[English] 日本語
Yorodumi
- PDB-7mkc: N74D mutant of the HIV-1 capsid protein in complex with PF-345007... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7mkc
TitleN74D mutant of the HIV-1 capsid protein in complex with PF-3450074 (PF74)
Componentscapsid proteinCapsid
KeywordsVIRAL PROTEIN / HIV-1 capsid protein / hexmer / CA-targeting antiviral
Function / homology
Function and homology information


viral process / viral nucleocapsid / host cell cytoplasm / virion membrane / structural molecule activity / RNA binding / zinc ion binding / cytoplasm
Similarity search - Function
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 knuckle ...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 knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
Chem-1B0 / IODIDE ION / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 Å
AuthorsKirby, K.A. / Sarafianos, S.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI120860 United States
CitationJournal: Viruses / Year: 2022
Title: TRIM5alpha Restriction of HIV-1-N74D Viruses in Lymphocytes Is Caused by a Loss of Cyclophilin A Protection.
Authors: Selyutina, A. / Simons, L.M. / Kirby, K.A. / Bulnes-Ramos, A. / Hu, P. / Sarafianos, S.G. / Hultquist, J.F. / Diaz-Griffero, F.
History
DepositionApr 23, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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: capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8188
Polymers25,6311
Non-polymers1,1877
Water28816
1
A: capsid protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)160,91048
Polymers153,7886
Non-polymers7,12242
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-y+1,x-y-1,z1
crystal symmetry operation3_765-x+y+2,-x+1,z1
crystal symmetry operation4_755-x+2,-y,z1
crystal symmetry operation5_665y+1,-x+y+1,z1
crystal symmetry operation6_545x-y,x-1,z1
Buried area20310 Å2
ΔGint-92 kcal/mol
Surface area63400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.358, 90.358, 55.695
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6

-
Components

#1: Protein capsid protein / Capsid / Gag polyprotein


Mass: 25631.410 Da / Num. of mol.: 1 / Mutation: N74D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: NL4-3 / Gene: gag / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: B6DRA0
#2: Chemical ChemComp-1B0 / N-METHYL-NALPHA-[(2-METHYL-1H-INDOL-3-YL)ACETYL]-N-PHENYL-L-PHENYLALANINAMIDE


Mass: 425.522 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H27N3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.97 % / Mosaicity: 0.42 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, NaI, Sodium Cacodylate, Glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03317 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 2.65→45.38 Å / Num. obs: 7562 / % possible obs: 98.5 % / Redundancy: 5.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.041 / Rrim(I) all: 0.101 / Net I/σ(I): 11.2 / Num. measured all: 41748
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.65-2.785.30.77452699850.6430.3590.858296.8
8.78-45.385.10.04311202200.9990.0190.04731.197.2

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.27 Å45.38 Å
Translation5.27 Å45.38 Å

-
Processing

Software
NameVersionClassificationNB
REFMAC5.8.0158refinement
XDSdata reduction
Aimless0.5.32data scaling
PHASER2.7.17phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XFX

4xfx


Resolution: 2.65→45.38 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.2435 / WRfactor Rwork: 0.177 / FOM work R set: 0.808 / SU B: 27.144 / SU ML: 0.253 / SU R Cruickshank DPI: 3.1466 / SU Rfree: 0.326 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 3.147 / ESU R Free: 0.326 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2421 366 4.8 %RANDOM
Rwork0.1828 ---
obs0.1858 7190 98.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 162.39 Å2 / Biso mean: 66.778 Å2 / Biso min: 32.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å2-0.15 Å20 Å2
2---0.31 Å2-0 Å2
3---0.99 Å2
Refinement stepCycle: final / Resolution: 2.65→45.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1725 0 38 16 1779
Biso mean--59.7 52.22 -
Num. residues----221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191800
X-RAY DIFFRACTIONr_bond_other_d0.0060.021668
X-RAY DIFFRACTIONr_angle_refined_deg1.961.9772447
X-RAY DIFFRACTIONr_angle_other_deg1.1383.0043886
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4885220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.57425.06577
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.2715307
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0931510
X-RAY DIFFRACTIONr_chiral_restr0.1130.2269
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211974
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02336
X-RAY DIFFRACTIONr_sphericity_free55.90551
X-RAY DIFFRACTIONr_sphericity_bonded63.80855
LS refinement shellResolution: 2.65→2.719 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.21 25 -
Rwork0.237 526 -
all-551 -
obs--98.92 %
Refinement TLS params.Method: refined / Origin x: 82.179 Å / Origin y: -26.197 Å / Origin z: -1.051 Å
111213212223313233
T0.0133 Å20.0005 Å2-0.0005 Å2-0.0156 Å20.0144 Å2--0.035 Å2
L0.7574 °2-0.2219 °2-0.2528 °2-0.1425 °2-0.0181 °2--0.2937 °2
S-0.0378 Å °0.0092 Å °-0.0207 Å °-0.0146 Å °0.003 Å °0.0286 Å °0.0558 Å °0.0281 Å °0.0348 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 221
2X-RAY DIFFRACTION1A300 - 306
3X-RAY DIFFRACTION1A401 - 416

+
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