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- PDB-4u0f: Hexameric HIV-1 CA in Complex with BI-2 -

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Basic information

Entry
Database: PDB / ID: 4u0f
TitleHexameric HIV-1 CA in Complex with BI-2
ComponentsCapsid protein p24
KeywordsVIRAL PROTEIN / Capsid / Inhibitor
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 / 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
Chem-3A8 / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.22 Å
AuthorsPrice, A.J. / Jacques, D.A. / James, L.C.
CitationJournal: Plos Pathog. / Year: 2014
Title: Host Cofactors and Pharmacologic Ligands Share an Essential Interface in HIV-1 Capsid That Is Lost upon Disassembly.
Authors: Price, A.J. / Jacques, D.A. / McEwan, W.A. / Fletcher, A.J. / Essig, S. / Chin, J.W. / Halambage, U.D. / Aiken, C. / James, L.C.
History
DepositionJul 11, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

Deposited unit
A: Capsid protein p24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8153
Polymers25,4611
Non-polymers3532
Water1,36976
1
A: Capsid protein p24
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)154,88818
Polymers152,7686
Non-polymers2,12012
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-y+1,x-y+2,z1
crystal symmetry operation3_465-x+y-1,-x+1,z1
crystal symmetry operation4_575-x,-y+2,z1
crystal symmetry operation5_455y-1,-x+y,z1
crystal symmetry operation6_665x-y+1,x+1,z1
Buried area14510 Å2
ΔGint-79 kcal/mol
Surface area58230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.880, 90.880, 56.580
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6
Detailsbiological unit is the same as asym.

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Components

#1: Protein Capsid protein p24 / / Pr55Gag


Mass: 25461.271 Da / Num. of mol.: 1 / Mutation: yes
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B
Strain: isolate NY5 / Gene: gag / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P12493
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-3A8 / (4S)-4-(4-hydroxyphenyl)-3-phenyl-4,5-dihydropyrrolo[3,4-c]pyrazol-6(1H)-one


Mass: 291.304 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H13N3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O

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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: 2.65 Å3/Da / Density % sol: 53.57 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 12% w/v PEG 4K, 0.1 M TRIS pH 8.5, 3% v/v ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.21→14.87 Å / Num. obs: 12460 / % possible obs: 93.4 % / Redundancy: 3.9 % / CC1/2: 0.986 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.096 / Net I/σ(I): 7.2 / Num. measured all: 48198 / Scaling rejects: 9
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.21-2.283.40.499330578970.4760.29472.5
8.84-14.8740.03624.76261570.9980.0271.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.59 Å14.87 Å
Translation5.59 Å14.87 Å

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Processing

Software
NameVersionClassification
Aimless0.2.7data scaling
PDB_EXTRACT3.14data extraction
PHASERphasing
REFMAC5.8.0049refinement
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H47

3h47


Resolution: 2.22→14.87 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.863 / WRfactor Rfree: 0.2398 / WRfactor Rwork: 0.2149 / FOM work R set: 0.7597 / SU B: 8.468 / SU ML: 0.204 / SU R Cruickshank DPI: 0.316 / SU Rfree: 0.2336 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.316 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2701 593 4.8 %RANDOM
Rwork0.2418 11864 --
obs0.2431 12457 93.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 79.71 Å2 / Biso mean: 36.167 Å2 / Biso min: 15.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20.14 Å20 Å2
2--0.28 Å20 Å2
3----0.92 Å2
Refinement stepCycle: final / Resolution: 2.22→14.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1558 0 26 76 1660
Biso mean--42.48 33.48 -
Num. residues----201
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191628
X-RAY DIFFRACTIONr_bond_other_d0.0010.021556
X-RAY DIFFRACTIONr_angle_refined_deg0.9181.9842215
X-RAY DIFFRACTIONr_angle_other_deg0.6973.0033581
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5445201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.74424.62767
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.81715274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.441510
X-RAY DIFFRACTIONr_chiral_restr0.0470.2250
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211814
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02351
X-RAY DIFFRACTIONr_mcbond_it3.4344.639804
X-RAY DIFFRACTIONr_mcbond_other3.4344.638803
X-RAY DIFFRACTIONr_mcangle_it4.7747.807999
LS refinement shellResolution: 2.222→2.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.481 40 -
Rwork0.4 817 -
all-857 -
obs--86.74 %

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