[English] 日本語
Yorodumi
- PDB-6usi: Barrier-to-autointegration factor soaked in 1,6-hexanediol: 1 of ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6usi
TitleBarrier-to-autointegration factor soaked in 1,6-hexanediol: 1 of 14 in MSCS set
ComponentsBarrier-to-autointegration factor
KeywordsDNA BINDING PROTEIN / alpha helical / MSCS / minor groove binder
Function / homology
Function and homology information


negative regulation of protein ADP-ribosylation / Nuclear Envelope Breakdown / mitotic nuclear membrane reassembly / Initiation of Nuclear Envelope (NE) Reformation / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / negative regulation of type I interferon production / negative regulation of viral genome replication / negative regulation of cGAS/STING signaling pathway / 2-LTR circle formation ...negative regulation of protein ADP-ribosylation / Nuclear Envelope Breakdown / mitotic nuclear membrane reassembly / Initiation of Nuclear Envelope (NE) Reformation / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / negative regulation of type I interferon production / negative regulation of viral genome replication / negative regulation of cGAS/STING signaling pathway / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / chromosome organization / condensed chromosome / negative regulation of innate immune response / DNA integration / response to virus / nuclear envelope / chromatin organization / response to oxidative stress / double-stranded DNA binding / chromatin / protein homodimerization activity / DNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Barrier- to-autointegration factor, BAF / Barrier-to-autointegration factor, BAF superfamily / : / Barrier to autointegration factor / Barrier to autointegration factor
Similarity search - Domain/homology
ETHANOL / Barrier-to-autointegration factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.653 Å
AuthorsAgarwal, S. / Smith, M. / De La Rosa, I. / Kliment, A.V. / Swartz, P. / Segura-Totten, M. / Mattos, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: Development of a structure-analysis pipeline using multiple-solvent crystal structures of barrier-to-autointegration factor.
Authors: Agarwal, S. / Smith, M. / De La Rosa, I. / Verba, K.A. / Swartz, P. / Segura-Totten, M. / Mattos, C.
History
DepositionOct 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 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: Barrier-to-autointegration factor
B: Barrier-to-autointegration factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2394
Polymers20,1472
Non-polymers922
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-4 kcal/mol
Surface area8520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.650, 41.650, 214.160
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Barrier-to-autointegration factor / Breakpoint cluster region protein 1


Mass: 10073.588 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BANF1, BAF, BCRG1 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O75531
#2: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.3 Å3/Da / Density % sol: 46.64 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 80 mM Tris pH 8.5, 16% Ethanol, 10% PEG-1450

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→40.884 Å / Num. obs: 23782 / % possible obs: 99.91 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.79
Reflection shellResolution: 1.65→1.71 Å / Rmerge(I) obs: 0.79 / Num. unique obs: 2285

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6URE

6ure


Resolution: 1.653→40.884 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.49
RfactorNum. reflection% reflection
Rfree0.2079 2000 8.41 %
Rwork0.1708 --
obs0.174 23770 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 152.63 Å2 / Biso mean: 36.7373 Å2 / Biso min: 15.76 Å2
Refinement stepCycle: final / Resolution: 1.653→40.884 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1402 0 18 142 1562
Biso mean--60.38 38.58 -
Num. residues----177
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.6531-1.69440.33811380.26391499
1.6944-1.74030.29971410.23771531
1.7403-1.79150.23831380.22091506
1.7915-1.84930.27871390.21081511
1.8493-1.91540.23691400.20341523
1.9154-1.99210.22671400.19381526
1.9921-2.08270.2571420.19441545
2.0827-2.19250.22781400.18621528
2.1925-2.32990.19861420.17061546
2.3299-2.50980.19631410.17341537
2.5098-2.76230.23571450.17781574
2.7623-3.16190.20661450.17051579
3.1619-3.98310.20361480.15521613
3.9831-40.8840.16491610.14611752
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)
10.2159-0.10220.10670.0362-0.04160.0926-0.28530.1003-0.0578-0.50050.08290.2272-0.0992-0.048-0.00040.3197-0.1447-0.02780.24850.00350.25216.0918-0.0333-1.5552
20.01940.0068-0.01130.00690.00680.014-0.0809-0.189-0.10620.112-0.09310.1596-0.0896-0.037500.3121-0.16570.06970.3867-0.07540.26766.1354-8.18719.9948
30.06870.02850.03140.05140.08810.2082-0.01310.05640.07690.00080.08130.06710.4361-0.21280.00410.2689-0.07890.02440.1965-0.03670.207219.2298-8.826310.35
40.04210.05060.02950.0335-0.02360.05770.0120.0389-0.0336-0.07440.0370.01870.01280.09770.02050.2462-0.1380.02460.2453-0.0330.205222.4371-5.03691.4483
50.19930.13370.15820.82780.31460.5113-0.24120.0376-0.0345-0.270.255-0.3937-0.21610.26890.0470.0957-0.0471-0.00960.2967-0.04130.246634.78976.036820.0194
60.0280.0340.06450.09630.07980.09970.0039-0.1006-0.01520.0814-0.0140.02670.2175-0.03160.00010.1776-0.01770.02260.2104-0.03720.206224.61470.420417.7418
70.04030.0320.02830.024-0.01920.056-0.1065-0.3779-0.12550.26460.00330.1339-0.1471-0.056-00.2227-0.01180.02220.2993-0.02990.21324.21433.097328.7166
80.04440.0403-0.01930.0573-0.08350.08-0.1154-0.10530.0421-0.02520.20.0012-0.1150.00190.00130.2292-0.07040.00750.2784-0.03440.212825.819510.871618.9308
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 27 )A1 - 27
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 37 )A28 - 37
3X-RAY DIFFRACTION3chain 'A' and (resid 38 through 70 )A38 - 70
4X-RAY DIFFRACTION4chain 'A' and (resid 71 through 89 )A71 - 89
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 37 )B2 - 37
6X-RAY DIFFRACTION6chain 'B' and (resid 38 through 55 )B38 - 55
7X-RAY DIFFRACTION7chain 'B' and (resid 56 through 70 )B56 - 70
8X-RAY DIFFRACTION8chain 'B' and (resid 71 through 89 )B71 - 89

+
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