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- PDB-2x7k: The crystal structure of PPIL1 in complex with cyclosporine A sug... -

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Basic information

Entry
Database: PDB / ID: 2x7k
TitleThe crystal structure of PPIL1 in complex with cyclosporine A suggests a binding mode for SKIP
Components
  • CYCLOSPORIN A
  • PEPTIDYL-PROLYL CIS-TRANS ISOMERASE-LIKE 1
KeywordsISOMERASE/IMMUNOSUPPRESSANT / ISOMERASE-IMMUNOSUPPRESSANT COMPLEX / ISOMERASE-CYCLOSPORIN COMPLEX / CYCLOSPORIN A / IMMUNOSUPPRESSANT
Function / homology
Function and homology information


embryonic brain development / U2-type catalytic step 2 spliceosome / cyclosporin A binding / protein peptidyl-prolyl isomerization / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / mRNA splicing, via spliceosome / disordered domain specific binding ...embryonic brain development / U2-type catalytic step 2 spliceosome / cyclosporin A binding / protein peptidyl-prolyl isomerization / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / mRNA splicing, via spliceosome / disordered domain specific binding / protein folding / nucleoplasm / nucleus
Similarity search - Function
Cyclophilin-type peptidyl-prolyl cis-trans isomerase, cyclophilin A-like / 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 ...Cyclophilin-type peptidyl-prolyl cis-trans isomerase, cyclophilin A-like / 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
Cyclosporin A / : / : / Peptidyl-prolyl cis-trans isomerase-like 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
TOLYPOCLADIUM INFLATUM (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.15 Å
AuthorsStegmann, C.M. / Luehrmann, R. / Wahl, M.C.
CitationJournal: Plos One / Year: 2010
Title: The Crystal Structure of Ppil1 Bound to Cyclosporine a Suggests a Binding Mode for a Linear Epitope of the Skip Protein.
Authors: Stegmann, C.M. / Luehrmann, R. / Wahl, M.C.
History
DepositionMar 1, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Structure summary / Version format compliance
Revision 1.2Nov 30, 2012Group: Other
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 16, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status ...exptl_crystal_grow / pdbx_database_status / reflns / reflns_shell
Item: _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf ..._exptl_crystal_grow.method / _pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs

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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-LIKE 1
B: CYCLOSPORIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7265
Polymers19,4782
Non-polymers2483
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-21.6 kcal/mol
Surface area8100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.218, 35.701, 45.851
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2063-

HOH

21A-2163-

HOH

31A-2169-

HOH

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Components

#1: Protein PEPTIDYL-PROLYL CIS-TRANS ISOMERASE-LIKE 1 / PPIASE / ROTAMASE / PPIL1


Mass: 18257.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-6-P1-PPIL1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA2 / Variant (production host): DE3 / References: UniProt: Q9Y3C6, peptidylprolyl isomerase
#2: Protein/peptide CYCLOSPORIN A / CICLOSPORIN / CICLOSPORINE


Type: Cyclic peptide / Class: Immunosuppressant / Mass: 1220.625 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: CYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. CYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI.
Source: (synth.) TOLYPOCLADIUM INFLATUM (fungus) / References: NOR: NOR00033, Cyclosporin A
#3: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. HERE, CYCLOSPORIN A IS REPRESENTED BY THE SEQUENCE (SEQRES) ...CYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. HERE, CYCLOSPORIN A IS REPRESENTED BY THE SEQUENCE (SEQRES) GROUP: 1 NAME: CYCLOSPORIN A CHAIN: B COMPONENT_1: PEPTIDE LIKE SEQUENCE RESIDUES 1 TO 11 DESCRIPTION: CYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. CYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI.

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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: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.1 M HEPES, PH 7.2, 0.7 M SODIUM ACETATE, 15 MM CDCL2 AND 50 MM GUANIDINE-HCL GROWN AT 4DEGC

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 21, 2009
Details: DOUBLE CRYSTAL MONOCHROMATOR WITH 2 SETS OF MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.15→50 Å / Num. obs: 62933 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Biso Wilson estimate: 8.13 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 8.9
Reflection shellResolution: 1.15→1.25 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.15→34.277 Å / SU ML: 0.09 / σ(F): 2 / Phase error: 11.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1487 3093 5.1 %
Rwork0.1282 --
obs0.1292 61160 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.022 Å2 / ksol: 0.389 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.5749 Å20 Å2-0 Å2
2--0.9631 Å20 Å2
3----2.538 Å2
Refinement stepCycle: LAST / Resolution: 1.15→34.277 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1355 0 3 294 1652
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091455
X-RAY DIFFRACTIONf_angle_d2.2051987
X-RAY DIFFRACTIONf_dihedral_angle_d17.997583
X-RAY DIFFRACTIONf_chiral_restr0.074200
X-RAY DIFFRACTIONf_plane_restr0.007264
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1496-1.16750.21261520.16952528X-RAY DIFFRACTION99
1.1675-1.18670.19441250.16512665X-RAY DIFFRACTION100
1.1867-1.20710.19621480.16032558X-RAY DIFFRACTION100
1.2071-1.22910.17971350.14892630X-RAY DIFFRACTION100
1.2291-1.25270.16331330.13462571X-RAY DIFFRACTION100
1.2527-1.27830.16371400.12972622X-RAY DIFFRACTION100
1.2783-1.30610.16421190.13042634X-RAY DIFFRACTION100
1.3061-1.33650.16171210.12472603X-RAY DIFFRACTION100
1.3365-1.36990.14621530.11482627X-RAY DIFFRACTION100
1.3699-1.40690.13181350.11212622X-RAY DIFFRACTION100
1.4069-1.44830.12651370.10612614X-RAY DIFFRACTION100
1.4483-1.49510.12621580.10422631X-RAY DIFFRACTION100
1.4951-1.54850.14331420.09882605X-RAY DIFFRACTION100
1.5485-1.61050.12141280.0992641X-RAY DIFFRACTION100
1.6105-1.68380.13911340.10032633X-RAY DIFFRACTION100
1.6838-1.77260.12711570.10422648X-RAY DIFFRACTION100
1.7726-1.88360.12991570.10612637X-RAY DIFFRACTION100
1.8836-2.02910.11461500.10812626X-RAY DIFFRACTION100
2.0291-2.23320.13451560.10832691X-RAY DIFFRACTION100
2.2332-2.55630.14761270.1232690X-RAY DIFFRACTION100
2.5563-3.22030.15751430.14652724X-RAY DIFFRACTION100
3.2203-34.29250.16471430.15742867X-RAY DIFFRACTION100

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