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- PDB-1awu: CYPA COMPLEXED WITH HVGPIA (PSEUDO-SYMMETRIC MONOMER) -

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Basic information

Entry
Database: PDB / ID: 1awu
TitleCYPA COMPLEXED WITH HVGPIA (PSEUDO-SYMMETRIC MONOMER)
Components
  • CYCLOPHILIN A
  • PEPTIDE FROM THE HIV-1 CAPSID PROTEIN
KeywordsCOMPLEX (ISOMERASE/PEPTIDE) / COMPLEX (ISOMERASE-PEPTIDE) / CYCLOPHILIN A / HIV-1 CAPSID / PSEUDO-SYMMETRY / COMPLEX (ISOMERASE-PEPTIDE) complex
Function / homology
Function and homology information


negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / negative regulation of viral life cycle / cell adhesion molecule production / lipid droplet organization / 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 / negative regulation of viral life cycle / cell adhesion molecule production / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication / virion binding / leukocyte chemotaxis / negative regulation of stress-activated MAPK cascade / endothelial cell activation / 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 / APOBEC3G mediated resistance to HIV-1 infection / viral release from host cell / Calcineurin activates NFAT / Binding and entry of HIV virion / positive regulation of viral genome replication / protein peptidyl-prolyl isomerization / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / : / activation of protein kinase B activity / negative regulation of protein phosphorylation / 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 / negative regulation of protein kinase activity / Assembly Of The HIV Virion / Budding and maturation of HIV virion / neuron differentiation / platelet aggregation / platelet activation / SARS-CoV-1 activates/modulates innate immune responses / unfolded protein binding / integrin binding / protein folding / Platelet degranulation / cellular response to oxidative stress / positive regulation of NF-kappaB transcription factor activity / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / positive regulation of MAPK cascade / positive regulation of protein phosphorylation / focal adhesion / Neutrophil degranulation / apoptotic process / protein-containing complex / extracellular space / RNA binding / extracellular exosome / extracellular region / membrane / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsVajdos, F.F.
CitationJournal: Protein Sci. / Year: 1997
Title: Crystal structure of cyclophilin A complexed with a binding site peptide from the HIV-1 capsid protein.
Authors: Vajdos, F.F. / Yoo, S. / Houseweart, M. / Sundquist, W.I. / Hill, C.P.
History
DepositionOct 5, 1997Processing site: BNL
Revision 1.0Mar 18, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYCLOPHILIN A
B: PEPTIDE FROM THE HIV-1 CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)18,4992
Polymers18,4992
Non-polymers00
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-5 kcal/mol
Surface area7510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.400, 52.400, 63.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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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) / Cellular location: CYTOPLASM / Gene: CYCLOPHILIN / Gene (production host): CYCLOPHILIN / Production host: Escherichia coli (E. coli) / References: UniProt: P62937, peptidylprolyl isomerase
#2: Protein/peptide PEPTIDE FROM THE HIV-1 CAPSID PROTEIN


Mass: 593.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.7 %
Crystal growpH: 8.4 / Details: pH 8.4
Crystal grow
*PLUS
Temperature: 21 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16 mg/mlpeptide11
244-54 %satammonium sulfate12
3100 mMTris-HCl12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.34→15 Å / Num. obs: 7251 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 21.6 Å2 / Rsym value: 0.047 / Net I/σ(I): 17.6
Reflection shellResolution: 2.34→2.38 Å / Rsym value: 0.114 / % possible all: 78.6
Reflection
*PLUS
Num. measured all: 48608 / Rmerge(I) obs: 0.047
Reflection shell
*PLUS
% possible obs: 78.6 % / Rmerge(I) obs: 0.114

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Processing

Software
NameVersionClassification
X-PLOR3.843model building
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.843phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CYH

2cyh


Resolution: 2.34→15 Å / Rfactor Rfree error: 0.018 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL USED A LARGE NUMBER OF ATOMS WERE SET TO ZERO OCCUPANCY FOR REFINEMENT PURPOSES SINCE THEY WERE NOT WELL-DEFINED BY THE ELECTRON DENSITY. REGARDING THE HIGH R-VALUE: THIS ...Details: BULK SOLVENT MODEL USED A LARGE NUMBER OF ATOMS WERE SET TO ZERO OCCUPANCY FOR REFINEMENT PURPOSES SINCE THEY WERE NOT WELL-DEFINED BY THE ELECTRON DENSITY. REGARDING THE HIGH R-VALUE: THIS IS THE STRUCTURE OF THE COMPLEX REFINED IN A PSEUDO-SPACE GROUP. THE DETAILS ARE ADDRESSED EXTENSIVELY IN THE PAPER. TO SUMMARIZE HERE, THE HIGH R-VALUE FOR THIS STRUCTURE STEMS FROM THE BREAKDOWN IN PSEUDO-SYMMETRY AT HIGH RESOLUTION.
RfactorNum. reflection% reflectionSelection details
Rfree0.351 387 5.5 %RANDOM
Rwork0.316 ---
obs0.316 7049 96.8 %-
Displacement parametersBiso mean: 27.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.58 Å0.45 Å
Luzzati d res low-5 Å
Luzzati sigma a0.7 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 2.34→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1258 0 42 13 1313
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.35
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it5.581.5
X-RAY DIFFRACTIONx_mcangle_it7.792
X-RAY DIFFRACTIONx_scbond_it7.552
X-RAY DIFFRACTIONx_scangle_it8.762.5
LS refinement shellResolution: 2.34→2.49 Å / Rfactor Rfree error: 0.061 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.469 59 5.6 %
Rwork0.438 990 -
obs--87 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2TIP3P.PARAMETERTIP3P.TOPOLOGY
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.35

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