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- PDB-7uxn: Structure of PPIA in complex with FP29103, a Helicon Polypeptide -

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Basic information

Entry
Database: PDB / ID: 7uxn
TitleStructure of PPIA in complex with FP29103, a Helicon Polypeptide
Components
  • FP29103
  • Peptidyl-prolyl cis-trans isomerase A
KeywordsISOMERASE / Complex / stapled
Function / homology
Function and homology information


negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / negative regulation of viral life cycle / lipid droplet organization / 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 / negative regulation of viral life cycle / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication / virion binding / leukocyte chemotaxis / negative regulation of stress-activated MAPK cascade / endothelial cell activation / Basigin interactions / protein peptidyl-prolyl isomerization / 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 / viral release from host cell / negative regulation of protein phosphorylation / Calcineurin activates NFAT / Binding and entry of HIV virion / positive regulation of viral genome replication / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / activation of protein kinase B activity / neutrophil chemotaxis / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / peptidyl-prolyl cis-trans isomerase activity / negative regulation of protein kinase activity / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / positive regulation of protein secretion / peptidylprolyl isomerase / Assembly Of The HIV Virion / Budding and maturation of HIV virion / platelet activation / platelet aggregation / neuron differentiation / positive regulation of NF-kappaB transcription factor activity / SARS-CoV-1 activates/modulates innate immune responses / integrin binding / unfolded protein binding / Platelet degranulation / protein folding / positive regulation of protein phosphorylation / 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-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
Similarity search - Domain/homology
N,N'-(1,4-phenylene)diacetamide / Peptidyl-prolyl cis-trans isomerase A
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsLi, K. / Agarwal, S. / Tokareva, O. / Thomson, T. / Tattersfield, H. / Wahl, S. / Verdine, G. / McGee, J.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: De novo mapping of alpha-helix recognition sites on protein surfaces using unbiased libraries.
Authors: Li, K. / Tokareva, O.S. / Thomson, T.M. / Wahl, S.C.T. / Travaline, T.L. / Ramirez, J.D. / Choudary, S.K. / Agarwal, S. / Walkup 4th, W.G. / Olsen, T.J. / Brennan, M.J. / Verdine, G.L. / McGee, J.H.
History
DepositionMay 5, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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: FP29103
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6283
Polymers19,4362
Non-polymers1921
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-11 kcal/mol
Surface area7980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.080, 48.010, 81.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 18093.555 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 FP29103


Mass: 1342.569 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Stapled peptide / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-WHL / N,N'-(1,4-phenylene)diacetamide


Mass: 192.214 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.13 Å3/Da / Density % sol: 42.18 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium acetate, 0.1 M Sodium cacodylate pH 6.5, 30% w/v PEG 8000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.36→41.41 Å / Num. obs: 36286 / % possible obs: 99.73 % / Redundancy: 12.3 % / Biso Wilson estimate: 16.7 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.044 / Net I/σ(I): 27.8
Reflection shellResolution: 1.36→1.41 Å / Rmerge(I) obs: 0.951 / Num. unique obs: 3474 / CC1/2: 0.755

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K0N

3k0n


Resolution: 1.36→41.41 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2166 2000 5.51 %
Rwork0.1933 34286 -
obs0.1946 36286 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 56.49 Å2 / Biso mean: 21.356 Å2 / Biso min: 10.49 Å2
Refinement stepCycle: final / Resolution: 1.36→41.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1351 0 14 197 1562
Biso mean--23.42 30.48 -
Num. residues----176
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.36-1.390.31051350.29952315245096
1.39-1.430.26711410.269724062547100
1.43-1.470.27161410.23824192560100
1.47-1.520.24061420.227124372579100
1.52-1.580.24461400.212924062546100
1.58-1.640.23321440.218124562600100
1.64-1.710.23531400.211124172557100
1.71-1.80.25751420.202924422584100
1.8-1.920.22551440.202624542598100
1.92-2.060.24081430.206824422585100
2.06-2.270.22081430.197824652608100
2.27-2.60.22011440.196324792623100
2.6-3.280.20851470.190425102657100
3.28-41.410.18381540.161926382792100

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