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- PDB-4dgb: TRIMCyp cyclophilin domain from Macaca mulatta: HIV-2 CA cyclophi... -

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Basic information

Entry
Database: PDB / ID: 4dgb
TitleTRIMCyp cyclophilin domain from Macaca mulatta: HIV-2 CA cyclophilin-binding loop complex
Components
  • TRIMCyp
  • capsid protein
KeywordsISOMERASE/VIRAL PROTEIN / anti-viral protein / ISOMERASE-VIRAL PROTEIN complex
Function / homology
Function and homology information


negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / negative regulation of viral life cycle / heparan sulfate binding / regulation of viral genome replication / leukocyte chemotaxis / negative regulation of stress-activated MAPK cascade / endothelial cell activation ...negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / negative regulation of viral life cycle / heparan sulfate binding / regulation of viral genome replication / leukocyte chemotaxis / negative regulation of stress-activated MAPK cascade / endothelial cell activation / protein peptidyl-prolyl isomerization / cyclosporin A binding / viral budding via host ESCRT complex / negative regulation of protein phosphorylation / activation of protein kinase B activity / positive regulation of viral genome replication / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of protein kinase activity / neutrophil chemotaxis / positive regulation of protein secretion / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / : / RING-type E3 ubiquitin transferase / platelet activation / autophagy / platelet aggregation / integrin binding / host multivesicular body / positive regulation of protein phosphorylation / protein folding / transferase activity / viral nucleocapsid / cellular response to oxidative stress / defense response to virus / positive regulation of MAPK cascade / protein ubiquitination / viral translational frameshifting / innate immune response / apoptotic process / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / protein-containing complex / RNA binding / extracellular region / zinc ion binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / Cyclophilin-like / B-box zinc finger / Cyclophilin / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site ...Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / Cyclophilin-like / B-box zinc finger / Cyclophilin / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / : / 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. / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Zinc finger, RING-type / 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 / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Zinc finger, RING/FYVE/PHD-type / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase A / Gag polyprotein / Peptidyl-prolyl cis-trans isomerase A
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
Human immunodeficiency virus 2
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.702 Å
AuthorsCaines, M.E.C. / Bichel, K. / Price, A.J. / McEwan, W.A. / James, L.C.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Diverse HIV viruses are targeted by a conformationally dynamic antiviral.
Authors: Caines, M.E. / Bichel, K. / Price, A.J. / McEwan, W.A. / Towers, G.J. / Willett, B.J. / Freund, S.M. / James, L.C.
History
DepositionJan 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 1.2Apr 18, 2012Group: Database references
Revision 1.3Sep 13, 2023Group: 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: TRIMCyp
B: capsid protein


Theoretical massNumber of molelcules
Total (without water)18,5672
Polymers18,5672
Non-polymers00
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint-3 kcal/mol
Surface area7800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.170, 55.720, 70.840
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TRIMCyp / Peptidyl-prolyl cis-trans isomerase


Mass: 18016.473 Da / Num. of mol.: 1 / Fragment: cyclophilin domain (UNP residues 304-468)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Gene: TRIMCyp / Plasmid: pOPT / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3)
References: UniProt: B0LJC8, UniProt: P62940*PLUS, peptidylprolyl isomerase
#2: Protein/peptide capsid protein


Mass: 550.647 Da / Num. of mol.: 1 / Fragment: cyclophilin-binding loop (UNP residues 221-226) / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 2 / References: UniProt: P04590
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 1.92 Å3/Da / Density % sol: 36.02 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 2.35 M ammonium phosphate dibasic, 0.1 M Tris-HCl, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.702→71.08 Å / Num. all: 16284 / Num. obs: 15839 / % possible obs: 95 % / Redundancy: 2.3 % / Biso Wilson estimate: 17.04 Å2 / Rsym value: 0.037 / Net I/σ(I): 14.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.702-1.792.30.1086.9935041440.10891.5
1.79-1.92.30.0828.9917240240.08292.8
1.9-2.032.30.06311.5866238010.06394.1
2.03-2.22.30.04714814935610.04795.1
2.2-2.412.30.05112.7747233070.05194.4
2.41-2.692.30.03718.2695330360.03796.8
2.69-3.112.30.03219.6620427150.03297.6
3.11-3.812.30.03318.9533823390.03398.6
3.81-5.382.30.02622.3412118200.02699
5.38-32.312.20.02425.8226810160.02498.2

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Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WLW

2wlw


Resolution: 1.702→30.34 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.2115 / WRfactor Rwork: 0.1775 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8878 / SU B: 3.89 / SU ML: 0.068 / SU R Cruickshank DPI: 0.128 / SU Rfree: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2103 806 5.1 %RANDOM
Rwork0.1775 ---
obs0.1791 15838 97.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 56.33 Å2 / Biso mean: 18.2559 Å2 / Biso min: 9.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2--0.16 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.702→30.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1286 0 0 225 1511
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221330
X-RAY DIFFRACTIONr_bond_other_d0.0010.02937
X-RAY DIFFRACTIONr_angle_refined_deg1.221.9441789
X-RAY DIFFRACTIONr_angle_other_deg0.7932279
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.195171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.63624.06859
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.37815222
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.746156
X-RAY DIFFRACTIONr_chiral_restr0.0730.2185
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211506
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02283
LS refinement shellResolution: 1.702→1.746 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42 52 -
Rwork0.375 966 -
all-1018 -
obs--94.79 %
Refinement TLS params.Method: refined / Origin x: 9.3657 Å / Origin y: -0.2112 Å / Origin z: 7.0043 Å
111213212223313233
T0.003 Å20.0041 Å20.001 Å2-0.0085 Å2-0.0045 Å2--0.0187 Å2
L1.2386 °20.402 °20.4476 °2-1.4115 °2-0.6688 °2--1.4452 °2
S-0.0185 Å °-0.0121 Å °0.0202 Å °-0.0017 Å °0.0004 Å °0.0676 Å °-0.0249 Å °-0.0411 Å °0.0181 Å °

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