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- PDB-1awv: CYPA COMPLEXED WITH HVGPIA -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1awv
TitleCYPA COMPLEXED WITH HVGPIA
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 / 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 ...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 / 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
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 / 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)110,99412
Polymers110,99412
Non-polymers00
Water3,153175
1
A: CYCLOPHILIN A
G: PEPTIDE FROM THE HIV-1 CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)18,4992
Polymers18,4992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-4 kcal/mol
Surface area7510 Å2
MethodPISA
2
C: CYCLOPHILIN A
I: PEPTIDE FROM THE HIV-1 CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)18,4992
Polymers18,4992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-3 kcal/mol
Surface area7300 Å2
MethodPISA
3
E: CYCLOPHILIN A
K: PEPTIDE FROM THE HIV-1 CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)18,4992
Polymers18,4992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-5 kcal/mol
Surface area7510 Å2
MethodPISA
4
D: CYCLOPHILIN A
J: PEPTIDE FROM THE HIV-1 CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)18,4992
Polymers18,4992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-4 kcal/mol
Surface area7410 Å2
MethodPISA
5
B: CYCLOPHILIN A
H: PEPTIDE FROM THE HIV-1 CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)18,4992
Polymers18,4992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: CYCLOPHILIN A
L: PEPTIDE FROM THE HIV-1 CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)18,4992
Polymers18,4992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-4 kcal/mol
Surface area7520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.000, 74.000, 190.400
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(0.999861, 0.001421, -0.016643), (-0.002204, 0.998888, -0.047093), (0.016558, 0.047123, 0.998752)-0.09511, 0.72127, 125.85183
2given(0.99375, 0.109133, 0.023496), (-0.109199, 0.994019, 0.001541), (-0.023188, -0.004097, 0.999723)-2.30208, 2.4448, 64.03819
3given(0.983917, 0.178561, 0.004839), (-0.178381, 0.983626, -0.025707), (-0.00935, 0.024431, 0.999658)33.72785, 41.14758, -0.18907
4given(0.998728, -0.050003, -0.006495), (0.049786, 0.998308, -0.03005), (0.007986, 0.029688, 0.999527)37.85891, 36.32781, 126.22861
5given(0.994504, 0.089688, 0.054024), (-0.096305, 0.986035, 0.135866), (-0.041085, -0.140322, 0.989253)35.25095, 38.86013, 67.00388

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Components

#1: Protein
CYCLOPHILIN 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: 593.695 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
#3: Water ChemComp-HOH / 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: 2.35 Å3/Da / Density % sol: 47.6 %
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: 42633 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 17.9 Å2 / Rsym value: 0.11 / Net I/σ(I): 4.7
Reflection shellResolution: 2.34→2.38 Å / Rsym value: 0.294 / % possible all: 80.1
Reflection
*PLUS
Num. measured all: 284842 / Rmerge(I) obs: 0.11
Reflection shell
*PLUS
% possible obs: 80.1 % / Rmerge(I) obs: 0.294

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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: 2.34→15 Å / Rfactor Rfree error: 0.011 / 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.
RfactorNum. reflection% reflectionSelection details
Rfree0.46 1781 5 %RANDOM
Rwork0.358 ---
obs0.358 35605 83.1 %-
Displacement parametersBiso mean: 16.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.66 Å0.47 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.34→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5032 0 126 175 5333
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_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.33
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_it3.352
X-RAY DIFFRACTIONx_scangle_it3.872.5
LS refinement shellResolution: 2.34→2.49 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.448 270 5.1 %
Rwork0.413 5004 -
obs--74.2 %
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
Refinement
*PLUS
Rfactor Rfree: 0.46
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.33

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