[English] 日本語
Yorodumi
- PDB-2je4: Atomic-resolution crystal structure of chemically-synthesized HIV... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2je4
TitleAtomic-resolution crystal structure of chemically-synthesized HIV-1 protease in complex with JG-365
Components
  • INHIBITOR MOLECULE JG365
  • PROTEASE
KeywordsHYDROLASE/HYDROLASE INHIBITOR / PROTEASE / HYDROLASE / HIGH RESOLUTION / ASPARTYL PROTEASE / HUMAN IMMUNODEFICIENCY VIRUS 1 / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


HIV-1 retropepsin / 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 ...HIV-1 retropepsin / 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 / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / 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 / virion membrane / structural molecule activity / 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 / Zinc finger, CCHC-type superfamily / Cathepsin D, subunit A; domain 1 / Acid Proteases / 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 / ACETATE ION / Protease / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHUMAN IMMUNODEFICIENCY VIRUS 1
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.07 Å
AuthorsMalito, E. / Johnson, E.C.B. / Tang, W.J.
CitationJournal: J.Am.Chem.Soc. / Year: 2007
Title: Modular Total Chemical Synthesis of a Human Immunodeficiency Virus Type 1 Protease.
Authors: Johnson, E.C.B. / Malito, E. / Shen, Y. / Rich, D. / Tang, W.J. / Kent, S.B.
History
DepositionJan 15, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Jul 20, 2011Group: Database references / Other / Source and taxonomy
Revision 1.3Mar 6, 2013Group: Other
Revision 1.4Dec 10, 2014Group: Data collection
Revision 1.5Feb 8, 2017Group: Data collection / Source and taxonomy
Revision 1.6Oct 18, 2017Group: Advisory / Data collection / Category: database_PDB_caveat / diffrn_radiation / Item: _diffrn_radiation.pdbx_diffrn_protocol
Revision 1.7May 22, 2019Group: Data collection / Derived calculations / Refinement description
Category: refine / struct_conn
Item: _refine.pdbx_ls_cross_valid_method / _struct_conn.pdbx_leaving_atom_flag
Revision 1.8Oct 16, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status ...exptl_crystal_grow / pdbx_database_status / reflns / reflns_shell
Item: _pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Dec 13, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEASE
B: PROTEASE
C: INHIBITOR MOLECULE JG365
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,32915
Polymers22,3363
Non-polymers99312
Water7,098394
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7140 Å2
ΔGint-73 kcal/mol
Surface area9480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.501, 58.853, 60.886
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Number of models2

-
Components

-
Protein / Protein/peptide , 2 types, 3 molecules ABC

#1: Protein PROTEASE / HIV1-PROTEASE


Mass: 10745.632 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) HUMAN IMMUNODEFICIENCY VIRUS 1 / References: UniProt: O38716, UniProt: P03369*PLUS
#2: Protein/peptide INHIBITOR MOLECULE JG365


Type: Peptide-like / Class: Inhibitor / Mass: 845.039 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) / References: JG-365

-
Non-polymers , 4 types, 406 molecules

#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.3 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop
Details: well solution 0.1 M citrate, 0.2 M sodium phosphate, 30% saturated ammonium sulfate, and 10% DMSO, pH 6.0

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11501
21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONAPS 14-BM-C10.987
SYNCHROTRONAPS 19-BM20.987
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.07→50 Å / Num. obs: 72978 / % possible obs: 93.9 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 28.2
Reflection shellResolution: 1.07→1.11 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 2.9 / % possible all: 82.8

-
Processing

Software
NameClassification
SHELXL-97refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 7HVP

7hvp


Resolution: 1.07→10 Å / Num. parameters: 18150 / Num. restraintsaints: 24635 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.184 3830 5.1 %RANDOM
all0.144 75585 --
obs0.143 -93.9 %-
Refine analyzeNum. disordered residues: 44 / Occupancy sum hydrogen: 1379.92 / Occupancy sum non hydrogen: 1791.98
Refinement stepCycle: LAST / Resolution: 1.07→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1567 0 59 394 2020
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.039
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.035
X-RAY DIFFRACTIONs_zero_chiral_vol0.106
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.087
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.043
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.007
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.061
X-RAY DIFFRACTIONs_approx_iso_adps0.098

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more