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- PDB-1m9d: X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal doma... -

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Basic information

Entry
Database: PDB / ID: 1m9d
TitleX-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) O-type chimera Complex.
Components
  • Cyclophilin APeptidylprolyl isomerase A
  • HIV-1 Capsid
KeywordsIsomerase/Viral protein / CAPSID / HIV-1 / CYCLOPHILIN A / ISOMERASE / ROTAMASE / Isomerase-Viral protein 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 / viral budding via host ESCRT complex / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Calcineurin activates NFAT / viral release from host cell / positive regulation of viral genome replication / Binding and entry of HIV virion / 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 / Assembly Of The HIV Virion / negative regulation of protein kinase activity / HIV-1 retropepsin / : / Budding and maturation of HIV virion / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / neuron differentiation / platelet aggregation / platelet activation / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / SARS-CoV-1 activates/modulates innate immune responses / RNA-directed DNA polymerase activity / unfolded protein binding / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / integrin binding / protein folding / Platelet degranulation / cellular response to oxidative stress / positive regulation of NF-kappaB transcription factor activity / viral nucleocapsid / secretory granule lumen / DNA recombination / vesicle / host cell cytoplasm / ficolin-1-rich granule lumen / positive regulation of MAPK cascade / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / positive regulation of protein phosphorylation / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / focal adhesion / lipid binding / apoptotic process / host cell nucleus / Neutrophil degranulation / structural molecule activity / host cell plasma membrane / virion membrane / protein-containing complex / proteolysis / DNA binding / extracellular space / RNA binding / extracellular exosome / zinc ion binding / extracellular region / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Gag protein p6 / Gag protein p6 / 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. ...Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Gag protein p6 / Gag protein p6 / 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 / gag protein p24 N-terminal domain / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Gag-Pol polyprotein / Peptidyl-prolyl cis-trans isomerase A / Gag polyprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHoward, B.R. / Vajdos, F.F. / Li, S. / Sundquist, W.I. / Hill, C.P.
CitationJournal: Nat.Struct.Biol. / Year: 2003
Title: Structural insights into the catalytic mechanism of cyclophilin A
Authors: Howard, B.R. / Vajdos, F.F. / Li, S. / Sundquist, W.I. / Hill, C.P.
History
DepositionJul 28, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 300BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 ...BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). Complex "A" consists of chains B and C; Complex "B" consists of chains A and D.
Remark 999SEQUENCE According to the authors, this apparent conflict is due to the use of HIV-1 strain NL4-3 ...SEQUENCE According to the authors, this apparent conflict is due to the use of HIV-1 strain NL4-3 which has a histidine at residue 120.

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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: HIV-1 Capsid
D: HIV-1 Capsid


Theoretical massNumber of molelcules
Total (without water)68,4564
Polymers68,4564
Non-polymers00
Water10,521584
1
A: Cyclophilin A
D: HIV-1 Capsid


Theoretical massNumber of molelcules
Total (without water)34,2282
Polymers34,2282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cyclophilin A
C: HIV-1 Capsid


Theoretical massNumber of molelcules
Total (without water)34,2282
Polymers34,2282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.900, 109.300, 67.700
Angle α, β, γ (deg.)90.00, 99.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cyclophilin A / Peptidylprolyl isomerase A / Peptidyl-prolyl cis-trans isomerase A / PPIase / Rotamase / Cyclosporin A-binding protein


Mass: 18036.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET3A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62937, peptidylprolyl isomerase
#2: Protein HIV-1 Capsid


Mass: 16191.552 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN / Mutation: L83T, V86P, H87A, A88M, I91L, A92P, M96I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: CA / Plasmid: PET11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q72497, UniProt: P12497*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 584 / 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: 2.07 Å3/Da / Density % sol: 36 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG 8K, Bicine, LiCl, Tris, Beta-mercaptoethanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 8 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.4 mMCypA-CAN1drop
21 mMbeta-mercaptoethanol1drop
310 mMTris1droppH8.0
415-25 %(w/v)PEG80001reservoir
51 M1reservoirLiCl
6100 mMBicine1reservoirpH7.0-9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1997
RadiationMonochromator: Single crystal Si(311) bent monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→67 Å / Num. all: 39417 / Num. obs: 37052 / % possible obs: 94 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 34.2 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 21.1
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 3 / Num. unique all: 1782 / Rsym value: 0.352 / % possible all: 82
Reflection
*PLUS
% possible obs: 94 % / Num. measured all: 219914
Reflection shell
*PLUS
% possible obs: 82 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
REFMAC5refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1AK4

1ak4


Resolution: 1.9→67.42 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.93 / SU B: 5.872 / SU ML: 0.175 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.193 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS But not output to the coordinate file
RfactorNum. reflection% reflectionSelection details
Rfree0.2324 3894 9.5 %RANDOM
Rwork0.16334 ---
all0.17005 39417 --
obs0.17 37052 94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.56 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å2-0.24 Å2
2--0.37 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.9→67.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4779 0 0 584 5363
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0214893
X-RAY DIFFRACTIONr_bond_other_d0.0020.024378
X-RAY DIFFRACTIONr_angle_refined_deg2.9221.9436610
X-RAY DIFFRACTIONr_angle_other_deg2.134310251
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7583616
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.5915913
X-RAY DIFFRACTIONr_chiral_restr0.1960.2707
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.025472
X-RAY DIFFRACTIONr_gen_planes_other0.0150.02958
X-RAY DIFFRACTIONr_nbd_refined0.2060.31053
X-RAY DIFFRACTIONr_nbd_other0.1440.34520
X-RAY DIFFRACTIONr_nbtor_other0.0030.51
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.5827
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0320.52
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1130.322
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1370.3104
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2050.563
X-RAY DIFFRACTIONr_mcbond_it3.00623072
X-RAY DIFFRACTIONr_mcangle_it4.31734945
X-RAY DIFFRACTIONr_scbond_it3.46121821
X-RAY DIFFRACTIONr_scangle_it5.12531665
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 186 -
Rwork0.183 2270 -
obs-1782 81.9 %
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 67 Å / % reflection Rfree: 10 % / Rfactor obs: 0.17 / Rfactor Rfree: 0.232 / Rfactor Rwork: 0.163
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.018
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.9
LS refinement shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 1.93 Å

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