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- PDB-3cyh: CYCLOPHILIN A COMPLEXED WITH DIPEPTIDE SER-PRO -

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Basic information

Entry
Database: PDB / ID: 3cyh
TitleCYCLOPHILIN A COMPLEXED WITH DIPEPTIDE SER-PRO
ComponentsCYCLOPHILIN A
KeywordsISOMERASE / CYCLOPHILIN / COMPLEX / BINDING PROTEIN FOR CYCLOSPORIN A / (ISOMERASE-DIPEPTIDE) COMPLEX
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 / leukocyte chemotaxis / virion binding ...: / 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 / leukocyte chemotaxis / virion binding / negative regulation of stress-activated MAPK cascade / endothelial cell activation / Basigin interactions / protein peptidyl-prolyl isomerization / 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 / positive regulation of protein secretion / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / Assembly Of The HIV Virion / positive regulation of NF-kappaB transcription factor activity / Budding and maturation of HIV virion / platelet activation / platelet aggregation / integrin binding / positive regulation of protein phosphorylation / neuron differentiation / SARS-CoV-1 activates/modulates innate immune responses / unfolded protein binding / Platelet degranulation / protein folding / cellular response to oxidative stress / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / positive regulation of MAPK cascade / focal adhesion / intracellular membrane-bounded organelle / apoptotic process / Neutrophil degranulation / protein-containing complex / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleus / membrane / 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
PROLINE / SERINE / Peptidyl-prolyl cis-trans isomerase A / Peptidyl-prolyl cis-trans isomerase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsZhao, Y. / Ke, H.
CitationJournal: Biochemistry / Year: 1996
Title: Mechanistic implication of crystal structures of the cyclophilin-dipeptide complexes.
Authors: Zhao, Y. / Ke, H.
History
DepositionFeb 27, 1996Processing site: BNL
Revision 1.0Jul 11, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYCLOPHILIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1263
Polymers17,9051
Non-polymers2202
Water97354
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.900, 52.400, 90.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CYCLOPHILIN A


Mass: 17905.307 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: XA90 / Gene: CYCLOPHILIN / Plasmid: PHN1+ / Gene (production host): CYCLOPHILIN / Production host: Escherichia coli (E. coli) / Strain (production host): XA90 F'
References: UniProt: P05092, UniProt: P62937*PLUS, peptidylprolyl isomerase
#2: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
#3: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE RESIDUES 201 AND 202 REPRESENT A DIPEPTIDE BOUND TO CYCLOPHILIN A

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 54 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8.5 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-15 mg/mlCyPA11
220 mMTris base12
32 mMEDTA12
42 mM2-mercaptoethanol12
50.5 mM12NaN3
66.7 %ethanol12
711-13 %PEG335012

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.9 Å / Num. obs: 14311 / % possible obs: 90 % / Redundancy: 4 % / Rmerge(I) obs: 0.056
Reflection
*PLUS
Num. measured all: 56836
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 2 Å / % possible obs: 74.4 %

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Processing

Software
NameClassification
X-PLORrefinement
RIGAKUdata reduction
RIGAKUdata scaling
RefinementResolution: 1.9→8 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.191 -
obs0.191 14075
Displacement parametersBiso mean: 19.5 Å2
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1544 0 18 162 1724
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Lowest resolution: 8 Å / Rfactor obs: 0.186 / Rfactor Rfree: 0.231 / Rfactor Rwork: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS

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