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- PDB-6pu1: Cysteine stabilized hexameric HIV-1 CA in complex with SEC24C peptide -

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Basic information

Entry
Database: PDB / ID: 6pu1
TitleCysteine stabilized hexameric HIV-1 CA in complex with SEC24C peptide
Components
  • Gag polyprotein
  • Protein transport protein Sec24C
KeywordsVIRAL PROTEIN / Capsid / co-factor / HIV
Function / homology
Function and homology information


COPII-coated vesicle cargo loading / COPII vesicle coat / Regulation of cholesterol biosynthesis by SREBP (SREBF) / Cargo concentration in the ER / COPII-mediated vesicle transport / viral budding via host ESCRT complex / endoplasmic reticulum exit site / endoplasmic reticulum to Golgi vesicle-mediated transport / MHC class II antigen presentation / SNARE binding ...COPII-coated vesicle cargo loading / COPII vesicle coat / Regulation of cholesterol biosynthesis by SREBP (SREBF) / Cargo concentration in the ER / COPII-mediated vesicle transport / viral budding via host ESCRT complex / endoplasmic reticulum exit site / endoplasmic reticulum to Golgi vesicle-mediated transport / MHC class II antigen presentation / SNARE binding / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / ER to Golgi transport vesicle membrane / host multivesicular body / ISG15 antiviral mechanism / viral nucleocapsid / in utero embryonic development / host cell cytoplasm / viral translational frameshifting / endoplasmic reticulum membrane / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / structural molecule activity / virion membrane / RNA binding / zinc ion binding / ATP binding / membrane / cytosol / cytoplasm
Similarity search - Function
: / Sec24-like, trunk domain / Zinc finger, Sec23/Sec24-type / Sec23/Sec24, trunk domain / Sec23/Sec24, helical domain / Sec23/Sec24 beta-sandwich / Zinc finger, Sec23/Sec24-type superfamily / Sec23/Sec24 helical domain superfamily / Sec23/Sec24 zinc finger / Sec23/Sec24 trunk domain ...: / Sec24-like, trunk domain / Zinc finger, Sec23/Sec24-type / Sec23/Sec24, trunk domain / Sec23/Sec24, helical domain / Sec23/Sec24 beta-sandwich / Zinc finger, Sec23/Sec24-type superfamily / Sec23/Sec24 helical domain superfamily / Sec23/Sec24 zinc finger / Sec23/Sec24 trunk domain / Sec23/Sec24 helical domain / Sec23/Sec24 beta-sandwich domain / Gelsolin-like domain superfamily / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like domain superfamily / Gag protein p6 / Gag protein p6 / : / gag protein p24 N-terminal domain / von Willebrand factor A-like domain superfamily / 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.
Similarity search - Domain/homology
IODIDE ION / Gag polyprotein / Gag polyprotein / Protein transport protein Sec24C
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsLindenberger, J.J. / Kvaratskhelia, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI062520 United States
CitationJournal: To Be Published
Title: Cysteine stabilized hexameric HIV-1 CA in complex with SEC24C peptide
Authors: Lindenberger, J.J. / Kvaratskhelia, M.
History
DepositionJul 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: 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

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Assembly

Deposited unit
A: Gag polyprotein
B: Protein transport protein Sec24C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3488
Polymers26,8612
Non-polymers4876
Water48627
1
A: Gag polyprotein
B: Protein transport protein Sec24C
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)164,08748
Polymers161,16512
Non-polymers2,92236
Water21612
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 area27000 Å2
ΔGint-323 kcal/mol
Surface area59590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.580, 92.580, 58.019
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6
Space group name HallP6
Symmetry operation#1: x,y,z
#2: x-y,x,z
#3: y,-x+y,z
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z

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Components

#1: Protein Gag polyprotein


Mass: 25461.271 Da / Num. of mol.: 1 / Mutation: A14C, E45C, W184A, M185A
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, UniProt: P12493*PLUS
#2: Protein/peptide Protein transport protein Sec24C / SEC24-related protein C


Mass: 1399.549 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P53992
#3: Chemical ChemComp-IOD / IODIDE ION


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


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.94 Å3/Da / Density % sol: 58.18 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 12% PEG3350, 24% glycerol, 0.35 M NaI, 50 mM sodium cacodylate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.28→47 Å / Num. obs: 13073 / % possible obs: 100 % / Redundancy: 10.2 % / Biso Wilson estimate: 55.89 Å2 / Rmerge(I) obs: 0.124 / Net I/σ(I): 11.8
Reflection shellResolution: 2.28→2.36 Å / Num. unique obs: 1264

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.16_3546refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U0A

4u0a


Resolution: 2.28→47 Å / SU ML: 0.3571 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.0912
RfactorNum. reflection% reflection
Rfree0.2724 578 4.46 %
Rwork0.2321 --
obs0.2338 12971 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 71.05 Å2
Refinement stepCycle: LAST / Resolution: 2.28→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1706 0 6 27 1739
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00231745
X-RAY DIFFRACTIONf_angle_d0.46882372
X-RAY DIFFRACTIONf_chiral_restr0.0367264
X-RAY DIFFRACTIONf_plane_restr0.0042312
X-RAY DIFFRACTIONf_dihedral_angle_d5.93091067
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.510.381590.3262991X-RAY DIFFRACTION97.1
2.51-2.870.30911410.27683095X-RAY DIFFRACTION99.88
2.87-3.620.26871430.24833116X-RAY DIFFRACTION99.97
3.62-470.24891350.20713191X-RAY DIFFRACTION99.97
Refinement TLS params.Method: refined / Origin x: -20.9293963818 Å / Origin y: -18.2546873472 Å / Origin z: -15.3463541017 Å
111213212223313233
T0.4751326991 Å2-0.133041440518 Å2-0.00371171646911 Å2-0.422532366028 Å20.00893761163169 Å2--0.397621929629 Å2
L2.01395493006 °2-0.976506599394 °2-0.504156209654 °2-3.23699448382 °21.38790089702 °2--2.90942311369 °2
S-0.14005471688 Å °0.0328037306678 Å °0.0524366605821 Å °0.162519657052 Å °0.0390359971699 Å °-0.0864328645579 Å °0.559492159279 Å °-0.289529689784 Å °0.0937392318192 Å °
Refinement TLS groupSelection details: all

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