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- PDB-4dge: TRIMCyp cyclophilin domain from Macaca mulatta: H70C mutant, HIV-... -

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Basic information

Entry
Database: PDB / ID: 4dge
TitleTRIMCyp cyclophilin domain from Macaca mulatta: H70C mutant, HIV-1 CA(O-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 / heparan sulfate binding / regulation of viral genome replication / leukocyte chemotaxis / endothelial cell activation / negative regulation of stress-activated MAPK cascade / cyclosporin A binding / viral budding via host ESCRT complex ...negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / heparan sulfate binding / regulation of viral genome replication / leukocyte chemotaxis / endothelial cell activation / negative regulation of stress-activated MAPK cascade / cyclosporin A binding / viral budding via host ESCRT complex / protein peptidyl-prolyl isomerization / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of protein dephosphorylation / activation of protein kinase B activity / neutrophil chemotaxis / negative regulation of protein phosphorylation / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / negative regulation of protein kinase activity / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / platelet activation / host multivesicular body / platelet aggregation / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / integrin binding / protein folding / positive regulation of NF-kappaB transcription factor activity / symbiont-mediated suppression of host gene expression / cellular response to oxidative stress / viral nucleocapsid / DNA recombination / host cell cytoplasm / positive regulation of MAPK cascade / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / response to hypoxia / protein ubiquitination / symbiont entry into host cell / positive regulation of protein phosphorylation / intracellular membrane-bounded organelle / lipid binding / apoptotic process / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / extracellular region / membrane / nucleus / cytoplasm / cytosol
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 / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Gag protein p6 / Gag protein p6 ...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 / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Gag protein p6 / Gag protein p6 / Cyclophilin-like / Cyclophilin / 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 / Reverse transcriptase connection / Reverse transcriptase connection domain / Zinc finger RING-type profile. / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Zinc finger, RING-type / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / 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. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Zinc finger, RING/FYVE/PHD-type / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase A / Gag-Pol polyprotein / Peptidyl-prolyl cis-trans isomerase A / Gag polyprotein
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 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 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRIMCyp
B: TRIMCyp
C: capsid protein
D: capsid protein


Theoretical massNumber of molelcules
Total (without water)68,3224
Polymers68,3224
Non-polymers00
Water3,603200
1
A: TRIMCyp
C: capsid protein


Theoretical massNumber of molelcules
Total (without water)34,1612
Polymers34,1612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-8 kcal/mol
Surface area14470 Å2
MethodPISA
2
B: TRIMCyp
D: capsid protein


Theoretical massNumber of molelcules
Total (without water)34,1612
Polymers34,1612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-9 kcal/mol
Surface area14830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.070, 59.710, 70.470
Angle α, β, γ (deg.)65.080, 83.870, 79.650
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Refine code: 4

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111VALVALGLUGLUAA2 - 1652 - 165
211VALVALGLUGLUBB2 - 1652 - 165
112PROPROVALVALCC1 - 32 - 4
212PROPROVALVALDD1 - 32 - 4
122VALVALARGARGCC11 - 14312 - 144
222VALVALARGARGDD11 - 14312 - 144

NCS ensembles :
ID
1
2

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Components

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


Mass: 17981.469 Da / Num. of mol.: 2 / Fragment: cyclophilin domain (UNP residues 304-468) / Mutation: H70C
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 capsid protein


Mass: 16179.579 Da / Num. of mol.: 2 / Fragment: cyclophilin-binding domain (UNP residues 133-277) / Mutation: yes
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: M-GROUP (NL4-3) / Gene: gag / Plasmid: pOPT / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q72497, UniProt: P12497*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.15 Å3/Da / Density % sol: 42.67 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 23.5% w/v PEG8000, 0.1 M HEPES, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jul 29, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→63.87 Å / Num. all: 27012 / Num. obs: 27012 / % possible obs: 93.8 % / Redundancy: 1.7 % / Biso Wilson estimate: 19.92 Å2 / Rsym value: 0.055 / Net I/σ(I): 9.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.2-2.321.60.1444.9609937130.14489.1
2.32-2.461.70.125.9624637550.1293.8
2.46-2.631.70.1017.1591635520.10194.4
2.63-2.841.70.0838.4551733250.08395.4
2.84-3.111.70.06610.2504630350.06695.6
3.11-3.481.70.05212.3466327870.05295.8
3.48-4.021.70.0416.5409724290.0495.4
4.02-4.921.70.03418.1354020650.03494.7
4.92-6.961.80.03617271015380.03692.8
6.96-38.4111.80.02820.514868130.02889.1

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2WLW AND 1AK4

2wlw

1ak4


Resolution: 2.2→63.87 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.89 / WRfactor Rfree: 0.2508 / WRfactor Rwork: 0.1849 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8347 / SU B: 12.914 / SU ML: 0.163 / SU R Cruickshank DPI: 0.3791 / SU Rfree: 0.2542 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.379 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1350 5 %RANDOM
Rwork0.186 ---
obs0.1894 27009 93.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 56.17 Å2 / Biso mean: 19.025 Å2 / Biso min: 3.66 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20.07 Å20.13 Å2
2---0.28 Å2-0.5 Å2
3---0.51 Å2
Refinement stepCycle: LAST / Resolution: 2.2→63.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4680 0 0 200 4880
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224794
X-RAY DIFFRACTIONr_bond_other_d0.0010.023292
X-RAY DIFFRACTIONr_angle_refined_deg1.3741.9496486
X-RAY DIFFRACTIONr_angle_other_deg0.8733.0018050
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0725604
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.84624.831207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.47415806
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8651520
X-RAY DIFFRACTIONr_chiral_restr0.0760.2699
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215348
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02926
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2148MEDIUM POSITIONAL0.450.5
1A2148MEDIUM THERMAL0.622
2C1775MEDIUM POSITIONAL0.990.5
2C1775MEDIUM THERMAL1.822
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 88 -
Rwork0.192 1703 -
all-1791 -
obs--85.29 %
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)
12.4478-0.19250.24691.9019-0.58691.6884-0.0237-0.104-0.03450.03550.0257-0.0244-0.00240.0137-0.00210.02830.00130.00140.01330.00410.0057-8.9701-15.003528.2197
22.15560.61870.14242.56150.55331.5739-0.0240.01430.0193-0.0038-0.01290.0069-0.0115-0.02640.03690.01050.0047-0.00040.00630.00250.0035-34.0468-17.993477.903
32.6367-1.1644-0.66053.94791.86832.2372-0.02230.0378-0.04810.1251-0.11650.28790.0156-0.17730.13880.0993-0.0210.02050.11740.00960.0275-30.069811.219345.3764
40.92210.3822-0.20974.6692-0.75761.08990.0044-0.0096-0.076-0.15560.0421-0.22170.04710.1133-0.04660.0623-0.0003-0.00270.1051-0.00490.0304-14.82696.592762.5227
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 165
2X-RAY DIFFRACTION2B2 - 165
3X-RAY DIFFRACTION3C1 - 143
4X-RAY DIFFRACTION4D1 - 145

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