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- PDB-5o2u: Llama VHH in complex with p24 -

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Basic information

Entry
Database: PDB / ID: 5o2u
TitleLlama VHH in complex with p24
Components
  • Capsid protein p24
  • VHH 59H10
KeywordsVIRUS / VHH Llama antibody HIV capsid protein complex
Function / homology
Function and homology information


viral budding via host ESCRT complex / ISG15 antiviral mechanism / host multivesicular body / viral nucleocapsid / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding / zinc ion binding / membrane
Similarity search - Function
Retrovirus capsid C-terminal domain / 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 domain / 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
Biological speciesHuman immunodeficiency virus 1
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsCaillat, C. / Verrips, T. / Weissenhorn, W.
CitationJournal: ACS Infect Dis / Year: 2017
Title: Unravelling the Molecular Basis of High Affinity Nanobodies against HIV p24: In Vitro Functional, Structural, and in Silico Insights.
Authors: Gray, E.R. / Brookes, J.C. / Caillat, C. / Turbe, V. / Webb, B.L.J. / Granger, L.A. / Miller, B.S. / McCoy, L.E. / El Khattabi, M. / Verrips, C.T. / Weiss, R.A. / Duffy, D.M. / Weissenhorn, W. / McKendry, R.A.
History
DepositionMay 22, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jan 17, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Capsid protein p24
B: VHH 59H10
C: Capsid protein p24
D: VHH 59H10


Theoretical massNumber of molelcules
Total (without water)139,6844
Polymers139,6844
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-24 kcal/mol
Surface area18780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.993, 72.228, 69.953
Angle α, β, γ (deg.)90.00, 91.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Capsid protein p24 /


Mass: 55895.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The following reagent was obtained through the NIH AIDS Reagent Program, Division of AIDS, NIAID, NIH: pWISP98-85 from Dr. Wes Sundquist.
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Escherichia coli (E. coli) / References: UniProt: P12493
#2: Antibody VHH 59H10


Mass: 13946.540 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Saccharomyces cerevisiae (brewer's yeast)

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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: 2.5 Å3/Da / Density % sol: 50.81 % / Description: needles
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100mM Tris base pH 8.0, Polyethylene glycol (PEG) 6000 25% Ethylene Glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976251 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976251 Å / Relative weight: 1
ReflectionResolution: 2.76→36.11 Å / Num. obs: 10360 / % possible obs: 97.73 % / Redundancy: 3 % / Biso Wilson estimate: 42.55 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.1424 / Rpim(I) all: 0.0983 / Net I/σ(I): 5.55
Reflection shellResolution: 2.76→2.91 Å / Redundancy: 3 % / Rmerge(I) obs: 0.712 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1508 / CC1/2: 0.572 / Rpim(I) all: 0.473 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
Aimlessdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5hgp and 4ldo

5hgp

4ldo


Resolution: 2.76→36.11 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.62
RfactorNum. reflection% reflection
Rfree0.256 512 4.94 %
Rwork0.2223 --
obs0.224 10360 97.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.76→36.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2890 0 0 0 2890
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032953
X-RAY DIFFRACTIONf_angle_d0.5783996
X-RAY DIFFRACTIONf_dihedral_angle_d14.5971788
X-RAY DIFFRACTIONf_chiral_restr0.042442
X-RAY DIFFRACTIONf_plane_restr0.004520
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.76-3.03770.35241100.31342473X-RAY DIFFRACTION98
3.0377-3.47690.30371240.26422470X-RAY DIFFRACTION99
3.4769-4.37930.25721360.2042454X-RAY DIFFRACTION98
4.3793-36.11710.20661420.18172451X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 33.1962 Å / Origin y: 15.334 Å / Origin z: 17.442 Å
111213212223313233
T0.2319 Å20.0659 Å20.0192 Å2-0.2344 Å20.0408 Å2--0.1997 Å2
L1.8688 °21.7215 °20.4323 °2-2.7751 °20.9862 °2--0.6509 °2
S0.0322 Å °-0.0249 Å °-0.0445 Å °0.0156 Å °0.0847 Å °-0.1371 Å °0.0068 Å °0.0755 Å °-0.1133 Å °
Refinement TLS groupSelection details: all

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