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- PDB-1awt: SECYPA COMPLEXED WITH HAGPIA -

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Basic information

Entry
Database: PDB / ID: 1awt
TitleSECYPA COMPLEXED WITH HAGPIA
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 / endothelial cell activation ...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 / endothelial cell activation / negative regulation of stress-activated MAPK cascade / 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 / protein peptidyl-prolyl isomerization / Calcineurin activates NFAT / Binding and entry of HIV virion / positive regulation of viral genome replication / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / : / neutrophil chemotaxis / activation of protein kinase B activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / negative regulation of protein phosphorylation / peptidylprolyl isomerase / positive regulation of protein secretion / 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 activation / platelet aggregation / SARS-CoV-1 activates/modulates innate immune responses / unfolded protein binding / integrin binding / protein folding / Platelet degranulation / positive regulation of NF-kappaB transcription factor activity / cellular response to oxidative stress / 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 / RNA binding / extracellular space / 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 / MAD / Resolution: 2.55 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 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)111,95112
Polymers111,95112
Non-polymers00
Water3,153175
1
A: CYCLOPHILIN A
G: PEPTIDE FROM THE HIV-1 CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)18,6592
Polymers18,6592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-3 kcal/mol
Surface area7440 Å2
MethodPISA
2
C: CYCLOPHILIN A
I: PEPTIDE FROM THE HIV-1 CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)18,6592
Polymers18,6592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-4 kcal/mol
Surface area7310 Å2
MethodPISA
3
E: CYCLOPHILIN A
K: PEPTIDE FROM THE HIV-1 CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)18,6592
Polymers18,6592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: CYCLOPHILIN A
J: PEPTIDE FROM THE HIV-1 CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)18,6592
Polymers18,6592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-4 kcal/mol
Surface area7370 Å2
MethodPISA
5
B: CYCLOPHILIN A
H: PEPTIDE FROM THE HIV-1 CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)18,6592
Polymers18,6592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-5 kcal/mol
Surface area7380 Å2
MethodPISA
6
F: CYCLOPHILIN A
L: PEPTIDE FROM THE HIV-1 CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)18,6592
Polymers18,6592
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-5 kcal/mol
Surface area7440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.200, 73.200, 189.600
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(0.999156, 0.03207, -0.025684), (-0.032094, 0.999485, -0.000521), (0.025654, 0.001345, 0.99967)-0.73243, 1.28372, 126.04409
2given(0.997887, 0.063136, 0.015329), (-0.062962, 0.997949, -0.011556), (-0.016027, 0.010567, 0.999816)-1.45689, 1.52184, 63.35123
3given(0.984487, 0.17543, 0.003197), (-0.175391, 0.984448, -0.009995), (-0.004901, 0.009279, 0.999945)33.3683, 40.68538, 0.04417
4given(0.998532, -0.05125, -0.01754), (0.050637, 0.998146, -0.033759), (0.019238, 0.032821, 0.999276)37.47346, 35.92854, 125.41647
5given(0.996721, 0.07396, 0.032813), (-0.077082, 0.991249, 0.10716), (-0.0246, -0.109338, 0.9937)35.11689, 37.9392, 65.77402

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Components

#1: Protein
CYCLOPHILIN A


Mass: 18092.887 Da / Num. of mol.: 6 / Mutation: SELENO-METHIONINE SUBSTITUTED
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: SELENOMETHIONINE SUBSTITUTED CYPA; / 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


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.27 Å3/Da / Density % sol: 45.76 %
Crystal growpH: 8.4 / Details: pH 8.4
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 8.2 / 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 AREA DETECTOR / Date: Jun 1, 1995
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.55→15 Å / Num. obs: 32487 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 18.1 Å2 / Rsym value: 0.075 / Net I/σ(I): 6
Reflection shellResolution: 2.55→2.59 Å / Rsym value: 0.206 / % possible all: 98
Reflection
*PLUS
Num. measured all: 159378 / Rmerge(I) obs: 0.075
Reflection shell
*PLUS
% possible obs: 98 % / Rmerge(I) obs: 0.206

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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: MAD / Resolution: 2.55→15 Å / Rfactor Rfree error: 0.012 / 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 PROTEIN IS SELENO-METHIONINE SUBSTITUTED, BUT THE SELENO-METHIONINE RESIDUES WERE REFINED AS METHIONINES. THE HIGH R-VALUE FOR THIS STRUCTURE STEMS FROM THE ...Details: BULK SOLVENT MODEL USED THE PROTEIN IS SELENO-METHIONINE SUBSTITUTED, BUT THE SELENO-METHIONINE RESIDUES WERE REFINED AS METHIONINES. 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.
RfactorNum. reflection% reflectionSelection details
Rfree0.465 1478 4.9 %RANDOM
Rwork0.378 ---
obs0.378 30093 93.3 %-
Displacement parametersBiso mean: 16.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.65 Å0.5 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.55→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5032 0 120 175 5327
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
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_d26
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.36
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: 2.55→2.71 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.479 261 5.3 %
Rwork0.407 4704 -
obs--92.1 %
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
Lowest resolution: 15 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.36

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