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- PDB-1ynd: Structure of human cyclophilin A in complex with the novel immuno... -

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Basic information

Entry
Database: PDB / ID: 1ynd
TitleStructure of human cyclophilin A in complex with the novel immunosuppressant sanglifehrin A at 1.6A resolution
ComponentsPeptidyl-prolyl cis-trans isomerase A
KeywordsISOMERASE / beta sandwich / cyclophilin-ligand complex / cyclosporin / rotamase
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 / virion binding / leukocyte chemotaxis / negative regulation of stress-activated MAPK cascade ...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 / virion binding / leukocyte chemotaxis / negative regulation of stress-activated MAPK cascade / endothelial cell activation / protein peptidyl-prolyl isomerization / Basigin interactions / cyclosporin A binding / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / Early Phase of HIV Life Cycle / Integration of provirus / negative regulation of protein phosphorylation / APOBEC3G mediated resistance to HIV-1 infection / viral release from host cell / Calcineurin activates NFAT / activation of protein kinase B activity / Binding and entry of HIV virion / positive regulation of viral genome replication / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of protein kinase activity / neutrophil chemotaxis / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / positive regulation of protein secretion / peptidyl-prolyl cis-trans isomerase activity / peptidylprolyl isomerase / Assembly Of The HIV Virion / positive regulation of NF-kappaB transcription factor activity / Budding and maturation of HIV virion / platelet activation / platelet aggregation / neuron differentiation / SARS-CoV-1 activates/modulates innate immune responses / integrin binding / unfolded protein binding / positive regulation of protein phosphorylation / Platelet degranulation / protein folding / cellular response to oxidative stress / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / positive regulation of MAPK cascade / focal adhesion / apoptotic process / Neutrophil degranulation / protein-containing complex / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleus / membrane / cytosol / cytoplasm
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
SANGLIFEHRIN A / Peptidyl-prolyl cis-trans isomerase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKallen, J. / Sedrani, R. / Zenke, G. / Wagner, J.
Citation
Journal: J.Biol.Chem. / Year: 2005
Title: Structure of human cyclophilin A in complex with the novel immunosuppressant sanglifehrin A at 1.6 A resolution.
Authors: Kallen, J. / Sedrani, R. / Zenke, G. / Wagner, J.
#1: Journal: J.Am.Chem.Soc. / Year: 2003
Title: Sanglifehrin-Cyclophilin Interaction: Degradation Work, Synthetic Macrocyclic Analogues, X-ray Crystal Structure, and Binding Data
Authors: Sedrani, R. / Kallen, J. / Cabrejas, L.M. / Papageorgiou, C.D. / Senia, F. / Rohrbach, S. / Wagner, D. / Thai, B. / Jutzi-Erne, A.M. / France, J.
History
DepositionJan 24, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)38,2544
Polymers36,0732
Non-polymers2,1812
Water6,521362
1
A: Peptidyl-prolyl cis-trans isomerase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1272
Polymers18,0371
Non-polymers1,0901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptidyl-prolyl cis-trans isomerase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1272
Polymers18,0371
Non-polymers1,0901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.600, 65.400, 76.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 18036.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPIA, CYPA / Plasmid: modified pkk 223-2 / Species (production host): Escherichia coli
Production host: Escherichia coli str. K12 substr. W3110 (bacteria)
Strain (production host): W3110 / References: UniProt: P62937, peptidylprolyl isomerase
#2: Chemical ChemComp-SFA / SANGLIFEHRIN A / (3S,6S,9R,10R,11S,12S,13E,15E,18S,21S)-18-{(1E,3E,7S,8S)-9-[(2S,3R,4S,5S,6R,9S,11S)-9-ETHYL-4-HYDROXY-3,5,11-TRIMETHYL- 8-OXO-1-OXA-7-AZASPIRO[5.5]UNDEC-2-YL]-8-HYDROXY-1,7-DIMETHYLNONA-1,3-DIENYL}-10,12-DIHYDROXY-3-(3-HYDROXYBENZYL)-6-ISOP ROPYL-11-METHYL-9-(3-OXOBUTYL)-19-OXA-1,4,7,25-TETRAAZABICYCLO[19.3.1]PENTACOSA-13,15-DIENE-2,5,8,20-TETRONE


Mass: 1090.390 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C60H91N5O13
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 2.2 Å3/Da / Density % sol: 42.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Mg acetate, Na cacodylate, PEG4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.873 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 18, 1997
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.6→15 Å / Num. obs: 41593 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 14.4 Å2 / Rsym value: 0.075 / Net I/σ(I): 16.4
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 4102 / Rsym value: 0.456 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CWA

1cwa


Resolution: 1.6→15 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.205 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.089 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18461 2096 5 %RANDOM
Rwork0.16332 ---
all0.1644 39452 --
obs0.1644 39452 98.81 %-
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: 14.282 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2---0.14 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2516 0 156 362 3034
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0212736
X-RAY DIFFRACTIONr_bond_other_d0.0010.022276
X-RAY DIFFRACTIONr_angle_refined_deg1.1832.0063680
X-RAY DIFFRACTIONr_angle_other_deg0.69435324
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5833326
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.72915464
X-RAY DIFFRACTIONr_chiral_restr0.0750.2392
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023012
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02554
X-RAY DIFFRACTIONr_nbd_refined0.2150.3430
X-RAY DIFFRACTIONr_nbd_other0.20.32122
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.5259
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0250.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.313
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2720.331
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2120.519
X-RAY DIFFRACTIONr_mcbond_it0.6481.51606
X-RAY DIFFRACTIONr_mcangle_it1.26322560
X-RAY DIFFRACTIONr_scbond_it1.77831130
X-RAY DIFFRACTIONr_scangle_it2.8494.51120
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.238 136
Rwork0.227 2710
obs-2710

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