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- PDB-2x82: Evolutionary basis of HIV restriction by the antiretroviral TRIMCyp -

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Basic information

Entry
Database: PDB / ID: 2x82
TitleEvolutionary basis of HIV restriction by the antiretroviral TRIMCyp
ComponentsCAPSID PROTEIN P24
KeywordsVIRAL PROTEIN / TRIM / RESTRICTION FACTOR IMMUNITY
Function / homologyHuman Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Orthogonal Bundle / Mainly Alpha
Function and homology information
Biological speciesHUMAN IMMUNODEFICIENCY VIRUS TYPE 2
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.6 Å
AuthorsPrice, A.J. / James, L.C.
CitationJournal: Plos Pathog. / Year: 2010
Title: Conformational Adaptation of Asian Macaque Trimcyp Directs Lineage Specific Antiviral Activity.
Authors: Ylinen, L.M. / Price, A.J. / Rasaiyaah, J. / Hue, S. / Rose, N.J. / Marzetta, F. / James, L.C. / Towers, G.J.
History
DepositionMar 5, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CAPSID PROTEIN P24
B: CAPSID PROTEIN P24
C: CAPSID PROTEIN P24
D: CAPSID PROTEIN P24


Theoretical massNumber of molelcules
Total (without water)65,1504
Polymers65,1504
Non-polymers00
Water1,00956
1
A: CAPSID PROTEIN P24
B: CAPSID PROTEIN P24


Theoretical massNumber of molelcules
Total (without water)32,5752
Polymers32,5752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-10.5 kcal/mol
Surface area15260 Å2
MethodPISA
2
C: CAPSID PROTEIN P24
D: CAPSID PROTEIN P24


Theoretical massNumber of molelcules
Total (without water)32,5752
Polymers32,5752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-11.3 kcal/mol
Surface area14960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.470, 116.770, 129.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
CAPSID PROTEIN P24 / CA


Mass: 16287.562 Da / Num. of mol.: 4 / Fragment: N-TERMINAL DOMAIN, RESIDUES 136-280
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS TYPE 2 (ISOLATE D194)
Production host: ESCHERICHIA COLI (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 50 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 22894 / % possible obs: 95.7 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Biso Wilson estimate: 34.1 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.6

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Processing

SoftwareName: REFMAC / Version: 5.5.0109 / Classification: refinement
RefinementMethod to determine structure: OTHER / Resolution: 2.6→86.68 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.859 / SU B: 32.425 / SU ML: 0.32 / Cross valid method: THROUGHOUT / ESU R: 1.586 / ESU R Free: 0.371 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27982 1110 5.1 %RANDOM
Rwork0.21547 ---
obs0.21869 20611 94.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.087 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2--3.15 Å20 Å2
3----3.08 Å2
Refinement stepCycle: LAST / Resolution: 2.6→86.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4576 0 0 56 4632
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225092
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5361.9396988
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5895656
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.42624.091264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.94915848
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5381548
X-RAY DIFFRACTIONr_chiral_restr0.1050.2728
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214100
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5461.53104
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.06325100
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.72731988
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9014.51876
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 76 -
Rwork0.281 1563 -
obs--98.97 %
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)
10.4481-0.46680.22281.7192-0.54321.37710.04470.01180.0402-0.0284-0.0270.05490.0515-0.0594-0.01770.0112-0.00150.010.09640.02410.13582.084321.65274.4224
21.4817-0.09130.03741.5357-0.66982.5337-0.0195-0.05670.06580.2170.0022-0.0916-0.20780.0350.01730.1157-0.01640.00730.00640.00250.12134.564812.683836.8939
30.5653-0.4134-0.03891.5721-0.61793.49870.1036-0.0745-0.0083-0.0583-0.10990.14820.2026-0.57140.00630.0683-0.1169-0.02040.264-0.0010.060120.2691-12.544633.5219
40.81310.579-0.39241.3350.79663.61830.0049-0.0347-0.0881-0.00250.0297-0.09750.52580.3134-0.03460.21970.1234-0.01540.08030.00070.089724.0971-13.09610.0134
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 146
2X-RAY DIFFRACTION2B2 - 146
3X-RAY DIFFRACTION3C2 - 146
4X-RAY DIFFRACTION4D2 - 146

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