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- PDB-1awr: CYPA COMPLEXED WITH HAGPIA -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1awr
TitleCYPA COMPLEXED WITH HAGPIA
Components
  • CYCLOPHILIN APeptidylprolyl isomerase 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 / negative regulation of viral life cycle / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication / leukocyte chemotaxis / negative regulation of stress-activated MAPK cascade / endothelial cell activation ...negative regulation of protein K48-linked ubiquitination / negative regulation of viral life cycle / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication / leukocyte chemotaxis / negative regulation of stress-activated MAPK cascade / endothelial cell activation / virion binding / 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 / Calcineurin activates NFAT / viral release from host cell / 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 / positive regulation of protein dephosphorylation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / activation of protein kinase B activity / 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 / Assembly Of The HIV Virion / Budding and maturation of HIV virion / neuron differentiation / platelet activation / platelet aggregation / 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 / apoptotic process / Neutrophil degranulation / 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: 1.58 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 4, 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 / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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: CYCLOPHILIN A
C: CYCLOPHILIN A
D: CYCLOPHILIN A
E: CYCLOPHILIN A
F: CYCLOPHILIN A
G: PEPTIDE FROM THE HIV-1 CAPSID PROTEIN
H: PEPTIDE FROM THE HIV-1 CAPSID PROTEIN
I: PEPTIDE FROM THE HIV-1 CAPSID PROTEIN
J: PEPTIDE FROM THE HIV-1 CAPSID PROTEIN
K: PEPTIDE FROM THE HIV-1 CAPSID PROTEIN
L: PEPTIDE FROM THE HIV-1 CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)110,82612
Polymers110,82612
Non-polymers00
Water3,153175
1
B: CYCLOPHILIN A
H: PEPTIDE FROM THE HIV-1 CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)18,4712
Polymers18,4712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-4 kcal/mol
Surface area7210 Å2
MethodPISA
2
E: CYCLOPHILIN A
K: PEPTIDE FROM THE HIV-1 CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)18,4712
Polymers18,4712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: CYCLOPHILIN A
I: PEPTIDE FROM THE HIV-1 CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)18,4712
Polymers18,4712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-3 kcal/mol
Surface area7200 Å2
MethodPISA
4
F: CYCLOPHILIN A
L: PEPTIDE FROM THE HIV-1 CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)18,4712
Polymers18,4712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-3 kcal/mol
Surface area7320 Å2
MethodPISA
5
A: CYCLOPHILIN A
G: PEPTIDE FROM THE HIV-1 CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)18,4712
Polymers18,4712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-3 kcal/mol
Surface area7370 Å2
MethodPISA
6
D: CYCLOPHILIN A
J: PEPTIDE FROM THE HIV-1 CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)18,4712
Polymers18,4712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-3 kcal/mol
Surface area7250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.910, 72.910, 188.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.999488, 0.029872, -0.011464), (-0.030147, 0.999242, -0.024632), (0.01072, 0.024965, 0.999631)-0.72019, 1.28644, 125.21173
2given(0.982366, 0.184037, 0.032984), (-0.184781, 0.982554, 0.021088), (-0.028528, -0.026811, 0.999233)-3.46054, 4.0898, 63.99939
3given(0.98891, 0.148517, 0.00019), (-0.148398, 0.98817, -0.038716), (-0.005938, 0.038259, 0.99925)33.69711, 40.01925, -0.4894
4given(0.999711, -0.023908, -0.002576), (0.023777, 0.998812, -0.042532), (0.00359, 0.042458, 0.999092)36.81032, 36.26115, 124.8375
5given(0.997627, 0.06161, 0.030747), (-0.063837, 0.994933, 0.077676), (-0.025805, -0.079455, 0.996504)35.2363, 37.48756, 64.87968

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Components

#1: Protein
CYCLOPHILIN A / Peptidylprolyl isomerase A


Mass: 17905.307 Da / Num. of mol.: 6
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: 565.642 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.26 Å3/Da / Density % sol: 45.58 %
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: NSLS / Beamline: X12C / Wavelength: 1.1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 28, 1995
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.58→15 Å / Num. obs: 147562 / % possible obs: 88.4 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 16.4 Å2 / Rsym value: 0.088 / Net I/σ(I): 4.2
Reflection shellResolution: 1.58→1.61 Å / Rsym value: 0.278 / % possible all: 54.8
Reflection
*PLUS
Num. measured all: 1295142 / Rmerge(I) obs: 0.088
Reflection shell
*PLUS
% possible obs: 54.8 % / Rmerge(I) obs: 0.278

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Processing

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

2cyh


Resolution: 1.58→15 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL USED THE HIGH R-VALUE FOR THIS STRUCTURE STEMS FROM THE EXTREME NON-RANDOM DISTRIBUTION OF STRUCTURE FACTOR AMPLITUDES IN THE DATA. THE STRUCTURE HAS BEEN CONFIRMED IN ...Details: BULK SOLVENT MODEL USED THE HIGH R-VALUE FOR THIS STRUCTURE STEMS FROM THE EXTREME NON-RANDOM DISTRIBUTION OF STRUCTURE FACTOR AMPLITUDES IN THE DATA. THE STRUCTURE HAS BEEN CONFIRMED IN BOTH THE PSEUDO-SPACE GROUP AND THE TRUE-SPACE GROUP BY THE MAD METHOD (PDB CODES 1AWS AND 1AWT FOR THE PSEUDO- AND TRUE- SPACE GROUPS, RESPECTIVELY).
RfactorNum. reflection% reflectionSelection details
Rfree0.461 5691 5.1 %RANDOM
Rwork0.394 ---
obs0.394 112527 88.3 %-
Displacement parametersBiso mean: 16.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 1.58→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5032 0 120 0 5152
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.013
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_d25.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.46
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.211.5
X-RAY DIFFRACTIONx_mcangle_it2.932
X-RAY DIFFRACTIONx_scbond_it3.312
X-RAY DIFFRACTIONx_scangle_it3.882.5
LS refinement shellResolution: 1.58→1.68 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.517 563 5 %
Rwork0.496 10619 -
obs--50.3 %
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_deg25.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.46

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