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- PDB-5hsv: X-Ray structure of a CypA-Alisporivir complex at 1.5 angstrom res... -

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Basic information

Entry
Database: PDB / ID: 5hsv
TitleX-Ray structure of a CypA-Alisporivir complex at 1.5 angstrom resolution
Components
  • Alisporivir
  • Peptidyl-prolyl cis-trans isomerase A
KeywordsISOMERASE / Cyclophilin PPIA CsA-derivative non-immunosuppressive
Function / homology
Function and homology information


: / negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / heparan sulfate binding / regulation of viral genome replication / leukocyte chemotaxis / endothelial cell activation / negative regulation of stress-activated MAPK cascade / cyclosporin A binding ...: / negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / heparan sulfate binding / regulation of viral genome replication / leukocyte chemotaxis / endothelial cell activation / negative regulation of stress-activated MAPK cascade / cyclosporin A binding / protein peptidyl-prolyl isomerization / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of protein dephosphorylation / activation of protein kinase B activity / neutrophil chemotaxis / negative regulation of protein phosphorylation / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / negative regulation of protein kinase activity / platelet activation / platelet aggregation / integrin binding / protein folding / positive regulation of NF-kappaB transcription factor activity / cellular response to oxidative stress / positive regulation of protein phosphorylation / apoptotic process / extracellular region / 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
Peptidyl-prolyl cis-trans isomerase A
Similarity search - Component
Biological speciesChlorocebus aethiops (grivet)
Tolypocladium inflatum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsDujardin, M. / Bouckaert, J. / Rucktooa, P. / Hanoulle, X.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR JCJC StruFunc5A5B France
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: X-ray structure of alisporivir in complex with cyclophilin A at 1.5 angstrom resolution.
Authors: Dujardin, M. / Bouckaert, J. / Rucktooa, P. / Hanoulle, X.
History
DepositionJan 26, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 10, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Jan 10, 2024Group: 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_ncs_dom_lim
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_label_atom_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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: Peptidyl-prolyl cis-trans isomerase A
E: Alisporivir
F: Alisporivir
G: Alisporivir
H: Alisporivir
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,34712
Polymers78,2068
Non-polymers1424
Water7,350408
1
A: Peptidyl-prolyl cis-trans isomerase A
E: Alisporivir
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5873
Polymers19,5512
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-16 kcal/mol
Surface area7700 Å2
MethodPISA
2
B: Peptidyl-prolyl cis-trans isomerase A
F: Alisporivir
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6224
Polymers19,5512
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-25 kcal/mol
Surface area7660 Å2
MethodPISA
3
C: Peptidyl-prolyl cis-trans isomerase A
G: Alisporivir
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5873
Polymers19,5512
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-21 kcal/mol
Surface area7710 Å2
MethodPISA
4
D: Peptidyl-prolyl cis-trans isomerase A
H: Alisporivir


Theoretical massNumber of molelcules
Total (without water)19,5512
Polymers19,5512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-8 kcal/mol
Surface area7770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.904, 68.443, 71.952
Angle α, β, γ (deg.)115.120, 103.170, 93.960
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24B
15A
25C
16B
26C
17B
27D
18B
28C
19C
29D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALGLNGLNAA2 - 1635 - 166
21VALVALGLNGLNBB2 - 1635 - 166
12VALVALGLUGLUAA2 - 1655 - 168
22VALVALGLUGLUCC2 - 1655 - 168
13VALVALGLUGLUAA2 - 1655 - 168
23VALVALGLUGLUDD2 - 1655 - 168
14HOHHOHHOHHOHAM301 - 311
24HOHHOHHOHHOHBN301 - 311
15HOHHOHHOHHOHAM301 - 311
25HOHHOHHOHHOHCO301 - 311
16VALVALGLNGLNBB2 - 1635 - 166
26VALVALGLNGLNCC2 - 1635 - 166
17VALVALGLNGLNBB2 - 1635 - 166
27VALVALGLNGLNDD2 - 1635 - 166
18HOHHOHHOHHOHBN301 - 311
28HOHHOHHOHHOHCO301 - 311
19VALVALGLUGLUCC2 - 1655 - 168
29VALVALGLUGLUDD2 - 1655 - 168

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9

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Components

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


Mass: 18318.777 Da / Num. of mol.: 4 / Fragment: Cyclophilin A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorocebus aethiops (grivet) / Gene: PPIA, CYPA / Production host: Escherichia coli (E. coli) / References: UniProt: P62938, peptidylprolyl isomerase
#2: Protein/peptide
Alisporivir


Mass: 1232.637 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Tolypocladium inflatum (fungus)
#3: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 408 / 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: 2.9 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 8.5 / Details: 0.1 M tris pH 8.5, 0.2 M MgCl2, 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.14→36.248 Å / Num. obs: 159748 / % possible obs: 69.3 % / Redundancy: 6.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.114 / Net I/σ(I): 7.2
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.14-1.162.33.2256802960.1312.1793.9120.32.6
6.23-36.257.10.048990213870.9980.0190.05228.399.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.4data scaling
PHASERphasing
REFMAC5.8.0107refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
MxCuBEdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CWA

1cwa


Resolution: 1.5→36.248 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.976 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.073
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1898 4807 4.9 %RANDOM
Rwork0.166 ---
obs0.1672 93703 98.2 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.3 Å
Displacement parametersBiso max: 129.05 Å2 / Biso mean: 29.699 Å2 / Biso min: 10.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0.55 Å2-0.41 Å2
2--0.29 Å2-0.49 Å2
3---0.31 Å2
Refinement stepCycle: final / Resolution: 1.5→36.248 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5366 0 4 408 5778
Biso mean--42.79 33.49 -
Num. residues----699
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0195515
X-RAY DIFFRACTIONr_bond_other_d00.025250
X-RAY DIFFRACTIONr_angle_refined_deg1.8441.9747417
X-RAY DIFFRACTIONr_angle_other_deg3.857312107
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.4715.122696
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.41824.181232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.01815890
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3881524
X-RAY DIFFRACTIONr_chiral_restr0.1270.2793
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0216406
X-RAY DIFFRACTIONr_gen_planes_other0.0310.021282
X-RAY DIFFRACTIONr_mcbond_it2.0141.2542819
X-RAY DIFFRACTIONr_mcbond_other2.0141.2542819
X-RAY DIFFRACTIONr_mcangle_it2.8141.8713518
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A193260.07
12B193260.07
21A194740.08
22C194740.08
31A194900.09
32D194900.09
41A9560.13
42B9560.13
51A9820.06
52C9820.06
61B192980.08
62C192980.08
71B192180.08
72D192180.08
81B9400.14
82C9400.14
91C197320.06
92D197320.06
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 367 -
Rwork0.343 6796 -
all-7163 -
obs--96.33 %
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)
13.231-0.91581.12963.58990.16452.80380.0985-0.1217-0.13470.1778-0.13850.1446-0.0815-0.1220.040.03570.018-0.01040.1869-0.0280.0248-14.68526.00532.226
22.6363-0.4430.93562.7256-0.38642.59310.0341-0.268-0.09450.2111-0.05040.1283-0.07-0.05260.01630.02430.0020.00690.1671-0.00750.01271.62559.28432.288
31.76130.47920.25352.490.33723.0763-0.05140.0822-0.0109-0.27540.16720.0587-0.0525-0.0397-0.11570.0722-0.0575-0.01850.05680.01740.01043.59138.92564.414
41.80230.48120.01783.25720.64573.5019-0.06810.01570.0104-0.28080.21110.0786-0.0641-0.0034-0.14310.0856-0.065-0.01730.06280.01540.0114-17.76172.97364.166
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 311
2X-RAY DIFFRACTION2B2 - 311
3X-RAY DIFFRACTION3C2 - 311
4X-RAY DIFFRACTION4D2 - 168

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