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- PDB-2x2d: acetyl-CypA:HIV-1 N-term capsid domain complex -

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Basic information

Entry
Database: PDB / ID: 2x2d
Titleacetyl-CypA:HIV-1 N-term capsid domain complex
Components
  • CAPSID PROTEIN P24
  • PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A
KeywordsISOMERASE/VIRAL PROTEIN / ISOMERASE-VIRAL PROTEIN COMPLEX / ISOMERASE VIRAL PROTEIN COMPLEX / VIRAL PROTEIN / ISOMERASE / HOST-VIRUS INTERACTION
Function / homology
Function and homology information


negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / negative regulation of viral life cycle / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication / virion binding / leukocyte chemotaxis / negative regulation of stress-activated MAPK cascade ...negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / negative regulation of viral life cycle / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication / virion binding / leukocyte chemotaxis / 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 / APOBEC3G mediated resistance to HIV-1 infection / viral release from host cell / negative regulation of protein phosphorylation / 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 / activation of protein kinase B activity / neutrophil chemotaxis / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / peptidyl-prolyl cis-trans isomerase activity / negative regulation of protein kinase activity / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / positive regulation of protein secretion / peptidylprolyl isomerase / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / Assembly Of The HIV Virion / Budding and maturation of HIV virion / host multivesicular body / DNA integration / platelet activation / ISG15 antiviral mechanism / viral genome integration into host DNA / RNA-directed DNA polymerase / platelet aggregation / establishment of integrated proviral latency / telomerase activity / viral penetration into host nucleus / RNA stem-loop binding / neuron differentiation / positive regulation of NF-kappaB transcription factor activity / RNA-DNA hybrid ribonuclease activity / SARS-CoV-1 activates/modulates innate immune responses / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / integrin binding / unfolded protein binding / Platelet degranulation / protein folding / host cell / positive regulation of protein phosphorylation / cellular response to oxidative stress / viral nucleocapsid / secretory granule lumen / DNA recombination / vesicle / ficolin-1-rich granule lumen / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / positive regulation of MAPK cascade / symbiont-mediated suppression of host gene expression / symbiont entry into host cell / viral translational frameshifting / focal adhesion / apoptotic process / lipid binding / Neutrophil degranulation / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / protein-containing complex / proteolysis / DNA binding / 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 / 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. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / 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. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H 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 polyprotein / Gag-Pol polyprotein / Peptidyl-prolyl cis-trans isomerase A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
HUMAN IMMUNODEFICIENCY VIRUS 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.95 Å
AuthorsLammers, M. / Neumann, H. / Chin, J.W. / James, L.C.
CitationJournal: Nat.Chem.Biol. / Year: 2010
Title: Acetylation Regulates Cyclophilin a Catalysis, Immunosuppression and HIV Isomerisation
Authors: Lammers, M. / Neumann, H. / Chin, J.W. / James, L.C.
History
DepositionJan 12, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 26, 2011Group: Database references / Derived calculations
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A
C: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A
D: CAPSID PROTEIN P24
E: CAPSID PROTEIN P24


Theoretical massNumber of molelcules
Total (without water)68,8274
Polymers68,8274
Non-polymers00
Water3,747208
1
C: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A
D: CAPSID PROTEIN P24


Theoretical massNumber of molelcules
Total (without water)34,4132
Polymers34,4132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-6.8 kcal/mol
Surface area18160 Å2
MethodPISA
2
B: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A
E: CAPSID PROTEIN P24


Theoretical massNumber of molelcules
Total (without water)34,4132
Polymers34,4132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-8.3 kcal/mol
Surface area17960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.542, 109.995, 67.567
Angle α, β, γ (deg.)90.00, 101.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A / PPIASE A / ROTAMASE A / CYCLOPHILIN A / CYCLOSPORIN A-BINDING PROTEIN / CYPA


Mass: 18077.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: POPTH / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P62937, peptidylprolyl isomerase
#2: Protein CAPSID PROTEIN P24 / CA / GAG POLYPROTEIN


Mass: 16335.771 Da / Num. of mol.: 2 / Fragment: RESIDUES 133-278 / Source method: isolated from a natural source / Source: (natural) HUMAN IMMUNODEFICIENCY VIRUS 1 / References: UniProt: P12493, UniProt: P12497*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.04 Å3/Da / Density % sol: 39.76 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.7
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 1.9→42.3 Å / Num. obs: 40235 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.16

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Processing

SoftwareName: REFMAC / Version: 5.5.0100 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.95→66.3 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.908 / SU B: 11.158 / SU ML: 0.142 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25695 1975 5 %RANDOM
Rwork0.19671 ---
obs0.19974 37521 98.16 %-
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: 27.394 Å2
Baniso -1Baniso -2Baniso -3
1--1.82 Å20 Å2-0.46 Å2
2--1.25 Å20 Å2
3---0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.95→66.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4720 0 0 208 4928
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0224827
X-RAY DIFFRACTIONr_bond_other_d0.0020.023325
X-RAY DIFFRACTIONr_angle_refined_deg1.7771.9466512
X-RAY DIFFRACTIONr_angle_other_deg1.0013.0018082
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7155603
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.82824.486214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.22115813
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6021524
X-RAY DIFFRACTIONr_chiral_restr0.1130.2696
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215379
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02955
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0761.53016
X-RAY DIFFRACTIONr_mcbond_other0.2971.51253
X-RAY DIFFRACTIONr_mcangle_it1.86624845
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8431811
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.454.51667
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 144 -
Rwork0.273 2829 -
obs--99.9 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7534-0.03530.15090.89120.29851.67260.01970.0360.0294-0.0178-0.0039-0.04760.0947-0.046-0.01580.019-0.01330.01470.0241-0.01170.027911.80152.006-18.6149
21.3501-0.53070.5322.02960.37771.87290.02890.0688-0.0165-0.2032-0.0220.0957-0.10.1167-0.00690.0429-0.0102-0.01580.01220.00160.0151-12.9064-41.3235-17.8416
30.7570.36260.52620.79160.49480.8476-0.04130.09910.06510.01310.0298-0.0626-0.0769-0.02860.01160.03140.00470.00960.03580.01260.08426.521-28.335911.8779
40.70440.4026-1.13881.0345-0.70612.1898-0.11080.21790.02130.1460.0752-0.00990.0606-0.24010.03560.0924-0.0743-0.02480.11960.00520.0643-8.6828-10.18912.1059
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B1 - 165
2X-RAY DIFFRACTION2C1 - 165
3X-RAY DIFFRACTION3D0 - 146
4X-RAY DIFFRACTION4E0 - 146

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