[English] 日本語
Yorodumi
- PDB-8quw: Hexameric HIV-1 CA in complex with DDD01044153 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8quw
TitleHexameric HIV-1 CA in complex with DDD01044153
ComponentsSpacer peptide 1
KeywordsVIRAL PROTEIN / Capsid
Function / homology
Function and homology information


viral budding via host ESCRT complex / ISG15 antiviral mechanism / host multivesicular body / viral nucleocapsid / viral translational frameshifting / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding ...viral budding via host ESCRT complex / ISG15 antiviral mechanism / host multivesicular body / viral nucleocapsid / viral translational frameshifting / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding / zinc ion binding / membrane
Similarity search - Function
Gag protein p6 / Gag protein p6 / : / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal ...Gag protein p6 / Gag protein p6 / : / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsPetit, A.P. / Fyfe, P.K.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Chemmedchem / Year: 2024
Title: Application of an NMR/Crystallography Fragment Screening Platform for the Assessment and Rapid Discovery of New HIV-CA Binding Fragments.
Authors: Lang, S. / Fletcher, D.A. / Petit, A.P. / Luise, N. / Fyfe, P. / Zuccotto, F. / Porter, D. / Hope, A. / Bellany, F. / Kerr, C. / Mackenzie, C.J. / Wyatt, P.G. / Gray, D.W.
#1: Journal: Biorxiv / Year: 2023
Title: Application of an NMR/crystallography fragment screening platform for the assessment and rapid discovery of new HIV-CA binding fragments
Authors: Lang, S. / Fletcher, D.A. / Petit, A.P. / Luise, N. / Fyfe, P.K. / Zuccotto, F. / Porter, D. / Hope, D. / Bellany, F. / Kerr, C. / MacKenzie, C.J. / Wyatt, P. / Gray, D.W.
History
DepositionOct 17, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2024Group: Database references / Category: citation / citation_author
Revision 1.2Jul 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Spacer peptide 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7633
Polymers25,4611
Non-polymers3012
Water3,765209
1
A: Spacer peptide 1
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)154,57618
Polymers152,7686
Non-polymers1,80812
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
Buried area16600 Å2
ΔGint-84 kcal/mol
Surface area59620 Å2
Unit cell
Length a, b, c (Å)90.472, 90.472, 56.688
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

-
Components

#1: Protein Spacer peptide 1 / SP1 / p2


Mass: 25461.271 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P12493
#2: Chemical ChemComp-WZR / (4~{R})-7-oxidanyl-4-phenyl-3,4-dihydro-1~{H}-quinolin-2-one


Mass: 239.269 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H13NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.24 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris buffer, pH 8.0 to 9.0, 10-15% PEG550MME, 0.15M KSCN

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.02→28.34 Å / Num. obs: 17180 / % possible obs: 98.5 % / Redundancy: 5.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.12 / Net I/σ(I): 11
Reflection shellResolution: 2.02→2.13 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3 / Num. unique obs: 2246 / CC1/2: 0.79 / % possible all: 89.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→28.34 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.916 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23048 870 5.1 %RANDOM
Rwork0.18926 ---
obs0.19133 16288 98.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.968 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20.16 Å20 Å2
2--0.31 Å20 Å2
3----1.02 Å2
Refinement stepCycle: 1 / Resolution: 2.02→28.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1664 0 22 209 1895
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191737
X-RAY DIFFRACTIONr_bond_other_d00.021601
X-RAY DIFFRACTIONr_angle_refined_deg1.771.9752366
X-RAY DIFFRACTIONr_angle_other_deg3.6923.0013725
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7735222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.46924.85770
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.77315287
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8481510
X-RAY DIFFRACTIONr_chiral_restr0.1140.2267
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211923
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02321
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4732.522879
X-RAY DIFFRACTIONr_mcbond_other2.4652.52878
X-RAY DIFFRACTIONr_mcangle_it3.6053.771098
X-RAY DIFFRACTIONr_mcangle_other3.6033.7731099
X-RAY DIFFRACTIONr_scbond_it2.82.693858
X-RAY DIFFRACTIONr_scbond_other2.82.693858
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2853.9481267
X-RAY DIFFRACTIONr_long_range_B_refined6.20130.9022122
X-RAY DIFFRACTIONr_long_range_B_other6.20130.9082123
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.024→2.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 62 -
Rwork0.302 977 -
obs--82.85 %

+
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