[English] 日本語
Yorodumi
- PDB-8gdv: Structure of M66I mutant of disulfide stabilized HIV-1 CA hexamer... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8gdv
TitleStructure of M66I mutant of disulfide stabilized HIV-1 CA hexamer in complex with CPSF6 peptide and IP6
Components
  • Cleavage and polyadenylation specificity factor subunit 6
  • Gag polyproteinGroup-specific antigen
KeywordsVIRAL PROTEIN / HIV-1 capsid / IP6 / CPSF6
Function / homology
Function and homology information


viral budding via host ESCRT complex / viral nucleocapsid / host cell cytoplasm / virion membrane / structural molecule activity / RNA binding / zinc ion binding / cytoplasm
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) / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retrovirus capsid, C-terminal / Retroviral matrix protein ...Gag protein p6 / Gag protein p6 / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / 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
INOSITOL HEXAKISPHOSPHATE / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsBriganti, L. / Schope, L. / Kvaratskhelia, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI157802 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI162665 United States
CitationJournal: To Be Published
Title: Structure of M66I mutant of disulfide stabilized HIV-1 CA hexamer in complex with CPSF6 peptide and IP6
Authors: Huang, S. / Briganti, L. / Kvaratskhelia, M.
History
DepositionMar 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Gag polyprotein
B: Gag polyprotein
C: Gag polyprotein
D: Gag polyprotein
E: Gag polyprotein
F: Gag polyprotein
M: Cleavage and polyadenylation specificity factor subunit 6
N: Cleavage and polyadenylation specificity factor subunit 6
O: Cleavage and polyadenylation specificity factor subunit 6
P: Cleavage and polyadenylation specificity factor subunit 6
Q: Cleavage and polyadenylation specificity factor subunit 6
R: Cleavage and polyadenylation specificity factor subunit 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,28414
Polymers161,96412
Non-polymers1,3202
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking, Hexamer confirmed by SEC and PAGE
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22790 Å2
ΔGint-183 kcal/mol
Surface area57470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.172, 133.172, 205.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein
Gag polyprotein / Group-specific antigen


Mass: 25443.234 Da / Num. of mol.: 6 / Mutation: A14C, E45C, W184A, M185A, M66I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D2ECD8
#2: Protein/peptide
Cleavage and polyadenylation specificity factor subunit 6 /


Mass: 1550.796 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / Phytic acid


Mass: 660.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H18O24P6
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 60.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.1 M Tris hydrochloride, 11% PEG 8000, 5% Glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.0722 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Jul 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0722 Å / Relative weight: 1
ReflectionResolution: 3.3→47.88 Å / Num. obs: 27382 / % possible obs: 95.37 % / Redundancy: 7.4 % / Biso Wilson estimate: 71.48 Å2 / CC1/2: 0.987 / Rpim(I) all: 0.1312 / Net I/σ(I): 6.56
Reflection shellResolution: 3.3→3.418 Å / Mean I/σ(I) obs: 1.41 / Num. unique obs: 2733 / CC1/2: 0.798 / % possible all: 97.18

-
Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7SNQ
Resolution: 3.3→47.88 Å / SU ML: 0.7 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 38.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3473 1354 4.98 %
Rwork0.3075 --
obs0.3094 27176 95.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→47.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9834 0 72 0 9906
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310290
X-RAY DIFFRACTIONf_angle_d0.54414042
X-RAY DIFFRACTIONf_dihedral_angle_d7.3241412
X-RAY DIFFRACTIONf_chiral_restr0.041593
X-RAY DIFFRACTIONf_plane_restr0.0041821
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.420.48131520.42912565X-RAY DIFFRACTION97
3.42-3.550.35671510.38992559X-RAY DIFFRACTION97
3.55-3.720.5111290.49492443X-RAY DIFFRACTION92
3.72-3.910.47641310.43312534X-RAY DIFFRACTION95
3.91-4.160.31561460.30632610X-RAY DIFFRACTION97
4.16-4.480.30671210.2742579X-RAY DIFFRACTION96
4.48-4.930.27911270.26062613X-RAY DIFFRACTION96
4.93-5.640.29021310.27812590X-RAY DIFFRACTION96
5.64-7.10.36651320.29632635X-RAY DIFFRACTION95
7.1-47.880.281340.21392694X-RAY DIFFRACTION92
Refinement TLS params.Method: refined / Origin x: 20.6463 Å / Origin y: 19.7585 Å / Origin z: 46.6826 Å
111213212223313233
T0.538 Å2-0.2194 Å2-0.0845 Å2-0.5014 Å20.1374 Å2--0.6409 Å2
L0.5775 °2-0.2519 °2-0.005 °2-0.8961 °2-0.3102 °2--2.5284 °2
S0.0987 Å °-0.1687 Å °-0.0792 Å °0.2527 Å °-0.2511 Å °-0.2099 Å °-0.4003 Å °0.0115 Å °0.1137 Å °
Refinement TLS groupSelection details: all

+
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