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- PDB-1ak4: HUMAN CYCLOPHILIN A BOUND TO THE AMINO-TERMINAL DOMAIN OF HIV-1 CAPSID -

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Basic information

Entry
Database: PDB / ID: 1ak4
TitleHUMAN CYCLOPHILIN A BOUND TO THE AMINO-TERMINAL DOMAIN OF HIV-1 CAPSID
Components
  • CYCLOPHILIN APeptidylprolyl isomerase A
  • HIV-1 CAPSID
KeywordsViral protein/isomerase / CAPSID / HIV-1 / CYCLOPHILIN A / ISOMERASE / ROTAMASE COMPLEX (CAPSID PROTEIN-CYCLOSPORIN) / Viral protein-isomerase 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 / 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 / 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 / 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 ...Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / 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 / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsHill, C.P. / Gamble, T.R. / Vajdos, F.F. / Worthylake, D.K. / Sundquist, W.I.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 1996
Title: Crystal structure of human cyclophilin A bound to the amino-terminal domain of HIV-1 capsid.
Authors: Gamble, T.R. / Vajdos, F.F. / Yoo, S. / Worthylake, D.K. / Houseweart, M. / Sundquist, W.I. / Hill, C.P.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Crystal Structure of Cyclophilin a Complexed with Substrate Ala-Pro Suggests a Solvent-Assisted Mechanism of Cis-Trans Isomerization
Authors: Ke, H. / Mayrose, D. / Cao, W.
History
DepositionMay 28, 1997Processing site: BNL
Revision 1.0Oct 15, 1997Provider: 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 / Other / Refinement description
Category: database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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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)68,3084
Polymers68,3084
Non-polymers00
Water1,928107
1
A: CYCLOPHILIN A
D: HIV-1 CAPSID


Theoretical massNumber of molelcules
Total (without water)34,1542
Polymers34,1542
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)34,1542
Polymers34,1542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.600, 113.100, 67.000
Angle α, β, γ (deg.)90.00, 100.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CYCLOPHILIN A / Peptidylprolyl isomerase A


Mass: 18036.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Gene: CYCLOPHILIN / Plasmid: WISP94-1 / Species (production host): Escherichia coli / Gene (production host): CYCLOPHILIN / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P62937, peptidylprolyl isomerase
#2: Protein HIV-1 CAPSID


Mass: 16117.495 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN / Mutation: DELETION MUTANT DEL(152-231)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Cell line: BL21 / Gene: CYCLOPHILIN / Plasmid: WISP95-69 / Species (production host): Escherichia coli / Gene (production host): CYCLOPHILIN / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P12497
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.1 Å3/Da / Density % sol: 36 %
Crystal growpH: 7
Details: THE PROTEIN SOLUTION WAS 0.25 MM CYPA AND 0.25 MM CA(151) IN 10 MM TRISHCL (PH 8.0) AND 1 MM 2-MERCAPTOETHANOL. THE RESERVOIR SOLUTION WAS 1ML OF 1.0 M LICL, 0.1 M BICINE (PH 7.0), AND 22% ...Details: THE PROTEIN SOLUTION WAS 0.25 MM CYPA AND 0.25 MM CA(151) IN 10 MM TRISHCL (PH 8.0) AND 1 MM 2-MERCAPTOETHANOL. THE RESERVOIR SOLUTION WAS 1ML OF 1.0 M LICL, 0.1 M BICINE (PH 7.0), AND 22% POLYETHYLENE GLYCOL 8000. THE INITIAL DROP WAS 6 MICROL OF A 1:1 MIX OF PROTEIN AND RESERVOIR SOLUTIONS.
Crystal grow
*PLUS
Temperature: 21 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.125 mMCyPA1drop
20.125 mMCA1511drop
35 mMTris-HCl1drop
40.5 mM2-mercaptoethanol1drop
50.50 M1dropLiCl
60.50 MBicine1drop
711 %PEG80001drop
81.0 M1reservoirLiCl
90.1 MBicine1reservoir
1022 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.978
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1996 / Details: COLLIMATOR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.36→20 Å / Num. obs: 21503 / % possible obs: 97 % / Observed criterion σ(I): 0 / Rsym value: 0.11 / Net I/σ(I): 10.5
Reflection shellResolution: 2.36→2.4 Å / Mean I/σ(I) obs: 3.5 / Rsym value: 0.399 / % possible all: 91
Reflection
*PLUS
Rmerge(I) obs: 0.11
Reflection shell
*PLUS
% possible obs: 91 % / Num. unique obs: 1049 / Rmerge(I) obs: 0.399

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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: MOLECULAR REPLACEMENT
Starting model: CYPA STRUCTURE (PDB ENTRY 2CYH)

2cyh


Resolution: 2.36→6 Å / Isotropic thermal model: INDIVIDUAL ATOMIC / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.306 --RANDOM
Rwork0.238 ---
obs0.238 21128 97 %-
Displacement parametersBiso mean: 25 Å2
Refinement stepCycle: LAST / Resolution: 2.36→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4777 0 0 107 4884
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
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_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.36→2.46 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.402 --
Rwork0.35 1049 -
obs--91 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CYPFRAG_PARTEST.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
LS refinement shell
*PLUS
Rfactor Rwork: 0.35

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