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- PDB-4dga: TRIMCyp cyclophilin domain from Macaca mulatta: HIV-1 CA(O-loop) ... -

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Basic information

Entry
Database: PDB / ID: 4dga
TitleTRIMCyp cyclophilin domain from Macaca mulatta: 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 / : / neutrophil chemotaxis / activation of protein kinase B activity / negative regulation of protein phosphorylation / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / negative regulation of protein kinase activity / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / platelet activation / platelet aggregation / host multivesicular body / 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 / symbiont-mediated suppression of host gene expression / 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 / 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 / host cell nucleus / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / extracellular region / membrane / nucleus / cytosol / 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 / 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 / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Zinc finger, RING-type / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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)68,3924
Polymers68,3924
Non-polymers00
Water6,287349
1
A: TRIMCyp
C: capsid protein


Theoretical massNumber of molelcules
Total (without water)34,1962
Polymers34,1962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TRIMCyp
D: capsid protein


Theoretical massNumber of molelcules
Total (without water)34,1962
Polymers34,1962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.590, 111.350, 67.760
Angle α, β, γ (deg.)90.000, 102.390, 90.000
Int Tables number4
Space group name H-MP1211
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
111THRTHRPHEPHEAA5 - 675 - 67
211THRTHRPHEPHEBB5 - 675 - 67
121GLYGLYLEULEUAA75 - 16475 - 164
221GLYGLYLEULEUBB75 - 16475 - 164
112PROPROALAALACC1 - 142 - 15
212PROPROALAALADD1 - 142 - 15
122ILEILEASNASNCC37 - 5738 - 58
222ILEILEASNASNDD37 - 5738 - 58
132THRTHRILEILECC72 - 14173 - 142
232THRTHRILEILEDD72 - 14173 - 142

NCS ensembles :
ID
1
2

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Components

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


Mass: 18016.473 Da / Num. of mol.: 2 / 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 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.: 349 / 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: 2.08 Å3/Da / Density % sol: 40.84 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% w/v PEG5000 MME, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.072 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 24, 2010
RadiationMonochromator: single crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 1.9→66.182 Å / Num. all: 41766 / Num. obs: 41766 / % possible obs: 95.1 % / Redundancy: 1.8 % / Biso Wilson estimate: 20.45 Å2 / Rsym value: 0.053 / Net I/σ(I): 9.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-21.70.1963.6904853220.19683.1
2-2.121.90.1345.11104259560.13498.2
2.12-2.271.90.0985.91044556140.09898.2
2.27-2.451.90.079.4957451540.0798.1
2.45-2.691.90.0698.5888847970.06998.1
2.69-31.90.05510.4799842940.05597.4
3-3.471.80.04412.5699637930.04497.2
3.47-4.251.80.03814.8580831750.03896
4.25-6.011.80.03813.5421323940.03894.5
6.01-42.6051.90.03118.2245912670.03189.2

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Processing

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

2wlw

1ak4


Resolution: 1.9→66.18 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.915 / WRfactor Rfree: 0.2547 / WRfactor Rwork: 0.2058 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8482 / SU B: 7.183 / SU ML: 0.112 / SU R Cruickshank DPI: 0.1918 / SU Rfree: 0.1687 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.192 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2431 2111 5.1 %RANDOM
Rwork0.1959 ---
obs0.1983 41697 94.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 67.29 Å2 / Biso mean: 25.0759 Å2 / Biso min: 9.45 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å2-0.21 Å2
2--1.3 Å20 Å2
3----1.27 Å2
Refinement stepCycle: LAST / Resolution: 1.9→66.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4554 0 0 349 4903
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194689
X-RAY DIFFRACTIONr_bond_other_d0.0010.023224
X-RAY DIFFRACTIONr_angle_refined_deg1.2041.956346
X-RAY DIFFRACTIONr_angle_other_deg0.83837895
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7855594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.23224.75200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.09615792
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7341519
X-RAY DIFFRACTIONr_chiral_restr0.0690.2687
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215210
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02917
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2029MEDIUM POSITIONAL0.290.5
1A2029MEDIUM THERMAL1.292
2C1241MEDIUM POSITIONAL0.280.5
2C1241MEDIUM THERMAL1.162
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 116 -
Rwork0.259 2261 -
all-2377 -
obs--73.77 %
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)
12.12820.0565-0.46563.07440.84192.61520.00040.029-0.1123-0.1341-0.0529-0.16970.22380.00560.05250.04070.0120.02020.01030.00810.02134.410225.842814.2441
23.32120.80351.00212.9902-0.80622.7677-0.14680.22770.3546-0.17540.12220.1898-0.32370.05570.02460.0805-0.0286-0.01560.030.02810.0437-21.7952-19.493514.7753
33.67910.4455-0.80431.5494-0.783.5795-0.06980.0243-0.12040.06310.02230.10450.1578-0.33180.04750.0301-0.0101-0.01380.0366-0.01990.0625-16.384113.047644.9698
44.48571.35021.60022.77071.56611.8884-0.0670.18370.06540.04860.0562-0.2034-0.09770.02920.01070.02270.00910.00070.01770.02180.0935-1.4831-5.475145.3712
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 164
2X-RAY DIFFRACTION2B2 - 165
3X-RAY DIFFRACTION3C1 - 145
4X-RAY DIFFRACTION4D1 - 142

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