[English] 日本語
Yorodumi
- PDB-2sam: STRUCTURE OF THE PROTEASE FROM SIMIAN IMMUNODEFICIENCY VIRUS: COM... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2sam
TitleSTRUCTURE OF THE PROTEASE FROM SIMIAN IMMUNODEFICIENCY VIRUS: COMPLEX WITH AN IRREVERSIBLE NON-PEPTIDE INHIBITOR
ComponentsSIV PROTEASE
KeywordsHYDROLASE(ACID PROTEASE)
Function / homology
Function and homology information


exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / aspartic-type endopeptidase activity / symbiont entry into host cell ...exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / aspartic-type endopeptidase activity / symbiont entry into host cell / proteolysis / DNA binding / zinc ion binding
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. / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / RNase H type-1 domain profile. / Ribonuclease H domain / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Cathepsin D, subunit A; domain 1 / Acid Proteases / 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 / Mainly Beta
Similarity search - Domain/homology
3-(4-NITRO-PHENOXY)-PROPAN-1-OL / Pol protein / Pol polyprotein
Similarity search - Component
Biological speciesSimian immunodeficiency virus
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsRose, R.B. / Rose, J.R. / Salto, R. / Craik, C.S. / Stroud, R.M.
CitationJournal: Biochemistry / Year: 1993
Title: Structure of the protease from simian immunodeficiency virus: complex with an irreversible nonpeptide inhibitor.
Authors: Rose, R.B. / Rose, J.R. / Salto, R. / Craik, C.S. / Stroud, R.M.
History
DepositionJul 8, 1994Processing site: BNL
Revision 1.0Oct 15, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET THE DIMER INTERFACE IS COMPOSED OF INTERDIGITATED N- AND C-TERMINI FROM BOTH SUBUNITS FORMING ...SHEET THE DIMER INTERFACE IS COMPOSED OF INTERDIGITATED N- AND C-TERMINI FROM BOTH SUBUNITS FORMING A FOUR-STRANDED ANTIPARALLEL BETA-SHEET. BECAUSE OF LIMITATIONS IMPOSED BY THE PROTEIN DATA BANK FORMAT IT IS NOT POSSIBLE TO PRESENT THIS SHEET ON SHEET RECORDS. INSTEAD THIS SHEET IS SPECIFIED IN THIS REMARK. STRANDS 1 AND 3 ARE FROM THE MOLECULE IN THIS ENTRY AND STRANDS 2 AND 4 ARE FROM THE SYMMETRY RELATED MOLECULE. I 4 PRO 1 THR 4 0 I 4 THR 96 PHE 99 -1 I 4 THR 96 PHE 99 -1 I 4 PRO 1 THR 4 -1

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SIV PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9802
Polymers10,7821
Non-polymers1971
Water43224
1
A: SIV PROTEASE
hetero molecules

A: SIV PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9594
Polymers21,5652
Non-polymers3942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4700 Å2
ΔGint-12 kcal/mol
Surface area9190 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)62.700, 32.200, 96.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Atom site foot note1: THE EPN INHIBITOR IS COVALENTLY BOUND TO OD2 OF ASP 25.
Components on special symmetry positions
IDModelComponents
11A-301-

HOH

DetailsTHE HIV-1 PROTEASE IS A DIMER. IN THE CRYSTAL THE TWO MONOMERS ARE RELATED BY A CRYSTALLOGRAPHIC TWO-FOLD AXIS. TO GENERATE THE SYMMETRY RELATED MONOMER, THE FOLLOWING TRANSFORMATION MUST BE APPLIED TO THE COORDINATES PRESENTED IN THIS ENTRY MTRIX1 1 1.000000 0.000000 0.000000 0.000000 MTRIX2 1 0.000000 -1.000000 0.000000 0.000000 MTRIX3 1 0.000000 0.000000 -1.000000 0.000000

-
Components

#1: Protein SIV PROTEASE


Mass: 10782.454 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian immunodeficiency virus / Genus: Lentivirus / References: UniProt: Q88016, UniProt: Q5QGH9*PLUS
#2: Chemical ChemComp-EPN / 3-(4-NITRO-PHENOXY)-PROPAN-1-OL


Mass: 197.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHE OCCUPANCY OF THE LIGAND, EPNP, WAS REFINED TO 0.5. THE STOICHIOMETRY OF BINDING OF EPNP TO SIV ...THE OCCUPANCY OF THE LIGAND, EPNP, WAS REFINED TO 0.5. THE STOICHIOMETRY OF BINDING OF EPNP TO SIV PROTEASE IS ONE MOLECULE PER PROTEASE DIMER; ONLY ONE OF THE ACTIVE-SITE ASPARTIC ACIDS PER DIMER BECOMES LABELLED BY EPNP. UPON EPNP BINDING TO THE DIMER, EACH INDIVIDUAL DIMER MOLECULE IS NO LONGER TWO-FOLD SYMMETRICAL AROUND THE CRYSTALLOGRAPHIC TWO-FOLD AXIS. THE DIMER TWO-FOLD IS STILL A CRYSTALLOGRAPHIC TWO-FOLD BECAUSE STATISTICALLY THROUGHOUT THE CRYSTAL THE EPNP IS LOCATED ON EITHER OF THE TWO ACTIVE-SITE ASPARTIC ACIDS WITH EQUAL PROBABILITY.
Sequence detailsSEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: POL_ ...SEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: POL_SIVM1 SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE SER 109 HIS 4 ARG 112 LYS 7 LEU 204 PHE 99 THE SEQUENCE IN THIS ENTRY IS FROM SIVMM239 (AS NAMED IN THE "HUMAN RETROVIRUS AND AIDS" LISTING OF SEQUENCES OF HIV GENOMES, PUBLISHED BY LOS ALAMOS NATIONAL LABORATORY. THIS SEQUENCE IS DIFFERENT THAN THE POL_SIVM1 SEQUENCE ABOVE IN TWO POSITIONS, AT RESIDUE 7 WHICH IS LYS IN THIS STRUCTURE AND ARG IN POL_SIVM1 AND AT RESIDUE 99 WHICH IS PHE IN THIS STRUCTURE AND LEU IN POL_SIMV1. THE HIS AT POSITION 4 IN THIS STRUCTURE IS A POINT MUTANT AND IS A SER IN THE WILD-TYPE SIVMM239 SEQUENCE. THIS POINT MUTATION AT RESIDUE 4 WAS ENGINEERED TO DECREASE THE PROTEASE'S SUSCEPTIBILITY TO AUTOPROTEOLYSIS.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.28 %
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop / Details: using macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
24-6 %sat1dropNaCl
3100 mMsodium cacodylate1drop
44-6 %sat1reservoirNaCl
5100 mMsodium cacodylate1reservoir
1protein1drop4ml

-
Data collection

Reflection
*PLUS
Highest resolution: 2.4 Å / Num. obs: 8824 / % possible obs: 92 % / Observed criterion σ(I): 1 / Num. measured all: 21880 / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
Highest resolution: 2.25 Å / Lowest resolution: 2.5 Å / % possible obs: 77 %

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.4→40 Å / σ(F): 1 /
RfactorNum. reflection
Rwork0.19 -
obs0.19 21880
Refinement stepCycle: LAST / Resolution: 2.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms742 0 14 24 780
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg3.2
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.2

+
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://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