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- PDB-2x83: Evolutionary basis of HIV restriction by the antiretroviral TRIMCyp -

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Basic information

Entry
Database: PDB / ID: 2x83
TitleEvolutionary basis of HIV restriction by the antiretroviral TRIMCyp
Components
  • HIV-1 CAPSID
  • TRIM5/CypA fusion protein
KeywordsVIRAL PROTEIN / TRIM / RESTRICTION FACTOR IMMUNITY
Function / homology
Function and homology information


cyclosporin A binding / peptidyl-prolyl cis-trans isomerase activity / protein folding / viral nucleocapsid / host cell cytoplasm / protein ubiquitination / viral translational frameshifting / host cell nucleus / structural molecule activity / RNA binding ...cyclosporin A binding / peptidyl-prolyl cis-trans isomerase activity / protein folding / viral nucleocapsid / host cell cytoplasm / protein ubiquitination / viral translational frameshifting / host cell nucleus / structural molecule activity / RNA binding / zinc ion binding / cytoplasm
Similarity search - Function
Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / B-box zinc finger / Cyclophilin-like / B-Box-type zinc finger / Cyclophilin / B-box-type zinc finger / Zinc finger B-box type profile. ...Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / B-box zinc finger / Cyclophilin-like / B-Box-type zinc finger / Cyclophilin / B-box-type zinc finger / Zinc finger B-box type profile. / : / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / gag protein p24 N-terminal domain / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Zinc finger RING-type profile. / Zinc finger, RING-type / 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, RING/FYVE/PHD-type / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Tripartite motif-containing protein 5 / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Macaca fascicularis (crab-eating macaque)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 1.7 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 1.3Apr 24, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Experimental preparation / Other / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_src_gen / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_entity_src_syn / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_biol / struct_ref / struct_ref_seq
Item: _citation.journal_id_ISSN / _citation.page_first ..._citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity.pdbx_description / _entity.src_method / _pdbx_database_status.recvd_author_approval / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Revision 1.4May 8, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
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

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Assembly

Deposited unit
A: HIV-1 CAPSID
B: TRIM5/CypA fusion protein
C: HIV-1 CAPSID
D: TRIM5/CypA fusion protein


Theoretical massNumber of molelcules
Total (without water)67,9244
Polymers67,9244
Non-polymers00
Water11,422634
1
A: HIV-1 CAPSID
B: TRIM5/CypA fusion protein


Theoretical massNumber of molelcules
Total (without water)33,9622
Polymers33,9622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: HIV-1 CAPSID
D: TRIM5/CypA fusion protein


Theoretical massNumber of molelcules
Total (without water)33,9622
Polymers33,9622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.520, 110.150, 67.760
Angle α, β, γ (deg.)90.00, 101.59, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HIV-1 CAPSID


Mass: 16204.573 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN, RESIDUES 401-564
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: LW12.3 ISOLATE / Gene: gag / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: E9MJX7
#2: Protein TRIM5/CypA fusion protein


Mass: 17757.213 Da / Num. of mol.: 2 / Fragment: RESIDUES 304-466
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca fascicularis (crab-eating macaque)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B0ZE32
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 634 / 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: 1.82 Å3/Da / Density % sol: 32.06 % / Description: NONE
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 0.33 mM each of Mafa Cyp and HIV-1 CAN in 20 mM HEPES pH 7, 50 mM NaCl, 1 mM DTT was mixed with reservoir solution (30% PEG 6000, 1 M LiCl, 0.1 M HEPES pH 7, 0.5% ethyl acetate

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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: 1.7→20 Å / Num. obs: 60435 / % possible obs: 95.1 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.1

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Processing

SoftwareName: REFMAC / Version: 5.5.0109 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.7→66.38 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.922 / SU B: 6.555 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.256 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.246 2942 5.1 %RANDOM
Rwork0.158 ---
obs0.163 55058 96 %-
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: 24 Å2
Baniso -1Baniso -2Baniso -3
1--2.03 Å20 Å2-1.22 Å2
2--1.72 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.7→66.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4751 0 0 634 5385
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0224896
X-RAY DIFFRACTIONr_bond_other_d0.0010.023346
X-RAY DIFFRACTIONr_angle_refined_deg1.8031.9426637
X-RAY DIFFRACTIONr_angle_other_deg1.05238160
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3525632
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.22324.615208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.30315808
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6231520
X-RAY DIFFRACTIONr_chiral_restr0.1120.2717
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215537
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02969
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_it1.9231.53108
X-RAY DIFFRACTIONr_mcbond_other0.6351.51286
X-RAY DIFFRACTIONr_mcangle_it2.96524995
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.53131788
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.5094.51642
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.9138242
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.75 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 186 -
Rwork0.212 3703 -
obs--85.96 %

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