[English] 日本語
Yorodumi
- PDB-1nmk: The Sanglifehrin-Cyclophilin Interaction: Degradation Work, Synth... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1nmk
TitleThe Sanglifehrin-Cyclophilin Interaction: Degradation Work, Synthetic Macrocyclic Analogues, X-ray Crystal Structure and Binding Data
ComponentsPeptidyl-prolyl cis-trans isomerase A
KeywordsISOMERASE / Beta Sandwich / Cyclophilin-Ligand Complex / Cyclosporin / Rotamase
Function / homology
Function and homology information


negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / negative regulation of viral life cycle / heparan sulfate binding / regulation of viral genome replication / virion binding / leukocyte chemotaxis / negative regulation of stress-activated MAPK cascade ...negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / negative regulation of viral life cycle / heparan sulfate binding / regulation of viral genome replication / virion binding / leukocyte chemotaxis / negative regulation of stress-activated MAPK cascade / endothelial cell activation / protein peptidyl-prolyl isomerization / Basigin interactions / cyclosporin A binding / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / Early Phase of HIV Life Cycle / Integration of provirus / negative regulation of protein phosphorylation / APOBEC3G mediated resistance to HIV-1 infection / viral release from host cell / Calcineurin activates NFAT / activation of protein kinase B activity / Binding and entry of HIV virion / positive regulation of viral genome replication / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of protein kinase activity / neutrophil chemotaxis / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / Assembly Of The HIV Virion / positive regulation of protein secretion / Budding and maturation of HIV virion / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / positive regulation of NF-kappaB transcription factor activity / platelet activation / platelet aggregation / SARS-CoV-1 activates/modulates innate immune responses / integrin binding / positive regulation of protein phosphorylation / neuron differentiation / unfolded protein binding / Platelet degranulation / protein folding / cellular response to oxidative stress / vesicle / secretory granule lumen / ficolin-1-rich granule lumen / positive regulation of MAPK cascade / focal adhesion / apoptotic process / Neutrophil degranulation / protein-containing complex / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleus / membrane / 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
Chem-SFM / Peptidyl-prolyl cis-trans isomerase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKallen, J. / Sedrani, R. / Wagner, J.
CitationJournal: J.Am.Chem.Soc. / Year: 2003
Title: Sanglifehrin-Cyclophilin Interaction: Degradation Work, Synthetic Macrocyclic Analogues, X-ray Crystal Structure and Binding Data
Authors: Sedrani, R. / Kallen, J. / Cabrejas, L.M.M. / Papageorgiou, C.D. / Senia, F. / Rohrbach, S. / Wagner, D. / Thai, B. / Eme, A.-M.J. / France, J. / Oberer, L. / Rihs, G. / Zenke, G. / Wagner, J.
History
DepositionJan 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 16, 2023Group: 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5554
Polymers36,0732
Non-polymers1,4822
Water3,747208
1
A: Peptidyl-prolyl cis-trans isomerase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7772
Polymers18,0371
Non-polymers7411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptidyl-prolyl cis-trans isomerase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7772
Polymers18,0371
Non-polymers7411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.200, 67.300, 78.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsthe biological assembly is a monomer of cyclophilinA/ligand

-
Components

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


Mass: 18036.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPIA OR CYPA / Plasmid: modified pKK 223-2 / Species (production host): Escherichia coli
Production host: Escherichia coli str. K12 substr. W3110 (bacteria)
Strain (production host): W3110 / References: UniProt: P62937, peptidylprolyl isomerase
#2: Chemical ChemComp-SFM / (13E,15E)-(3S,6S,9R,10R,11S,12S,18S,21S)-10,12-DIHYDROXY-3-(3-HYDROXYBEN-ZYL)-18-((E)-3-HYDROXY-1-METHYLPROPENYL)-6-ISOPROPYL-11-METHYL-9-(3-OXO-BUTYL)-19-OXA-1,4,7,25-TETRAAZA-BICYCLO[19.3.1]PENTACOSA-13,15-DIENE-2,5,8,20-TETRAONE / ANALOGUE OF MACROLIDE FROM DEGRADED SANGLIFEHRIN A


Mass: 740.883 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C39H56N4O10
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE LIGAND NAMED SFM IN THE STRUCTURE IS AN ANALOGUE OF THE DEGRADED PRODUCT OF SANGLIFEHRIN A

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 35.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 6000, tris-HCl, NaCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: unknown

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Feb 26, 1997
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→15 Å / Num. all: 18318 / Num. obs: 18318 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 22 Å2 / Rsym value: 0.088 / Net I/σ(I): 15.9
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 4.1 / Num. unique all: 1808 / Rsym value: 0.403 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CWA

1cwa


Resolution: 2.1→15 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.566 / SU ML: 0.15 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.242 / ESU R Free: 0.164 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18891 940 5.1 %RANDOM
Rwork0.1632 ---
all0.1645 18282 --
obs0.16453 17342 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20 Å20 Å2
2--0.44 Å20 Å2
3----0.9 Å2
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2532 0 106 208 2846
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212698
X-RAY DIFFRACTIONr_bond_other_d0.0010.022294
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.9833618
X-RAY DIFFRACTIONr_angle_other_deg0.74335366
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.073328
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.73215465
X-RAY DIFFRACTIONr_chiral_restr0.0910.2376
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023012
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02556
X-RAY DIFFRACTIONr_nbd_refined0.210.3470
X-RAY DIFFRACTIONr_nbd_other0.210.32175
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.5222
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0290.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.310
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2240.328
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1850.57
X-RAY DIFFRACTIONr_mcbond_it0.8491.51616
X-RAY DIFFRACTIONr_mcangle_it1.65122576
X-RAY DIFFRACTIONr_scbond_it2.40731082
X-RAY DIFFRACTIONr_scangle_it4.024.51042
LS refinement shellResolution: 2.1→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 67 -
Rwork0.186 1209 -
obs-1209 99.9 %
Refinement
*PLUS
Highest resolution: 2.1 Å / Rfactor Rwork: 0.164
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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