[English] 日本語
Yorodumi
- PDB-1jq7: HCMV protease dimer-interface mutant, S225Y complexed to Inhibito... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1jq7
TitleHCMV protease dimer-interface mutant, S225Y complexed to Inhibitor BILC 408
ComponentsASSEMBLIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Herpesvirus / cytomegalovirus / serine protease / dimerization / enzyme activity regulation / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


assemblin / viral release from host cell / host cell cytoplasm / serine-type endopeptidase activity / host cell nucleus / proteolysis / identical protein binding
Similarity search - Function
Serine Protease, Human Cytomegalovirus Protease; Chain A / Herpesvirus/Caudovirus protease domain / Peptidase S21 / Herpesvirus protease superfamily / Assemblin (Peptidase family S21) / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
N-(6-aminohexanoyl)-3-methyl-L-valyl-3-methyl-L-valyl-N~4~,N~4~-dimethyl-N~1~-[(1R)-1-methyl-2,3-dioxo-3-{[(1S)-1- phenylpropyl]amino}propyl]-L-aspartamide / Chem-0FP / Capsid scaffolding protein
Similarity search - Component
Biological speciesHuman herpesvirus 5
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBatra, R. / Khayat, R. / Tong, L.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Molecular mechanism for dimerization to regulate the catalytic activity of human cytomegalovirus protease.
Authors: Batra, R. / Khayat, R. / Tong, L.
History
DepositionAug 3, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2001Provider: 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
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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
Revision 1.6Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ASSEMBLIN
B: ASSEMBLIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8494
Polymers56,4132
Non-polymers1,4362
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-18 kcal/mol
Surface area17890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.250, 74.250, 215.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein ASSEMBLIN / / PROTEASE


Mass: 28206.641 Da / Num. of mol.: 2 / Mutation: A143Q, S225Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 5 / Production host: Escherichia coli (E. coli) / References: UniProt: P16753, assemblin
#2: Chemical ChemComp-0FP / N-(6-aminohexanoyl)-3-methyl-L-valyl-3-methyl-L-valyl-N~1~-[(2S,3S)-3-hydroxy-4-oxo-4-{[(1R)-1-phenylpropyl]amino}butan-2-yl]-N~4~,N~4~-dimethyl-L-aspartamide / BILC 408


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 717.939 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C37H63N7O7 / Details: This peptide was chemically synthesized.
References: N-(6-aminohexanoyl)-3-methyl-L-valyl-3-methyl-L-valyl-N~4~,N~4~-dimethyl-N~1~-[(1R)-1-methyl-2,3-dioxo-3-{[(1S)-1- phenylpropyl]amino}propyl]-L-aspartamide
Nonpolymer detailsTHE INHIBITOR 0FP IS COVALENTLY CONNECTED AT CARBON C4 TO THE ACTIVE SITE SERINES (A 1132 AND B ...THE INHIBITOR 0FP IS COVALENTLY CONNECTED AT CARBON C4 TO THE ACTIVE SITE SERINES (A 1132 AND B 1432) VIA HEMIKETAL LINKAGES

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, HEPES, sodium chloride, glycerol, spermine tetrahydrochloride, DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
Temperature: 21 ℃ / Details: Tong, L., (1998) Nature Struct. Biol., 5, 819.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
17 mg/mlprotein1drop
218 %PEG40001reservoir
30.1 MHEPES1reservoirpH7.5
40.2 M1reservoirNaCl
510 %glycerol1reservoir
650 mMspermine1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 2, 2001
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3→19.9 Å / Num. all: 48246 / Num. obs: 10900 / % possible obs: 85.5 % / Observed criterion σ(F): 7 / Observed criterion σ(I): 5
Reflection shellResolution: 3→3.19 Å / % possible all: 97
Reflection
*PLUS
Num. measured all: 48246 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
Rmerge(I) obs: 0.129

-
Processing

Software
NameVersionClassification
COMOphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WPO (dimer)

2wpo


Resolution: 3→19.99 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 2061042.99 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 7 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.339 809 7.4 %RANDOM
Rwork0.26 ---
all0.28 48246 --
obs-10900 85.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.250918 e/Å3
Displacement parametersBiso mean: 28 Å2
Baniso -1Baniso -2Baniso -3
1-10.71 Å20 Å20 Å2
2--10.71 Å20 Å2
3----21.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.58 Å0.41 Å
Luzzati d res low-7 Å
Luzzati sigma a-0.11 Å
Refinement stepCycle: LAST / Resolution: 3→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3309 0 86 0 3395
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_mcbond_it0.921.5
X-RAY DIFFRACTIONc_mcangle_it1.562
X-RAY DIFFRACTIONc_scbond_it1.152
X-RAY DIFFRACTIONc_scangle_it1.732.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.36 96 7.5 %
Rwork0.281 1185 -
obs-1200 62.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2C408.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 7 / % reflection Rfree: 7.4 % / Rfactor obs: 0.26 / Rfactor Rwork: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.89
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.36 / % reflection Rfree: 7.5 % / Rfactor Rwork: 0.281

+
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