[English] 日本語
Yorodumi
- PDB-5w4o: Structure of the R18A mutant of the HIV-1 capsid protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5w4o
TitleStructure of the R18A mutant of the HIV-1 capsid protein
ComponentsCapsid protein p24
KeywordsVIRAL PROTEIN / capsid protein
Function / homology
Function and homology information


viral budding via host ESCRT complex / viral process / ISG15 antiviral mechanism / host multivesicular body / viral nucleocapsid / host cell cytoplasm / host cell nucleus / structural molecule activity / host cell plasma membrane / virion membrane ...viral budding via host ESCRT complex / viral process / ISG15 antiviral mechanism / host multivesicular body / viral nucleocapsid / host cell cytoplasm / host cell nucleus / structural molecule activity / host cell plasma membrane / virion membrane / RNA binding / zinc ion binding / membrane / cytoplasm
Similarity search - Function
Retrovirus capsid C-terminal domain / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Gag protein p6 / Gag protein p6 / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / 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 ...Retrovirus capsid C-terminal domain / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Gag protein p6 / Gag protein p6 / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / 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. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
IODIDE ION / Gag polyprotein / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.093 Å
AuthorsGres, A.T. / Kirby, K.A. / Sarafianos, S.G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103368 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI120860 United States
CitationJournal: MBio / Year: 2019
Title: Novel Intersubunit Interaction Critical for HIV-1 Core Assembly Defines a Potentially Targetable Inhibitor Binding Pocket.
Authors: Craveur, P. / Gres, A.T. / Kirby, K.A. / Liu, D. / Hammond, J.A. / Deng, Y. / Forli, S. / Goodsell, D.S. / Williamson, J.R. / Sarafianos, S.G. / Olson, A.J.
History
DepositionJun 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Capsid protein p24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,93517
Polymers25,5441
Non-polymers1,39016
Water2,018112
1
A: Capsid protein p24
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)161,608102
Polymers153,2666
Non-polymers8,34296
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 area29020 Å2
ΔGint-563 kcal/mol
Surface area61600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.921, 92.921, 58.053
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6

-
Components

#1: Protein Capsid protein p24 /


Mass: 25544.311 Da / Num. of mol.: 1 / Fragment: residues 133-363 / Mutation: R18A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B6DRA0, UniProt: P12493*PLUS
#2: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.57 % / Description: hexagonal plate-like crystals
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG3350, NaI, Sodium cacodylate, Glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033203 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033203 Å / Relative weight: 1
ReflectionResolution: 2.09→47.08 Å / Num. obs: 16952 / % possible obs: 99.8 % / Redundancy: 5.6 % / Biso Wilson estimate: 44.79 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.037 / Rrim(I) all: 0.087 / Net I/σ(I): 12.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
2.09-2.155.40.8420.6330.3910.9397.8
8.88-47.085.20.0460.9960.0230.05199.2

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.44 Å47.08 Å
Translation5.44 Å47.08 Å

-
Processing

Software
NameVersionClassification
Aimless0.5.31data scaling
PHASER2.7.17phasing
PHENIX(1.11.1-2575_1692)refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 4XFX

4xfx


Resolution: 2.093→46.46 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.39
RfactorNum. reflection% reflection
Rfree0.2462 936 5.53 %
Rwork0.2174 --
obs0.219 16932 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 139.22 Å2 / Biso mean: 57.3416 Å2 / Biso min: 28.37 Å2
Refinement stepCycle: final / Resolution: 2.093→46.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1683 0 16 112 1811
Biso mean--67.65 54.58 -
Num. residues----218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021726
X-RAY DIFFRACTIONf_angle_d0.5142350
X-RAY DIFFRACTIONf_chiral_restr0.04266
X-RAY DIFFRACTIONf_plane_restr0.004305
X-RAY DIFFRACTIONf_dihedral_angle_d14.5531055
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0932-2.20360.3451370.332224236198
2.2036-2.34160.37071280.349522842412100
2.3416-2.52240.34331400.278722752415100
2.5224-2.77620.2661080.252522952403100
2.7762-3.17790.26191340.236522752409100
3.1779-4.00350.21271160.195323212437100
4.0035-46.47190.21841730.17923222495100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.44990.1635-0.5050.88-0.36141.35520.6194-0.8351-0.14021.05550.645-0.0492-1.03761.38920.06780.7940.0162-0.12160.8146-0.00490.6708-1.9814-12.38315.8484
20.41850.5830.28220.87850.44270.64270.0230.13710.5007-0.3873-0.0962-0.41150.20330.0506-0.00090.3438-0.01130.02060.30460.03430.57012.7168-17.484-3.7237
31.6173-0.5992-1.28381.4938-0.9342.0038-0.19140.06860.02730.1471-0.0324-0.08650.27680.0718-0.00180.3813-0.0009-00.2578-0.01260.3585-3.544-29.52863.6348
4-0.1106-0.1204-0.10520.0147-0.05360.21320.0356-0.4004-0.00660.5747-0.17750.09970.06670.50800.7524-0.0470.13390.5648-0.01180.3828-7.7445-34.206222.9358
51.63910.2096-0.02963.1052-1.84521.3201-0.1104-0.42030.03620.7215-0.0824-0.3377-0.39080.2207-0.00020.43790.0082-0.05930.40530.02340.3837-0.884-27.445811.1696
60.4060.5162-0.03770.23050.75211.4142-0.04630.56390.0344-0.08110.07170.13430.2033-0.0854-00.43520.07520.0370.40070.07310.346821.1259-27.1041-16.0739
71.65741.1837-0.91051.1531-0.66940.6175-0.5846-0.0924-0.6360.65880.5428-0.23240.2568-0.4043-0.02480.73020.24950.07720.59180.13450.537524.6288-34.9034-6.9958
81.70790.1902-0.59840.77910.27010.2631-0.25760.06150.0838-0.07580.238-0.21240.33540.6473-0.00010.42540.12990.04030.63330.02320.42835.9123-25.7121-14.7345
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 16 )A1 - 16
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 43 )A17 - 43
3X-RAY DIFFRACTION3chain 'A' and (resid 44 through 83 )A44 - 83
4X-RAY DIFFRACTION4chain 'A' and (resid 84 through 104 )A84 - 104
5X-RAY DIFFRACTION5chain 'A' and (resid 105 through 144 )A105 - 144
6X-RAY DIFFRACTION6chain 'A' and (resid 145 through 174 )A145 - 174
7X-RAY DIFFRACTION7chain 'A' and (resid 175 through 192 )A175 - 192
8X-RAY DIFFRACTION8chain 'A' and (resid 193 through 221 )A193 - 221

+
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