[English] 日本語
Yorodumi
- PDB-6fk1: Cyclophilin A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6fk1
TitleCyclophilin A
ComponentsPeptidyl-prolyl cis-trans isomerase A
KeywordsISOMERASE / Cyclophilin / PPiase / Chaperone
Function / homology
Function and homology information


Basigin interactions / : / negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication / leukocyte chemotaxis / endothelial cell activation ...Basigin interactions / : / negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication / leukocyte chemotaxis / endothelial cell activation / negative regulation of stress-activated MAPK cascade / cyclosporin A binding / 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 / activation of protein kinase B activity / Neutrophil degranulation / neutrophil chemotaxis / negative regulation of protein phosphorylation / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / positive regulation of protein secretion / negative regulation of protein kinase activity / neuron differentiation / platelet activation / platelet aggregation / integrin binding / protein folding / myelin sheath / positive regulation of NF-kappaB transcription factor activity / cellular response to oxidative stress / positive regulation of protein phosphorylation / intracellular membrane-bounded organelle / apoptotic process / protein-containing complex / extracellular space / 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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.299 Å
AuthorsLisboa, J. / dos Santos, N.M.S.
Funding support Portugal, 2items
OrganizationGrant numberCountry
FCTPOCI-01-0145-FEDER-016608 Portugal
COMPETE 2020Norte-01-0145-FEDER-000012 Portugal
CitationJournal: To Be Published
Title: Production, crystallization and structure determination of cyclophilin A from Mus musculus
Authors: Lisboa, J. / dos Santos, N.M.S.
History
DepositionJan 23, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1913
Polymers19,0671
Non-polymers1242
Water1,982110
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint5 kcal/mol
Surface area8090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.717, 61.717, 93.130
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Peptidyl-prolyl cis-trans isomerase A / PPIase A / Cyclophilin A / Cyclosporin A-binding protein / Rotamase A / SP18


Mass: 19066.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ppia / Production host: Escherichia coli (E. coli) / References: UniProt: P17742, peptidylprolyl isomerase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.85 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 3.5M Sodium formate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98005 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98005 Å / Relative weight: 1
ReflectionResolution: 1.299→46.36 Å / Num. obs: 51157 / % possible obs: 99.86 % / Redundancy: 10.9 % / Biso Wilson estimate: 20.86 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.0433 / Rpim(I) all: 0.01364 / Rrim(I) all: 0.04544 / Net I/σ(I): 24.47
Reflection shellResolution: 1.299→1.346 Å / Redundancy: 10.7 % / Mean I/σ(I) obs: 0.79 / Num. unique obs: 5010 / CC1/2: 0.392 / Rpim(I) all: 0.6622 / % possible all: 98.89

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2cpl

2cpl


Resolution: 1.299→46.357 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.49
RfactorNum. reflection% reflection
Rfree0.1811 2594 5.07 %
Rwork0.1627 --
obs0.1636 51120 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.299→46.357 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1300 0 8 110 1418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141364
X-RAY DIFFRACTIONf_angle_d1.3721833
X-RAY DIFFRACTIONf_dihedral_angle_d3.464804
X-RAY DIFFRACTIONf_chiral_restr0.114189
X-RAY DIFFRACTIONf_plane_restr0.009244
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2993-1.32290.35071470.36442437X-RAY DIFFRACTION98
1.3229-1.34830.38141350.36842551X-RAY DIFFRACTION100
1.3483-1.37590.3211270.35872513X-RAY DIFFRACTION100
1.3759-1.40580.32061220.34242544X-RAY DIFFRACTION100
1.4058-1.43850.3651400.32162503X-RAY DIFFRACTION100
1.4385-1.47450.37721360.29672539X-RAY DIFFRACTION100
1.4745-1.51430.25211170.25342547X-RAY DIFFRACTION100
1.5143-1.55890.2561460.20112518X-RAY DIFFRACTION100
1.5589-1.60920.19141270.16282543X-RAY DIFFRACTION100
1.6092-1.66670.16781290.14312560X-RAY DIFFRACTION100
1.6667-1.73350.1781580.14332501X-RAY DIFFRACTION100
1.7335-1.81240.16451480.14732544X-RAY DIFFRACTION100
1.8124-1.90790.16181270.14672544X-RAY DIFFRACTION100
1.9079-2.02750.15391490.14432562X-RAY DIFFRACTION100
2.0275-2.1840.16711190.14372591X-RAY DIFFRACTION100
2.184-2.40380.19141340.14762574X-RAY DIFFRACTION100
2.4038-2.75160.17971550.16922573X-RAY DIFFRACTION100
2.7516-3.46650.15721390.15872632X-RAY DIFFRACTION100
3.4665-46.38610.16371390.13962750X-RAY DIFFRACTION100
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)
10.40060.16010.47120.62190.20930.4564-0.1134-0.05120.0089-0.02180.00260.0474-0.07390.0236-00.2318-0.03470.01060.2136-0.0180.2122-6.199243.863499.3109
20.81910.77530.41050.79950.24440.4341-0.10940.0420.0258-0.11030.09780.0864-0.25410.18160.00040.2328-0.0299-0.00240.1891-0.00290.1886-5.224141.25793.2499
30.18680.12030.18050.1180.12450.1744-0.0183-0.0690.1105-0.0589-0.05350.5328-0.2477-0.184-0.00020.28590.0124-0.04090.2405-0.01650.2912-16.1144.169494.7474
40.30840.2405-0.15530.186-0.07650.13020.0523-0.1661-0.09650.153-0.04650.39550.1499-0.2812-00.2648-0.0331-0.00680.24570.00890.2878-17.005932.139498.2706
50.67510.56040.40450.82940.3450.8304-0.07230.0744-0.0626-0.01970.06180.0533-0.0139-0.023400.1938-0.032-0.00360.1961-0.00320.1958-10.921931.222189.15
60.2565-0.0666-0.18690.2198-0.09750.2059-0.03280.0713-0.15170.09770.10330.03920.02960.15940.00070.2065-0.0227-0.01190.2004-0.0180.2139-4.025331.529793.2173
70.08490.0720.01310.10570.1160.13620.0432-0.1519-0.28950.1448-0.12860.00350.4017-0.0024-0.00050.3124-0.0482-0.0060.2231-0.00310.2316-8.501433.0398108.658
80.07460.02790.01280.0744-0.05430.05520.02510.0235-0.10560.4011-0.01070.26850.3239-0.4968-0.02050.4449-0.13450.14380.3844-0.06150.4259-20.647829.9546107.5192
90.0485-0.0255-0.01560.36290.2010.1069-0.0401-0.05810.3-0.0670.03160.0628-0.06930.003800.248-0.02180.0020.2193-0.0080.2402-4.4847.121398.931
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 14 )
2X-RAY DIFFRACTION2chain 'A' and (resid 15 through 41 )
3X-RAY DIFFRACTION3chain 'A' and (resid 42 through 54 )
4X-RAY DIFFRACTION4chain 'A' and (resid 55 through 69 )
5X-RAY DIFFRACTION5chain 'A' and (resid 70 through 122 )
6X-RAY DIFFRACTION6chain 'A' and (resid 123 through 135 )
7X-RAY DIFFRACTION7chain 'A' and (resid 136 through 145 )
8X-RAY DIFFRACTION8chain 'A' and (resid 146 through 155 )
9X-RAY DIFFRACTION9chain 'A' and (resid 156 through 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