[English] 日本語
Yorodumi
- PDB-7t13: Hexameric HIV-1 (M-group) CA Q50Y mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7t13
TitleHexameric HIV-1 (M-group) CA Q50Y mutant
ComponentsCapsid protein p24
KeywordsVIRAL PROTEIN / Capsid
Function / homology
Function and homology information


viral process / viral nucleocapsid / host cell cytoplasm / host cell nucleus / structural molecule activity / virion membrane / RNA binding / zinc ion binding / ATP 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
Biological speciesHIV-1 group M (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.15 Å
AuthorsJacques, D.A. / James, L.C.
Funding support Australia, United Kingdom, European Union, 6items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP180101384 Australia
National Health and Medical Research Council (NHMRC, Australia)GNT1158338 Australia
Wellcome Trust214344/Z/18/Z United Kingdom
Wellcome Trust108183 United Kingdom
Wellcome Trust220863 United Kingdom
European Research Council (ERC)339223European Union
CitationJournal: Nat Microbiol / Year: 2022
Title: Evasion of cGAS and TRIM5 defines pandemic HIV.
Authors: Zuliani-Alvarez, L. / Govasli, M.L. / Rasaiyaah, J. / Monit, C. / Perry, S.O. / Sumner, R.P. / McAlpine-Scott, S. / Dickson, C. / Rifat Faysal, K.M. / Hilditch, L. / Miles, R.J. / Bibollet- ...Authors: Zuliani-Alvarez, L. / Govasli, M.L. / Rasaiyaah, J. / Monit, C. / Perry, S.O. / Sumner, R.P. / McAlpine-Scott, S. / Dickson, C. / Rifat Faysal, K.M. / Hilditch, L. / Miles, R.J. / Bibollet-Ruche, F. / Hahn, B.H. / Boecking, T. / Pinotsis, N. / James, L.C. / Jacques, D.A. / Towers, G.J.
History
DepositionDec 1, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2022Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 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 p24
B: Capsid protein p24
C: Capsid protein p24
D: Capsid protein p24
E: Capsid protein p24
F: Capsid protein p24


Theoretical massNumber of molelcules
Total (without water)152,9786
Polymers152,9786
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14650 Å2
ΔGint-92 kcal/mol
Surface area59700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.289, 156.609, 118.890
Angle α, β, γ (deg.)90.000, 107.330, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 25 or resid 27...
21(chain B and (resid 1 through 25 or resid 27...
31(chain C and (resid 1 through 25 or resid 27...
41(chain D and (resid 1 through 25 or resid 27...
51(chain E and (resid 1 through 25 or resid 27...
61(chain F and (resid 1 through 25 or resid 27...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 1 through 25 or resid 27...A1 - 25
121(chain A and (resid 1 through 25 or resid 27...A27 - 35
131(chain A and (resid 1 through 25 or resid 27...A37
141(chain A and (resid 1 through 25 or resid 27...A39 - 82
151(chain A and (resid 1 through 25 or resid 27...A0
161(chain A and (resid 1 through 25 or resid 27...A86
171(chain A and (resid 1 through 25 or resid 27...A1 - 219
181(chain A and (resid 1 through 25 or resid 27...A1 - 219
211(chain B and (resid 1 through 25 or resid 27...B1 - 25
221(chain B and (resid 1 through 25 or resid 27...B27 - 35
231(chain B and (resid 1 through 25 or resid 27...B37
241(chain B and (resid 1 through 25 or resid 27...B39 - 82
251(chain B and (resid 1 through 25 or resid 27...B84 - 86
261(chain B and (resid 1 through 25 or resid 27...B96 - 149
271(chain B and (resid 1 through 25 or resid 27...B151 - 156
281(chain B and (resid 1 through 25 or resid 27...B158 - 179
291(chain B and (resid 1 through 25 or resid 27...B180
2101(chain B and (resid 1 through 25 or resid 27...B1 - 219
2111(chain B and (resid 1 through 25 or resid 27...B1 - 219
2121(chain B and (resid 1 through 25 or resid 27...B1 - 219
2131(chain B and (resid 1 through 25 or resid 27...B1 - 219
311(chain C and (resid 1 through 25 or resid 27...C1 - 25
321(chain C and (resid 1 through 25 or resid 27...C27 - 35
331(chain C and (resid 1 through 25 or resid 27...C37
341(chain C and (resid 1 through 25 or resid 27...C3
351(chain C and (resid 1 through 25 or resid 27...C151 - 1567
361(chain C and (resid 1 through 25 or resid 27...C1 - 219
371(chain C and (resid 1 through 25 or resid 27...C1 - 219
381(chain C and (resid 1 through 25 or resid 27...C1 - 219
391(chain C and (resid 1 through 25 or resid 27...C1 - 219
411(chain D and (resid 1 through 25 or resid 27...D1 - 25
421(chain D and (resid 1 through 25 or resid 27...D27 - 35
431(chain D and (resid 1 through 25 or resid 27...D37
441(chain D and (resid 1 through 25 or resid 27...D0
451(chain D and (resid 1 through 25 or resid 27...D1
461(chain D and (resid 1 through 25 or resid 27...D151 - 156
471(chain D and (resid 1 through 25 or resid 27...D1 - 219
481(chain D and (resid 1 through 25 or resid 27...D183 - 185
491(chain D and (resid 1 through 25 or resid 27...D1 - 219
4101(chain D and (resid 1 through 25 or resid 27...D1 - 219
4111(chain D and (resid 1 through 25 or resid 27...D1 - 219
4121(chain D and (resid 1 through 25 or resid 27...D1 - 219
4131(chain D and (resid 1 through 25 or resid 27...D1 - 219
511(chain E and (resid 1 through 25 or resid 27...E1 - 25
521(chain E and (resid 1 through 25 or resid 27...E27 - 35
531(chain E and (resid 1 through 25 or resid 27...E37
541(chain E and (resid 1 through 25 or resid 27...E39 - 82
551(chain E and (resid 1 through 25 or resid 27...E96 - 149
561(chain E and (resid 1 through 25 or resid 27...E1 - 219
571(chain E and (resid 1 through 25 or resid 27...E51 - 15679
581(chain E and (resid 1 through 25 or resid 27...E1 - 219
591(chain E and (resid 1 through 25 or resid 27...E180
5101(chain E and (resid 1 through 25 or resid 27...E1 - 219
5111(chain E and (resid 1 through 25 or resid 27...E1 - 219
5121(chain E and (resid 1 through 25 or resid 27...E1 - 219
5131(chain E and (resid 1 through 25 or resid 27...E1 - 219
611(chain F and (resid 1 through 25 or resid 27...F1 - 25
621(chain F and (resid 1 through 25 or resid 27...F27 - 35
631(chain F and (resid 1 through 25 or resid 27...F37
641(chain F and (resid 1 through 25 or resid 27...F39 - 82
651(chain F and (resid 1 through 25 or resid 27...F0
661(chain F and (resid 1 through 25 or resid 27...F86
671(chain F and (resid 1 through 25 or resid 27...F1 - 219
681(chain F and (resid 1 through 25 or resid 27...F1 - 219

-
Components

#1: Protein
Capsid protein p24


Mass: 25496.318 Da / Num. of mol.: 6 / Mutation: A14C, E45C, Q50Y, W184A, M185A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HIV-1 group M (virus) / Gene: gag / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: B6DRA0

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.1 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Crystallant: 19% (v/v) PEG 550MME, 100 mM TRIS (pH 8.0), 150 mM KSCN, 10 mM ATP, 3% (v/v) 3,5-hexanediol. Crystals grew in 2 ul protein (13 mg/ml) + 2 ul crystallant. Cryoprotected in 20% (v/v) MPD

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 3.15→78.3 Å / Num. obs: 25912 / % possible obs: 95.4 % / Redundancy: 2.5 % / CC1/2: 0.943 / Rmerge(I) obs: 0.198 / Rpim(I) all: 0.146 / Rrim(I) all: 0.247 / Net I/σ(I): 3.6 / Num. measured all: 65258 / Scaling rejects: 56
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
3.15-3.372.40.5391092746360.630.4140.6821.994.2
8.91-78.32.50.089290011440.9610.0660.1115.993.8

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.27 Å78.3 Å
Translation6.27 Å78.3 Å

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.5.27data scaling
PHASER2.6.1phasing
PHENIX1.14refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H47

3h47


Resolution: 3.15→78.3 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.239 1230 4.75 %
Rwork0.2046 24664 -
obs0.2062 25894 94.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 214.2 Å2 / Biso mean: 37.8194 Å2 / Biso min: 7.73 Å2
Refinement stepCycle: final / Resolution: 3.15→78.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9873 0 0 0 9873
Num. residues----1281
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3474X-RAY DIFFRACTION3.238TORSIONAL
12B3474X-RAY DIFFRACTION3.238TORSIONAL
13C3474X-RAY DIFFRACTION3.238TORSIONAL
14D3474X-RAY DIFFRACTION3.238TORSIONAL
15E3474X-RAY DIFFRACTION3.238TORSIONAL
16F3474X-RAY DIFFRACTION3.238TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.15-3.27620.31991430.2667268593
3.2762-3.42530.2751240.2448271295
3.4253-3.60580.27391370.2197280296
3.6058-3.83180.23581330.2163276096
3.8318-4.12760.22891560.194274595
4.1276-4.54290.20821390.1807271994
4.5429-5.20020.20791260.1721277696
5.2002-6.55120.26121360.2156274094
6.5512-78.30.21311360.1886272593

+
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://pdbjlvh1.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