[English] 日本語
Yorodumi
- PDB-8r7u: Crystal Structure of Cyclophilin TgCyp23 from Toxoplasma gondii i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8r7u
TitleCrystal Structure of Cyclophilin TgCyp23 from Toxoplasma gondii in complex with dihydro Cyclosporin A
Components
  • Dihydrocyclosporin A
  • Peptidyl-prolyl cis-trans isomerase
KeywordsISOMERASE / CYCLOPHILIN COMPLEX / peptidylprolyl isomerase activity
Function / homology
Function and homology information


cyclosporin A binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / cytoplasm
Similarity search - Function
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
: / Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsJimenez-Faraco, E. / Hermoso, J.A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Agencia Estatal de Investigacion (AEI)PID2020-115331GB-I00 Spain
Citation
Journal: Protein Sci. / Year: 2024
Title: Evaluating the potential of non-immunosuppressive cyclosporin analogs for targeting Toxoplasma gondii cyclophilin: Insights from structural studies.
Authors: Favretto, F. / Jimenez-Faraco, E. / Catucci, G. / Di Matteo, A. / Travaglini-Allocatelli, C. / Sadeghi, S.J. / Dominici, P. / Hermoso, J.A. / Astegno, A.
#1: Journal: ACS Infect Dis / Year: 2023
Title: Structural Basis for Cyclosporin Isoform-Specific Inhibition of Cyclophilins from Toxoplasma gondii in complex with Cyclosporin A at 1.1 Angstroms resolution
Authors: Jimenez-Faraco, E. / Hermoso, J.A.
History
DepositionNov 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Peptidyl-prolyl cis-trans isomerase
A: Peptidyl-prolyl cis-trans isomerase
C: Dihydrocyclosporin A
D: Dihydrocyclosporin A


Theoretical massNumber of molelcules
Total (without water)48,8324
Polymers48,8324
Non-polymers00
Water8,071448
1
B: Peptidyl-prolyl cis-trans isomerase
D: Dihydrocyclosporin A


Theoretical massNumber of molelcules
Total (without water)24,4162
Polymers24,4162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-8 kcal/mol
Surface area9120 Å2
MethodPISA
2
A: Peptidyl-prolyl cis-trans isomerase
C: Dihydrocyclosporin A


Theoretical massNumber of molelcules
Total (without water)24,4162
Polymers24,4162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-9 kcal/mol
Surface area9070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.346, 118.109, 47.460
Angle α, β, γ (deg.)90.000, 103.670, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein Peptidyl-prolyl cis-trans isomerase / PPIase


Mass: 23193.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: There are two additional residues in N-term, that remain after the His tag cleavage and are not observed in density. Glycine (-1) Histidine (0)
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: TGRH88_026260 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7J6KAD1, peptidylprolyl isomerase
#2: Protein/peptide Dihydrocyclosporin A


Type: Cyclic peptide / Class: Inhibitor / Mass: 1222.641 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Analogue of cyclosporine A. It is a cyclic undecapeptide. Cyclization is achieved by linking the N- and the C- termini.
Source: (synth.) synthetic construct (others) / References: BIRD: PRD_002553
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 448 / 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) Dihydrocyclosporin A, is a derivative of cyclosporin A that is not immunosuppressive. It has been shown to inhibit growth of Leishmania donovani.
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M citric acid pH 3.5, and 25% polyethylene glycol 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.2→42.96 Å / Num. obs: 125896 / % possible obs: 98.67 % / Redundancy: 6.8 % / Biso Wilson estimate: 15.96 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.019 / Net I/σ(I): 16.8
Reflection shellResolution: 1.2→1.243 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.028 / Mean I/σ(I) obs: 1.45 / Num. unique obs: 12366 / CC1/2: 0.752 / Rpim(I) all: 0.418 / % possible all: 97.04

-
Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
PHENIX1.20.1refinement
XDS0.86data reduction
Aimless0.7.13data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→42.96 Å / SU ML: 0.1502 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.9965
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1866 6379 5.07 %
Rwork0.1716 119462 -
obs0.1723 125841 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.07 Å2
Refinement stepCycle: LAST / Resolution: 1.2→42.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3080 0 170 448 3698
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01133352
X-RAY DIFFRACTIONf_angle_d1.52244548
X-RAY DIFFRACTIONf_chiral_restr0.0886486
X-RAY DIFFRACTIONf_plane_restr0.011595
X-RAY DIFFRACTIONf_dihedral_angle_d22.5863516
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.210.37191920.37273942X-RAY DIFFRACTION96.86
1.21-1.230.35151900.35173872X-RAY DIFFRACTION97.11
1.23-1.240.3432140.32223940X-RAY DIFFRACTION97.15
1.24-1.260.2851820.30323901X-RAY DIFFRACTION97.24
1.26-1.280.28812000.28283987X-RAY DIFFRACTION97.3
1.28-1.290.29411940.26513928X-RAY DIFFRACTION97.75
1.29-1.310.24552550.24423894X-RAY DIFFRACTION97.67
1.31-1.330.252040.2273942X-RAY DIFFRACTION97.64
1.33-1.350.24742200.22143924X-RAY DIFFRACTION98.18
1.35-1.370.21762020.21313976X-RAY DIFFRACTION97.85
1.37-1.40.22812250.21053937X-RAY DIFFRACTION98.14
1.4-1.420.21752270.20563948X-RAY DIFFRACTION98.42
1.42-1.450.22242060.20763949X-RAY DIFFRACTION98.41
1.45-1.480.2242310.21413991X-RAY DIFFRACTION98.51
1.48-1.510.21462060.19583939X-RAY DIFFRACTION98.5
1.51-1.550.18712150.17713968X-RAY DIFFRACTION98.77
1.55-1.590.17852020.16984015X-RAY DIFFRACTION98.78
1.59-1.630.18952420.1633944X-RAY DIFFRACTION98.82
1.63-1.680.18552270.1624010X-RAY DIFFRACTION99.04
1.68-1.730.18272140.16474009X-RAY DIFFRACTION99.48
1.73-1.790.19172030.17114017X-RAY DIFFRACTION99.58
1.79-1.860.17722170.17063995X-RAY DIFFRACTION99.65
1.86-1.950.20792200.17144026X-RAY DIFFRACTION99.74
1.95-2.050.16262150.16744056X-RAY DIFFRACTION99.86
2.05-2.180.15732320.16224002X-RAY DIFFRACTION99.95
2.18-2.350.1752000.16934070X-RAY DIFFRACTION99.95
2.35-2.590.19952150.17444055X-RAY DIFFRACTION100
2.59-2.960.19972320.17544057X-RAY DIFFRACTION100
2.96-3.730.18251920.15414058X-RAY DIFFRACTION100
3.73-42.960.14192050.13364110X-RAY DIFFRACTION99.77
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)
10.971744818238-0.1884184271260.4575739398972.131891541480.1584434186431.19958687025-0.0620375757504-0.1262336464270.001185315132210.1913959431670.100720268075-0.1506623844910.00255025571334-0.0734285259362-0.02724205012040.09063680232160.0247883768107-0.01999597173830.114492304299-0.03654527919850.1221129881019.09275437196-20.861917039216.3629011466
21.579821577181.405852455950.2226389426913.806535899520.458326484070.7864739000530.146967819333-0.202534212967-0.02666359970420.224613665667-0.236502359104-0.107778855107-0.006244088703620.009206910416240.08020598707990.122260194124-0.0329085040828-0.02094455864940.1232852021310.04034950866150.1153418341460.0164069530185-55.65284462067.77444035449
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 13 - 301 / Label seq-ID: 1

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain B and resseq 13:301)BA - B
22(chain A and resseq 12:301)AC - D

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more