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- PDB-7mn0: N74D mutant of the HIV-1 capsid protein -

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Basic information

Entry
Database: PDB / ID: 7mn0
TitleN74D mutant of the HIV-1 capsid protein
Componentscapsid protein
KeywordsVIRAL PROTEIN / HIV-1 capsid protein / hexmer / mutant
Function / homology
Function and homology information


viral process / viral nucleocapsid / host cell cytoplasm / host cell nucleus / structural molecule activity / virion membrane / RNA binding / zinc ion binding / ATP binding / cytoplasm
Similarity search - Function
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 knuckle ...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 knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
IODIDE ION / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 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)R01 AI120860 United States
CitationJournal: Viruses / Year: 2022
Title: TRIM5alpha Restriction of HIV-1-N74D Viruses in Lymphocytes Is Caused by a Loss of Cyclophilin A Protection.
Authors: Selyutina, A. / Simons, L.M. / Kirby, K.A. / Bulnes-Ramos, A. / Hu, P. / Sarafianos, S.G. / Hultquist, J.F. / Diaz-Griffero, F.
History
DepositionApr 30, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3937
Polymers25,6311
Non-polymers7616
Water00
1
A: capsid protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)158,35742
Polymers153,7886
Non-polymers4,56936
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
crystal symmetry operation4_775-x+2,-y+2,z1
crystal symmetry operation5_565y,-x+y+1,z1
crystal symmetry operation6_655x-y+1,x,z1
Buried area21270 Å2
ΔGint-98 kcal/mol
Surface area60610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.741, 91.741, 57.163
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 capsid protein / Gag polyprotein


Mass: 25631.410 Da / Num. of mol.: 1 / Mutation: N74D
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) / Variant (production host): RIL / References: UniProt: B6DRA0
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: I
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: 2.71 Å3/Da / Density % sol: 54.6 % / Mosaicity: 0.21 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, NaI, Sodium Cacodylate, Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00003 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Oct 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.9→45.87 Å / Num. obs: 6190 / % possible obs: 99.8 % / Redundancy: 11.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.039 / Rrim(I) all: 0.129 / Net I/σ(I): 16.7 / Num. measured all: 69089
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.9-3.0810.61.134105789990.6940.3641.1912.199.4
8.71-45.8710.30.034253924710.0110.03663.698.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.39 Å45.87 Å
Translation5.39 Å45.87 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0158refinement
XDSdata reduction
Aimless0.5.32data scaling
PHASER2.7.17phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XFX

4xfx


Resolution: 2.9→45.87 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.2365 / WRfactor Rwork: 0.188 / FOM work R set: 0.7396 / SU B: 48.943 / SU ML: 0.38 / SU R Cruickshank DPI: 0.3612 / SU Rfree: 0.4337 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.434 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2736 323 5.2 %RANDOM
Rwork0.2194 ---
obs0.2222 5866 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 152.39 Å2 / Biso mean: 83.079 Å2 / Biso min: 45.67 Å2
Baniso -1Baniso -2Baniso -3
1-1.4 Å20.7 Å2-0 Å2
2--1.4 Å20 Å2
3----4.53 Å2
Refinement stepCycle: final / Resolution: 2.9→45.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1680 0 6 0 1686
Biso mean--81.91 --
Num. residues----216
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191719
X-RAY DIFFRACTIONr_bond_other_d0.0070.021602
X-RAY DIFFRACTIONr_angle_refined_deg1.9041.9582337
X-RAY DIFFRACTIONr_angle_other_deg1.07233732
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2985214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.60324.79573
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.97815295
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8141510
X-RAY DIFFRACTIONr_chiral_restr0.090.2263
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211880
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02314
X-RAY DIFFRACTIONr_sphericity_bonded29.20456
LS refinement shellResolution: 2.903→2.978 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.474 12 -
Rwork0.37 436 -
all-448 -
obs--99.56 %
Refinement TLS params.Method: refined / Origin x: 64.3555 Å / Origin y: 58.764 Å / Origin z: -0.2068 Å
111213212223313233
T0.0521 Å20.019 Å20.0539 Å2-0.0414 Å2-0.0312 Å2--0.1759 Å2
L0.1536 °20.2489 °2-0.0774 °2-0.7449 °2-0.5951 °2--0.7338 °2
S0.0688 Å °0.0099 Å °0.0343 Å °0.0427 Å °-0.0896 Å °0.0796 Å °0.0686 Å °0.127 Å °0.0208 Å °

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