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- PDB-4ipz: SmBz bound to Cyclophilin A -

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Basic information

Entry
Database: PDB / ID: 4ipz
TitleSmBz bound to Cyclophilin A
Components
  • Peptidyl-prolyl cis-trans isomerase A
  • cyclosporine SmBz-CsA
KeywordsIsomerase/isomerase inhibitor / Cyclophilin fold / Peptidyl-prolyl Isomerase / Cyclosporine A / Isomerase-isomerase inhibitor complex
Function / homology
Function and homology information


negative regulation of protein K48-linked ubiquitination / negative regulation of viral life cycle / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication / leukocyte chemotaxis / endothelial cell activation / virion binding ...negative regulation of protein K48-linked ubiquitination / negative regulation of viral life cycle / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication / leukocyte chemotaxis / endothelial cell activation / virion binding / Basigin interactions / negative regulation of stress-activated MAPK cascade / cyclosporin A binding / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Calcineurin activates NFAT / viral release from host cell / Binding and entry of HIV virion / positive regulation of viral genome replication / protein peptidyl-prolyl isomerization / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of protein dephosphorylation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / activation of protein kinase B activity / neutrophil chemotaxis / negative regulation of protein phosphorylation / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / positive regulation of protein secretion / Assembly Of The HIV Virion / negative regulation of protein kinase activity / Budding and maturation of HIV virion / neuron differentiation / platelet activation / platelet aggregation / SARS-CoV-1 activates/modulates innate immune responses / unfolded protein binding / integrin binding / protein folding / Platelet degranulation / positive regulation of NF-kappaB transcription factor activity / cellular response to oxidative stress / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / positive regulation of MAPK cascade / response to hypoxia / positive regulation of protein phosphorylation / focal adhesion / apoptotic process / Neutrophil degranulation / protein-containing complex / RNA binding / extracellular space / extracellular exosome / extracellular region / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
SmBz, cyclosporin A derivative / : / Peptidyl-prolyl cis-trans isomerase A
Similarity search - Component
Biological speciesHomo sapiens (human)
Tolypocladium inflatum (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.67 Å
AuthorsPrice, A.J. / Jacques, D.A. / James, L.C.
CitationJournal: Nature / Year: 2013
Title: HIV-1 evades innate immune recognition through specific cofactor recruitment.
Authors: Rasaiyaah, J. / Tan, C.P. / Fletcher, A.J. / Price, A.J. / Blondeau, C. / Hilditch, L. / Jacques, D.A. / Selwood, D.L. / James, L.C. / Noursadeghi, M. / Towers, G.J.
History
DepositionJan 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2013Group: Database references
Revision 1.2Aug 29, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: entity / entity_src_nat / pdbx_entity_src_syn
Item: _entity.pdbx_description / _entity.pdbx_mutation / _entity.src_method
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0May 8, 2024Group: Atomic model / Category: atom_site / atom_site_anisotrop
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.type_symbol

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase A
B: cyclosporine SmBz-CsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4624
Polymers19,3912
Non-polymers712
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-20 kcal/mol
Surface area7640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.180, 64.600, 80.070
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
DetailsThe biological assembly is a heterodimer formed between entity 1 and entity 2. There is one biological assembly in the asymmetric unit.

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase A / PPIase A / Cyclophilin A / Cyclosporin A-binding protein / Rotamase A


Mass: 18036.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPIA, CYPA / Production host: Escherichia coli (E. coli) / References: UniProt: P62937, peptidylprolyl isomerase
#2: Protein/peptide cyclosporine SmBz-CsA


Type: Cyclic peptide / Class: Immunosuppressant / Mass: 1354.757 Da / Num. of mol.: 1 / Mutation: (sar)7(1JM) / Source method: obtained synthetically / Details: CsA has been modified at position 4 (sarcosine) / Source: (synth.) Tolypocladium inflatum (fungus) / References: NOR: NOR00033, SmBz, cyclosporin A derivative
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 1.81 Å3/Da / Density % sol: 31.91 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 1M LiCl, 0.1M MES, 30% (w/v) PEG6000, 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: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.67→50.277 Å / Num. all: 16480 / Num. obs: 16480 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rsym value: 0.061 / Net I/σ(I): 17.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.67-1.765.80.5621.41257221820.56291.1
1.76-1.8660.3492.21342422440.34998.5
1.86-1.9960.2073.71287021320.20799.2
1.99-2.156.10.1315.81219920040.13199.3
2.15-2.356.10.0878.81123218450.08799.5
2.35-2.636.20.06711.31037816870.06799.9
2.63-3.046.10.04814.9921915040.048100
3.04-3.726.20.04514.3786712780.045100
3.72-5.276.10.02724.5616210150.027100
5.27-32.35.70.02921.233675890.02999.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.67 Å32.3 Å
Translation1.67 Å32.3 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.20data scaling
PHASER2.5.2phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CWA

1cwa


Resolution: 1.67→32.32 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.2014 / WRfactor Rwork: 0.159 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8783 / SU B: 4.274 / SU ML: 0.075 / SU R Cruickshank DPI: 0.1177 / SU Rfree: 0.1163 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2178 831 5 %RANDOM
Rwork0.172 ---
obs0.1743 16479 98.86 %-
all-16479 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 53.77 Å2 / Biso mean: 21.1822 Å2 / Biso min: 11.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å2-0 Å20 Å2
2--0.62 Å20 Å2
3----1.13 Å2
Refinement stepCycle: LAST / Resolution: 1.67→32.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1330 0 2 184 1516
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0191375
X-RAY DIFFRACTIONr_bond_other_d0.0010.021330
X-RAY DIFFRACTIONr_angle_refined_deg1.0821.9911817
X-RAY DIFFRACTIONr_angle_other_deg1.3693.0033053
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5895165
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.52724.03557
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.97815214
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.528156
X-RAY DIFFRACTIONr_chiral_restr0.0590.2199
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211517
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02323
X-RAY DIFFRACTIONr_mcbond_it1.0111.865701
X-RAY DIFFRACTIONr_mcbond_other1.011.865700
X-RAY DIFFRACTIONr_mcangle_it1.6263.119842
LS refinement shellResolution: 1.671→1.714 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 58 -
Rwork0.341 1099 -
all-1157 -
obs--95.7 %
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)
10.41040.16020.52810.11420.2051.178-0.0180.0858-0.02160.03320.04210.0054-0.0410.0841-0.02410.0489-0.0015-0.00590.0359-0.00630.030714.051815.192690.7715
21.2225-2.1627-0.26063.83980.48740.1059-0.03350.0142-0.1180.1224-0.00460.21340.10050.02070.03810.16920.046-00.0184-0.02340.09355.29073.674984.4388
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 165
2X-RAY DIFFRACTION2B1 - 11

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