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- PDB-7uxm: Structure of PPIA in complex with FP29092, a Helicon Polypeptide -

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Basic information

Entry
Database: PDB / ID: 7uxm
TitleStructure of PPIA in complex with FP29092, a Helicon Polypeptide
Components
  • FP29092
  • Peptidyl-prolyl cis-trans isomerase A
KeywordsISOMERASE / Complex / stapled
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 / negative regulation of stress-activated MAPK cascade / endothelial cell activation ...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 / negative regulation of stress-activated MAPK cascade / endothelial cell activation / virion binding / Basigin interactions / 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 / cellular response to oxidative stress / positive regulation of NF-kappaB transcription factor activity / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / positive regulation of MAPK cascade / positive regulation of protein phosphorylation / focal adhesion / apoptotic process / Neutrophil degranulation / protein-containing complex / extracellular space / RNA binding / extracellular exosome / extracellular region / membrane / nucleus / 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
AMINO GROUP / 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: 1.2 Å
AuthorsLi, K. / Agarwal, S. / Tokareva, O. / Thomson, T. / Wahl, S. / Verdine, G. / McGee, J.
Funding support1items
OrganizationGrant numberCountry
Other private
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

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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: Peptidyl-prolyl cis-trans isomerase A
C: Peptidyl-prolyl cis-trans isomerase A
D: FP29092
E: FP29092
F: FP29092
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,84924
Polymers60,4796
Non-polymers1,37018
Water12,052669
1
A: Peptidyl-prolyl cis-trans isomerase A
D: FP29092
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4305
Polymers20,1602
Non-polymers2703
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-2 kcal/mol
Surface area8870 Å2
MethodPISA
2
B: Peptidyl-prolyl cis-trans isomerase A
E: FP29092
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6789
Polymers20,1602
Non-polymers5197
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-3 kcal/mol
Surface area8300 Å2
MethodPISA
3
C: Peptidyl-prolyl cis-trans isomerase A
F: FP29092
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,74010
Polymers20,1602
Non-polymers5818
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint1 kcal/mol
Surface area8090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.000, 73.270, 113.210
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

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Protein / Protein/peptide , 2 types, 6 molecules ABCDEF

#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.: 3
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 FP29092


Mass: 2066.261 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: Stapled peptide / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 687 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NH2 / AMINO GROUP / Amine


Mass: 16.023 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NH2
#5: Chemical ChemComp-WHL / N,N'-(1,4-phenylene)diacetamide


Mass: 192.214 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H12N2O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 669 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 1.92 Å3/Da / Density % sol: 35.94 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.15 M Potassium bromide, 30% w/v Polyethylene glycol monomethyl ether 2,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→44.79 Å / Num. obs: 145752 / % possible obs: 99.96 % / Redundancy: 13.3 % / Biso Wilson estimate: 11.44 Å2 / CC1/2: 0.999 / Net I/σ(I): 13.3
Reflection shellResolution: 1.2→1.24 Å / Rmerge(I) obs: 1.38 / Num. unique obs: 14438 / CC1/2: 0.753

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Processing

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

3k0n


Resolution: 1.2→44.79 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1896 7216 4.95 %
Rwork0.1612 138536 -
obs0.1625 145752 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.92 Å2 / Biso mean: 16.7783 Å2 / Biso min: 7.37 Å2
Refinement stepCycle: final / Resolution: 1.2→44.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4192 0 93 669 4954
Biso mean--25.57 27.91 -
Num. residues----543
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.2-1.210.30722290.252945894818
1.21-1.230.27492530.250345404793
1.23-1.240.25892400.234345854825
1.24-1.260.24552220.221245594781
1.26-1.280.26652600.217845684828
1.28-1.290.24962270.220845424769
1.29-1.310.23852330.208245854818
1.31-1.330.2452510.207345854836
1.33-1.350.22442400.201445834823
1.35-1.370.24492410.18745604801
1.37-1.40.20982460.175345874833
1.4-1.420.22122460.175245514797
1.42-1.450.20212210.165246094830
1.45-1.480.20222340.157245864820
1.48-1.510.17232420.152346144856
1.51-1.550.19152440.145245824826
1.55-1.590.19182300.145146134843
1.59-1.630.17262390.141645864825
1.63-1.680.17282380.141346254863
1.68-1.730.1892430.145146004843
1.73-1.790.18062620.144345904852
1.79-1.860.16542480.140346324880
1.86-1.950.17752520.142446134865
1.95-2.050.16522340.138946324866
2.05-2.180.16912360.143246754911
2.18-2.350.16862710.147946224893
2.35-2.590.18732370.166246744911
2.59-2.960.19882450.173447094954
2.96-3.730.18972020.154648085010
3.73-44.790.16812500.158849325182

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