
6X-RAY DIFFRACTION6chain 'A' and (resid 126 through 145 )A126 - 145
7X-RAY DIFFRACTION7chain 'A' and (resid 146 through 160 )A146 - 160
8X-RAY DIFFRACTION8chain 'A' and (resid 161 through 174 )A161 - 174
9X-RAY DIFFRACTION9chain 'A' and (resid 175 through 192 )A175 - 192
10X-RAY DIFFRACTION10chain 'A' and (resid 193 through 221 )A193 - 221

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