[English] 日本語
Yorodumi
- PDB-7b5g: Crystal structure of E.coli LexA in complex with nanobody NbSOS3(... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7b5g
TitleCrystal structure of E.coli LexA in complex with nanobody NbSOS3(Nb14527)
Components
  • LexA repressor
  • Nanobody Nb14527, NbSOS3
KeywordsTRANSCRIPTION / Transcriptional repressor DNA binding autoproteolysis Nanobodies
Function / homology
Function and homology information


repressor LexA / SOS response / DNA-binding transcription repressor activity / protein-DNA complex / DNA replication / transcription cis-regulatory region binding / serine-type endopeptidase activity / DNA repair / negative regulation of DNA-templated transcription / DNA-templated transcription ...repressor LexA / SOS response / DNA-binding transcription repressor activity / protein-DNA complex / DNA replication / transcription cis-regulatory region binding / serine-type endopeptidase activity / DNA repair / negative regulation of DNA-templated transcription / DNA-templated transcription / DNA damage response / proteolysis / DNA binding / identical protein binding / cytosol
Similarity search - Function
LexA repressor, DNA-binding domain / Transcription regulator LexA / LexA DNA binding domain / Peptidase S24, LexA-like / : / LexA-like / Peptidase S24/S26A/S26B/S26C / Peptidase S24-like / LexA/Signal peptidase-like superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Biological speciesEscherichia coli K-12 (bacteria)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMaso, L. / Vascon, F. / Chinellato, M. / Pardon, E. / Steyaert, J. / Angelini, A. / Tondi, D. / Cendron, L.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Ministry of Education Italy
CitationJournal: Structure / Year: 2022
Title: Nanobodies targeting LexA autocleavage disclose a novel suppression strategy of SOS-response pathway.
Authors: Maso, L. / Vascon, F. / Chinellato, M. / Goormaghtigh, F. / Bellio, P. / Campagnaro, E. / Van Melderen, L. / Ruzzene, M. / Pardon, E. / Angelini, A. / Celenza, G. / Steyaert, J. / Tondi, D. / Cendron, L.
History
DepositionDec 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 16, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LexA repressor
B: Nanobody Nb14527, NbSOS3
C: LexA repressor
D: Nanobody Nb14527, NbSOS3
E: LexA repressor
F: Nanobody Nb14527, NbSOS3
G: LexA repressor
H: Nanobody Nb14527, NbSOS3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,12514
Polymers146,7538
Non-polymers3726
Water2,126118
1
A: LexA repressor
B: Nanobody Nb14527, NbSOS3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8124
Polymers36,6882
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: LexA repressor
D: Nanobody Nb14527, NbSOS3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9376
Polymers36,6882
Non-polymers2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: LexA repressor
F: Nanobody Nb14527, NbSOS3


Theoretical massNumber of molelcules
Total (without water)36,6882
Polymers36,6882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: LexA repressor
H: Nanobody Nb14527, NbSOS3


Theoretical massNumber of molelcules
Total (without water)36,6882
Polymers36,6882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.067, 57.081, 122.506
Angle α, β, γ (deg.)84.530, 83.210, 68.430
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
LexA repressor


Mass: 22388.713 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: First 70 residues are not visible in the electron density maps.
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: lexA, exrA, spr, tsl, umuA, b4043, JW4003 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A7C2, repressor LexA
#2: Antibody
Nanobody Nb14527, NbSOS3


Mass: 14299.536 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: N-term and fusion tag are not visible in the electron density maps
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 42.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 0.15 M sodium chloride, 0.05 M HEPES, 24 % w/v PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.979499 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979499 Å / Relative weight: 1
ReflectionResolution: 2.4→53.06 Å / Num. obs: 47061 / % possible obs: 98.2 % / Redundancy: 2.4 % / CC1/2: 0.923 / Rmerge(I) obs: 0.084 / Net I/σ(I): 5.9
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 1 / Num. unique obs: 4685

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JHF

1jhf


Resolution: 2.4→49.61 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.252 --RANDOM
Rwork0.206 ---
obs-46989 98.04 %-
Displacement parametersBiso max: 130.69 Å2 / Biso mean: 46.1177 Å2 / Biso min: 14.01 Å2
Refinement stepCycle: LAST / Resolution: 2.4→49.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7789 0 24 118 7931

+
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