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- PDB-1m9e: X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal doma... -

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Basic information

Entry
Database: PDB / ID: 1m9e
TitleX-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) M-type H87A Complex.
Components
  • Cyclophilin 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 / 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 / positive regulation of NF-kappaB transcription factor activity / Budding and maturation of HIV virion / platelet activation / platelet aggregation / integrin binding / 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 / host cell cytoplasm / 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 / cytoplasm / cytosol
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: 1.72 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)68,0904
Polymers68,0904
Non-polymers00
Water6,846380
1
A: Cyclophilin A
D: HIV-1 Capsid


Theoretical massNumber of molelcules
Total (without water)34,0452
Polymers34,0452
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)34,0452
Polymers34,0452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.289, 110.989, 67.685
Angle α, β, γ (deg.)90.00, 101.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 17907.389 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: 16137.505 Da / Num. of mol.: 2 / Fragment: N-terminal domain / Mutation: H87A
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / 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
Details: PEG 8K, Bicine, LiCl, Tris, Beta-mercaptoethanol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal grow
*PLUS
Temperature: 21 ℃ / 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: BL1-5 / Wavelength: 1.07 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 12, 1998
RadiationMonochromator: double crystal monochromator Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 1.72→26 Å / Num. all: 52624 / Num. obs: 41047 / % possible obs: 78 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 30.3 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 9.4
Reflection shellResolution: 1.72→1.82 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1721 / Rsym value: 0.304 / % possible all: 31
Reflection
*PLUS
Lowest resolution: 26 Å / % possible obs: 78 % / Num. measured all: 188143
Reflection shell
*PLUS
% possible obs: 31 %

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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: 1.72→25.73 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.72 / SU ML: 0.147 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.165 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS But not output to the atomic coordinate file.
RfactorNum. reflection% reflectionSelection details
Rfree0.22571 4623 10.1 %RANDOM
Rwork0.17286 ---
all0.17811 52624 --
obs0.178 41047 77.7 %-
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: 20.181 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å20 Å2-0.35 Å2
2--1.29 Å20 Å2
3----0.75 Å2
Refinement stepCycle: LAST / Resolution: 1.72→25.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4677 0 0 380 5057
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0214786
X-RAY DIFFRACTIONr_bond_other_d00.024287
X-RAY DIFFRACTIONr_angle_refined_deg3.0341.9416461
X-RAY DIFFRACTIONr_angle_other_deg1.218310027
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0813603
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.41715884
X-RAY DIFFRACTIONr_chiral_restr0.1810.2691
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.025361
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02949
X-RAY DIFFRACTIONr_nbd_refined0.2410.31136
X-RAY DIFFRACTIONr_nbd_other0.2140.34512
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.5745
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0680.54
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.30.317
X-RAY DIFFRACTIONr_symmetry_vdw_other0.260.380
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2290.542
X-RAY DIFFRACTIONr_mcbond_it2.87523003
X-RAY DIFFRACTIONr_mcangle_it3.99834825
X-RAY DIFFRACTIONr_scbond_it3.19521783
X-RAY DIFFRACTIONr_scangle_it4.7631636
LS refinement shellResolution: 1.72→1.764 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 102 -
Rwork0.291 1019 -
obs-1721 31 %
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 26 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.226 / Rfactor Rwork: 0.173
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_deg3
LS refinement shell
*PLUS
Highest resolution: 1.72 Å / Lowest resolution: 1.82 Å

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