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- PDB-3gi0: Crystal structure of a chemically synthesized 203 amino acid 'cov... -

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Basic information

Entry
Database: PDB / ID: 3gi0
TitleCrystal structure of a chemically synthesized 203 amino acid 'covalent dimer' [l-ala51,d-ala51'] hiv-1 protease molecule complexed with jg-365 inhibitor
Components
  • COVALENT DIMER [L-ALA51,D-ALA51'] HIV-1 PROTEASE
  • JG-365 inhibitor
KeywordsHYDROLASE/HYDROLASE INHIBITOR / beta-barrel / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
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 ...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 / Cathepsin D, subunit A; domain 1 / Acid Proteases / 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. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
JG-365 / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTorbeev, V.Y. / Kent, S.B.H.
CitationJournal: To be Published
Title: Correlations of protein dynamics with function in HIV-1 protease catalysis
Authors: Torbeev, V.Y. / Kent, S.B.H.
History
DepositionMar 4, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Other
Revision 1.2Jun 7, 2017Group: Database references / Structure summary
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _pdbx_validate_peptide_omega.auth_comp_id_1 / _pdbx_validate_peptide_omega.auth_comp_id_2 / _pdbx_validate_peptide_omega.auth_seq_id_1 / _pdbx_validate_peptide_omega.auth_seq_id_2 / _pdbx_validate_peptide_omega.omega / _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
A: COVALENT DIMER [L-ALA51,D-ALA51'] HIV-1 PROTEASE
B: COVALENT DIMER [L-ALA51,D-ALA51'] HIV-1 PROTEASE
C: JG-365 inhibitor
D: JG-365 inhibitor


Theoretical massNumber of molelcules
Total (without water)45,5294
Polymers45,5294
Non-polymers00
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-7 kcal/mol
Surface area9410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.172, 58.456, 60.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein COVALENT DIMER [L-ALA51,D-ALA51'] HIV-1 PROTEASE


Mass: 21919.703 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: total chemical protein synthesis / Source: (synth.) Homo sapiens (human) / References: UniProt: P03369, HIV-1 retropepsin
#2: Protein/peptide JG-365 inhibitor


Type: Peptide-like / Class: Inhibitor / Mass: 845.039 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: chemical peptide synthesis / Source: (synth.) synthetic construct (others) / References: JG-365
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
Compound detailsSEE REMARK 999
Sequence detailsBOTH THE HIV-1 PROTEASE COVALENT DIMER [L-ALA51,D-ALA51'] (CHAINS A AND B) AND JG-365 INHIBITOR ...BOTH THE HIV-1 PROTEASE COVALENT DIMER [L-ALA51,D-ALA51'] (CHAINS A AND B) AND JG-365 INHIBITOR (CHAINS C AND D) WERE CHEMICALLY SYNTHESIZED WITH NON-NATURAL AMINO ACIDS INTRODUCED AT SEVERAL POSITIONS. THE HIV-1 PROTEASE DIMER HAS TWO COVALENTLY LINKED MONOMER PARTS, RESIDUES 1-99 AND RESIDUES 105-203, BOTH REPRESENTING ANALOGUE OF HIV-1 PROTEASE CORRESPONDING TO THE RESIDUES 491-589 OF UNP ENTRY P03369. THE REGION 1-99 OF THE FIRST HALF AND 105-203 OF THE SECOND HALF SHARE THE SAME SEQUENCE EXCEPT FOR THE 51ST RESIDUE, WHICH IS L-ALA(ALA51) IN REGION 1-99 AND D-ALA (DAL155) IN REGION 105-203. THERE IS A SHORT LINKER REGION (RESIDUES 100-104). THE TWO REGIONS (HALVES) ARE RELATED BY INTRA-MOLECULAR PSEUDO-2-FOLD SYMMETRY, I.E. REGIONS 1-99 AND 105-203 HAVE SIMILAR STRUCTURES BUT DO NOT SUPERIMPOSE COMPLETELY. MOREOVER, THERE IS A DISORDER WITH RESPECT TO THE NON-CRYSTALLOGRAPHIC PSEUDO-2-FOLD SYMMETRY AXIS OF THE COVELENT DIMER HIV-1 PROTEASE. SUCH CONCLUSION IS BASED ON THE SPLIT OF THE DENSITY AT THE BETA-TURN REGIONS FOR RESIDUES 49-52 AND 153-156, ALTHOUGH THE IS NO DENSITY SPLIT BETWEEN TWO CONFORMERS FOR MOST OF THE ATOMS. TO ACCOUNT FOR SUCH DISORDER, CHAINS A AND B, EACH REPRESENTING THE SAME 203-AMINO ACID RESIDUE COVALENT DIMER HIV-1 PROTEASE WERE INTRODUCED IN THE STRUCTURE SOLUTION. SO WERE CHAINS C AND D FOR THE PEPTIDOMIMETIC JG-365 INHIBITOR, WHERE CHAIN C OF INHIBITOR CORRESPONDS TO THE MODEL A OF THE COVELENT DIMER HIV-1 PROTEASE AND CHAIN D CORRESPONDS TO MODEL B. THESE TWO MODELS, OR TWO CONFORMATIONS OF ONE POLYMER CHAIN ARE RELATED TO EACH OTHER BY PSEUDO-2-FOLD SYMMETRY. THE OCCUPANCIES WERE DETERMINED TO BE 0.65 FOR CHAINS A AND C AND 0.35 FOR CHAINS B AND D, RESPECTIVELY.

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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 Å3/Da / Density % sol: 38.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M CITRATE, 0.2M SODIUM PHOPHATE,30% (W/V) AMMONIUM SULFATE, 10% (V/V) DMSO , PH 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 10, 2007
Details: double crystal monochromator and K-B pair of biomorph mirrors for vertical and horizontal focusing
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 17520 / Num. obs: 17520 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 26.22
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 3.86 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPv.5phasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3FSM

3fsm


Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.929 / SU B: 5.486 / SU ML: 0.086 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SEE REMARK 999 FOR THE SPECIAL STRUCTURAL SOLUTION
RfactorNum. reflection% reflectionSelection details
Rfree0.23682 883 5.1 %RANDOM
Rwork0.18778 ---
obs0.19016 16579 99.9 %-
all-16579 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.294 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å20 Å20 Å2
2--0.23 Å20 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3212 0 0 96 3308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221774
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6731.9822403
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.435228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.13925.08261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.53315303
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.514159
X-RAY DIFFRACTIONr_chiral_restr0.1230.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021259
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.2745
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.320.21163
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2106
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0440.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.252
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0571.51171
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.55721839
X-RAY DIFFRACTIONr_scbond_it2.5693685
X-RAY DIFFRACTIONr_scangle_it3.9314.5564
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.801→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 59 -
Rwork0.181 1206 -
obs--100 %

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