[English] 日本語
Yorodumi
- PDB-8u3s: Structure of human TIRR in complex with VHH4 nanobody -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8u3s
TitleStructure of human TIRR in complex with VHH4 nanobody
Components
  • Nanobody
  • Tudor-interacting repair regulator protein
KeywordsRNA BINDING PROTEIN / TIRR / nanobody / RNA / 53BP1 / p53 / NEAT1 / DNA damage response / DNA double-strand break repair / Cell cycle
Function / homology: / U8 snoRNA-decapping enzyme-like / negative regulation of double-strand break repair via nonhomologous end joining / snoRNA binding / NUDIX hydrolase-like domain superfamily / RNA binding / nucleus / Tudor-interacting repair regulator protein
Function and homology information
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsBotuyan, M.V. / Mer, G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM136262 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA132878 United States
CitationJournal: Nat Commun / Year: 2024
Title: NEAT1 modulates the TIRR/53BP1 complex to maintain genome integrity.
Authors: Kilgas, S. / Syed, A. / Toolan-Kerr, P. / Swift, M.L. / Roychoudhury, S. / Sarkar, A. / Wilkins, S. / Quigley, M. / Poetsch, A.R. / Botuyan, M.V. / Cui, G. / Mer, G. / Ule, J. / Drane, P. / Chowdhury, D.
History
DepositionSep 8, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_entry_details / pdbx_modification_feature
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tudor-interacting repair regulator protein
B: Nanobody


Theoretical massNumber of molelcules
Total (without water)36,7752
Polymers36,7752
Non-polymers00
Water1,874104
1
A: Tudor-interacting repair regulator protein

A: Tudor-interacting repair regulator protein

B: Nanobody

B: Nanobody


Theoretical massNumber of molelcules
Total (without water)73,5504
Polymers73,5504
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation4_554y+1/2,-x+1/2,z-1/41
crystal symmetry operation5_555-x+1/2,y+1/2,-z+1/41
Buried area7080 Å2
ΔGint-31 kcal/mol
Surface area26770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.076, 48.076, 238.906
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-321-

HOH

-
Components

#1: Protein Tudor-interacting repair regulator protein / NUDT16-like protein 1 / Protein syndesmos


Mass: 23038.943 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT16L1, SDOS, TIRR / Plasmid: pBB75 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BRJ7
#2: Antibody Nanobody


Mass: 13736.084 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Plasmid: pHISPP / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.88 Å3/Da / Density % sol: 34.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: Crystals were produced by the hanging-drop vapor diffusion method by mixing 2 microliters of the protein (in 10 mM HEPES, 50 mM NaCl, 2 mM TCEP, pH 7.5) and 2 microliters of the reservoir ...Details: Crystals were produced by the hanging-drop vapor diffusion method by mixing 2 microliters of the protein (in 10 mM HEPES, 50 mM NaCl, 2 mM TCEP, pH 7.5) and 2 microliters of the reservoir solution made up of 8% Tacsimate, pH 5, and 20% PEG 3,350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 23137 / % possible obs: 85.4 % / Redundancy: 5.5 % / Biso Wilson estimate: 33.86 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.1288 / Rpim(I) all: 0.05998 / Rrim(I) all: 0.1433 / Net I/σ(I): 7.89
Reflection shellResolution: 1.85→1.916 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.9244 / Mean I/σ(I) obs: 0.82 / Num. unique obs: 2231 / CC1/2: 0.583 / CC star: 0.858 / Rpim(I) all: 0.4911 / Rrim(I) all: 1.056 / % possible all: 73.15

-
Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→50 Å / SU ML: 0.2445 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.7687 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2708 1628 7.58 %
Rwork0.2144 19843 -
obs0.2187 21471 85.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.01 Å2
Refinement stepCycle: LAST / Resolution: 1.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2451 0 0 104 2555
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072519
X-RAY DIFFRACTIONf_angle_d0.9053406
X-RAY DIFFRACTIONf_chiral_restr0.0505368
X-RAY DIFFRACTIONf_plane_restr0.0053441
X-RAY DIFFRACTIONf_dihedral_angle_d5.42061699
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.36931210.30861351X-RAY DIFFRACTION72.76
1.9-1.970.38331250.29461487X-RAY DIFFRACTION79.84
1.97-2.040.28481350.26381676X-RAY DIFFRACTION88.21
2.04-2.120.33661320.24711709X-RAY DIFFRACTION89.89
2.12-2.210.31651480.23191735X-RAY DIFFRACTION91.94
2.21-2.330.31521450.21641789X-RAY DIFFRACTION93.43
2.33-2.480.25821470.21681790X-RAY DIFFRACTION93.53
2.48-2.670.24481480.20691858X-RAY DIFFRACTION95.3
2.67-2.940.31571440.23181777X-RAY DIFFRACTION92.76
2.94-3.360.241400.21821695X-RAY DIFFRACTION85.83
3.36-4.230.25971180.19751442X-RAY DIFFRACTION72.06
4.23-47.150.2451250.19291534X-RAY DIFFRACTION71.17

+
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