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- PDB-1m9y: X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal doma... -

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Basic information

Entry
Database: PDB / ID: 1m9y
TitleX-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) M-type H87A,G89A Complex.
Components
  • Cyclophilin A
  • HIV-1 Capsid
KeywordsIsomerase/Viral protein / CAPSID / HIV-1 / CYCLOPHILIN A / ROTAMASE / Isomerase-Viral protein 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 / viral budding via host ESCRT complex / 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 / : / Budding and maturation of HIV virion / platelet activation / platelet aggregation / integrin binding / host multivesicular body / positive regulation of protein phosphorylation / neuron differentiation / SARS-CoV-1 activates/modulates innate immune responses / unfolded protein binding / Platelet degranulation / protein folding / viral nucleocapsid / cellular response to oxidative stress / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / positive regulation of MAPK cascade / viral translational frameshifting / focal adhesion / apoptotic process / Neutrophil degranulation / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / protein-containing complex / extracellular space / RNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleus / membrane / 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. / : ...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 / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / 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. / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
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 30, 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, 3, 4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF ...BIOMOLECULE: 1, 2, 3, 4 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; Complex A' consists of chains F and G; Complex B' consists of chains E and H.
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
E: Cyclophilin A
F: Cyclophilin A
G: HIV-1 Capsid
H: HIV-1 Capsid


Theoretical massNumber of molelcules
Total (without water)136,7528
Polymers136,7528
Non-polymers00
Water20,2311123
1
A: Cyclophilin A
D: HIV-1 Capsid


Theoretical massNumber of molelcules
Total (without water)34,1882
Polymers34,1882
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)34,1882
Polymers34,1882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Cyclophilin A
H: HIV-1 Capsid


Theoretical massNumber of molelcules
Total (without water)34,1882
Polymers34,1882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
F: Cyclophilin A
G: HIV-1 Capsid


Theoretical massNumber of molelcules
Total (without water)34,1882
Polymers34,1882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.426, 111.223, 67.780
Angle α, β, γ (deg.)89.99, 101.45, 89.75
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 18036.504 Da / Num. of mol.: 4
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: 16151.530 Da / Num. of mol.: 4 / Fragment: N-terminal domain / Mutation: H87A,G89A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Plasmid: PET11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q72497
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1123 / 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: 2.08 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: 0.97 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 8, 2001
RadiationMonochromator: Single crystal Si(311) bent monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 86252 / Num. obs: 84527 / % possible obs: 98 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2.05 % / Biso Wilson estimate: 32.8 Å2 / Rmerge(I) obs: 0.04 / Rsym value: 0.04 / Net I/σ(I): 19
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 1.95 % / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 2.5 / Num. unique all: 4202 / Rsym value: 0.251 / % possible all: 96
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 98 % / Num. measured all: 173271 / Rmerge(I) obs: 0.04
Reflection shell
*PLUS
% possible obs: 96 % / Mean I/σ(I) obs: 2.9

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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→19.69 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.808 / SU ML: 0.113 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.179 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23417 8529 10.1 %RANDOM
Rwork0.16204 ---
all0.16914 84527 --
obs0.16914 84527 97.58 %-
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: 27.376 Å2
Baniso -1Baniso -2Baniso -3
1--1.29 Å2-0.1 Å2-0.46 Å2
2--1.79 Å2-0.18 Å2
3----0.69 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9408 0 0 1123 10531
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0219626
X-RAY DIFFRACTIONr_bond_other_d00.028622
X-RAY DIFFRACTIONr_angle_refined_deg2.5891.9412998
X-RAY DIFFRACTIONr_angle_other_deg1.059320168
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.54631212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.99151763
X-RAY DIFFRACTIONr_chiral_restr0.1560.21394
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0210780
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021904
X-RAY DIFFRACTIONr_nbd_refined0.2340.32235
X-RAY DIFFRACTIONr_nbd_other0.210.39081
X-RAY DIFFRACTIONr_nbtor_other0.0180.51
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2120.51712
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1650.57
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2470.342
X-RAY DIFFRACTIONr_symmetry_vdw_other0.230.3153
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2530.5114
X-RAY DIFFRACTIONr_symmetry_hbond_other0.0590.51
X-RAY DIFFRACTIONr_mcbond_it2.54226040
X-RAY DIFFRACTIONr_mcangle_it3.79939708
X-RAY DIFFRACTIONr_scbond_it2.78823586
X-RAY DIFFRACTIONr_scangle_it4.18733290
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 641 -
Rwork0.199 5472 -
obs-4202 96 %
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor obs: 0.169 / Rfactor Rfree: 0.234 / Rfactor Rwork: 0.162
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_deg2.6
LS refinement shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 1.93 Å

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