[English] 日本語
Yorodumi
- PDB-5hsv: X-Ray structure of a CypA-Alisporivir complex at 1.5 angstrom res... -

+
Open data


ID or keywords:

Loading...

-
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 / negative regulation of stress-activated MAPK cascade / endothelial cell activation / protein peptidyl-prolyl isomerization / 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 / negative regulation of stress-activated MAPK cascade / endothelial cell activation / protein peptidyl-prolyl isomerization / cyclosporin A binding / negative regulation of protein phosphorylation / activation of protein kinase B activity / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of protein kinase activity / neutrophil chemotaxis / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / : / platelet activation / platelet aggregation / integrin binding / positive regulation of protein phosphorylation / protein folding / cellular response to oxidative stress / positive regulation of MAPK cascade / apoptotic process / extracellular region / nucleus / cytosol / cytoplasm
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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

+
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://pdbjlvh1.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