[English] 日本語
Yorodumi
- PDB-1k2b: Combining Mutations in HIV-1 Protease to Understand Mechanisms of... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1k2b
TitleCombining Mutations in HIV-1 Protease to Understand Mechanisms of Resistance
ComponentsPROTEASE RETROPEPSIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HIV-1 PROTEASE / 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 / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / viral translational frameshifting / lipid binding / symbiont entry into host cell / 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. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retrovirus capsid, C-terminal / Retroviral matrix protein / Cathepsin D, subunit A; domain 1 / Acid Proteases / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / 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. / 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
N-[(2R)-2-({N~5~-[amino(iminio)methyl]-L-ornithyl-L-valyl}amino)-4-methylpentyl]-L-phenylalanyl-L-alpha-glutamyl- L-alanyl-L-norleucinamide / Chem-0Q4 / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMahalingam, B. / Boross, P. / Wang, Y.-F. / Louis, J.M. / Fischer, C. / Tozser, J. / W Harrison, R. / Weber, I.T.
CitationJournal: Proteins / Year: 2002
Title: Combining mutations in HIV-1 protease to understand mechanisms of resistance.
Authors: Mahalingam, B. / Boross, P. / Wang, Y.F. / Louis, J.M. / Fischer, C.C. / Tozser, J. / Harrison, R.W. / Weber, I.T.
History
DepositionSep 26, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations / Refinement description
Category: database_2 / software ...database_2 / software / struct_ref_seq_dif / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.classification / _software.name / _struct_ref_seq_dif.details / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEASE RETROPEPSIN
B: PROTEASE RETROPEPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3523
Polymers21,5192
Non-polymers8331
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-30 kcal/mol
Surface area9120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.759, 57.541, 60.841
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein PROTEASE RETROPEPSIN / Retropepsin / PR


Mass: 10759.699 Da / Num. of mol.: 2 / Mutation: Q7K, l33I, L63I, C67A, C95A, N88D, L90M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Production host: Escherichia coli (E. coli) / References: UniProt: P04587, HIV-1 retropepsin
#2: Chemical ChemComp-0Q4 / N-[(2R)-2-({N~5~-[amino(iminio)methyl]-L-ornithyl-L-valyl}amino)-4-methylpentyl]-L-phenylalanyl-L-alpha-glutamyl-L-alanyl-L-norleucinamide / Inhibitor analogues of CA-p2


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 833.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H70N11O8
References: N-[(2R)-2-({N~5~-[amino(iminio)methyl]-L-ornithyl-L-valyl}amino)-4-methylpentyl]-L-phenylalanyl-L-alpha-glutamyl- L-alanyl-L-norleucinamide
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE INHIBITOR 0Q4 WAS CHEMICALLY SYNTHESIZED AND IS ANALOGOUS TO THE CA-P2 PROCESSING SITE ...THE INHIBITOR 0Q4 WAS CHEMICALLY SYNTHESIZED AND IS ANALOGOUS TO THE CA-P2 PROCESSING SITE INHIBITOR IN HIV-1 IT HAS A REDUCED PEPTIDE (-CH2-NH) INSTEAD OF THE NORMAL PEPTIDE LINK (-CO-NH).
Sequence detailsMUTATIONS Q7K, L33I, L63I, C67A, C95A, HAVE BEEN MADE TO STABILIZE THE PROTEASE FROM ...MUTATIONS Q7K, L33I, L63I, C67A, C95A, HAVE BEEN MADE TO STABILIZE THE PROTEASE FROM AUTOPROTEOLYSIS, WHILE RETAINING ACTIVITY SIMILAR TO WILD-TYPE HIV-1 PROTEASE

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 20-50% Saturated Ammonium Sulphate, 10% DMSO, 0.25M citrate/0.5M phosphate buffer, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
PH range low: 6.5 / PH range high: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.25 Mcitrate1reservoir
20.5 Mphosphate1reservoirpH5-6.5
310 %DMSO1reservoir
410 mMdithiothreitol1reservoir
520-50 %satammonium sulfate1reservoir
62-10 mg/mlprotein1drop

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.037 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 8, 1999
RadiationMonochromator: Double-crystal, fixed-exit Si-III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.037 Å / Relative weight: 1
ReflectionResolution: 1.7→25 Å / Num. all: 20000 / Num. obs: 20000 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 10.8
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 5.1 / Num. unique all: 1958 / % possible all: 98.4
Reflection
*PLUS
Lowest resolution: 8 Å / % possible obs: 99 % / Rmerge(I) obs: 0.042
Reflection shell
*PLUS
Rmerge(I) obs: 0.248

-
Processing

Software
NameClassification
AMoREphasing
X-PLORrefinement
Adxvdata processing
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DAZ

1daz


Resolution: 1.7→8 Å / Isotropic thermal model: Isotropic / Cross valid method: FREE R / σ(F): 2 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflectionSelection details
Rfree0.278 1972 RANDOM
Rwork0.215 --
obs-19780 -
Refinement stepCycle: LAST / Resolution: 1.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1512 0 59 128 1699
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_d2.183
X-RAY DIFFRACTIONx_dihedral_angle_d25.523
X-RAY DIFFRACTIONx_improper_angle_d1.446
LS refinement shellResolution: 1.7→1.76 Å
RfactorNum. reflection
Rfree0.3784 183
Rwork0.3196 -
obs-1886
Refinement
*PLUS
Rfactor Rfree: 0.275 / Rfactor Rwork: 0.216
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg2.183
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.523
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.446
X-RAY DIFFRACTIONx_bond_d0.011
LS refinement shell
*PLUS
Highest resolution: 1.7 Å / Rfactor Rfree: 0.3784 / Rfactor Rwork: 0.3196

+
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