[English] 日本語
Yorodumi
- PDB-6kea: crystal structure of MBP-tagged REV7-IpaB complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6kea
Titlecrystal structure of MBP-tagged REV7-IpaB complex
ComponentsMaltose-binding periplasmic protein,LINKER,hREV7,LINKER,Invasin IpaB,hREV3
KeywordsCELL CYCLE / REV7 / MAD2B / MAD2L2 / Shigella Invasin IpaB
Function / homology
Function and homology information


somatic diversification of immunoglobulins involved in immune response / DNA damage response, signal transduction resulting in transcription / telomere maintenance in response to DNA damage / negative regulation of transcription regulatory region DNA binding / zeta DNA polymerase complex / positive regulation of isotype switching / positive regulation of extracellular matrix assembly / negative regulation of transcription by competitive promoter binding / negative regulation of cell-cell adhesion mediated by cadherin / negative regulation of epithelial to mesenchymal transition ...somatic diversification of immunoglobulins involved in immune response / DNA damage response, signal transduction resulting in transcription / telomere maintenance in response to DNA damage / negative regulation of transcription regulatory region DNA binding / zeta DNA polymerase complex / positive regulation of isotype switching / positive regulation of extracellular matrix assembly / negative regulation of transcription by competitive promoter binding / negative regulation of cell-cell adhesion mediated by cadherin / negative regulation of epithelial to mesenchymal transition / JUN kinase binding / negative regulation of ubiquitin protein ligase activity / detection of maltose stimulus / maltose transport complex / mitotic spindle assembly checkpoint signaling / positive regulation of double-strand break repair via nonhomologous end joining / maltose binding / maltose transport / maltodextrin transmembrane transport / carbohydrate transport / carbohydrate transmembrane transporter activity / host cell membrane / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / negative regulation of double-strand break repair via homologous recombination / error-prone translesion synthesis / positive regulation of epithelial to mesenchymal transition / Translesion synthesis by REV1 / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / Translesion synthesis by POLK / Translesion synthesis by POLI / actin filament organization / regulation of cell growth / double-strand break repair via homologous recombination / negative regulation of canonical Wnt signaling pathway / negative regulation of protein catabolic process / negative regulation of DNA-binding transcription factor activity / DNA-templated DNA replication / spindle / double-strand break repair / positive regulation of peptidyl-serine phosphorylation / site of double-strand break / chromosome / 4 iron, 4 sulfur cluster binding / outer membrane-bounded periplasmic space / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-directed DNA polymerase / periplasmic space / DNA-directed DNA polymerase activity / cell division / nucleotide binding / DNA damage response / host cell nucleus / chromatin / nucleolus / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / DNA binding / extracellular region / nucleoplasm / membrane / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Type III secretion system, invasin protein B / Invasin IpaB, N-terminal / Type III cell invasion protein SipB / Secretion system effector C, SseC-like / Secretion system effector C (SseC) like family / Domain of unknown function DUF4683 / Domain of unknown function (DUF4683) / DNA polymerase zeta catalytic subunit / C4-type zinc-finger of DNA polymerase delta / C4-type zinc-finger of DNA polymerase delta ...Type III secretion system, invasin protein B / Invasin IpaB, N-terminal / Type III cell invasion protein SipB / Secretion system effector C, SseC-like / Secretion system effector C (SseC) like family / Domain of unknown function DUF4683 / Domain of unknown function (DUF4683) / DNA polymerase zeta catalytic subunit / C4-type zinc-finger of DNA polymerase delta / C4-type zinc-finger of DNA polymerase delta / Mad2-like / HORMA domain / HORMA domain / HORMA domain profile. / HORMA domain superfamily / DNA polymerase family B, thumb domain / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
DNA polymerase zeta catalytic subunit / Maltose/maltodextrin-binding periplasmic protein / Type 3 secretion system translocon protein SctE / Mitotic spindle assembly checkpoint protein MAD2B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
Homo sapiens (human)
Shigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsWang, X. / Pernicone, N. / Pertz, L. / Hua, D.P. / Zhang, T.Q. / Listovsky, T. / Xie, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31600605 China
CitationJournal: J.Biol.Chem. / Year: 2019
Title: REV7 has a dynamic adaptor region to accommodate small GTPase RAN/ShigellaIpaB ligands, and its activity is regulated by the RanGTP/GDP switch.
Authors: Wang, X. / Pernicone, N. / Pertz, L. / Hua, D. / Zhang, T. / Listovsky, T. / Xie, W.
History
DepositionJul 4, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Nov 22, 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: Maltose-binding periplasmic protein,LINKER,hREV7,LINKER,Invasin IpaB,hREV3
B: Maltose-binding periplasmic protein,LINKER,hREV7,LINKER,Invasin IpaB,hREV3
C: Maltose-binding periplasmic protein,LINKER,hREV7,LINKER,Invasin IpaB,hREV3
D: Maltose-binding periplasmic protein,LINKER,hREV7,LINKER,Invasin IpaB,hREV3


Theoretical massNumber of molelcules
Total (without water)275,8544
Polymers275,8544
Non-polymers00
Water5,963331
1
A: Maltose-binding periplasmic protein,LINKER,hREV7,LINKER,Invasin IpaB,hREV3


Theoretical massNumber of molelcules
Total (without water)68,9641
Polymers68,9641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Maltose-binding periplasmic protein,LINKER,hREV7,LINKER,Invasin IpaB,hREV3


Theoretical massNumber of molelcules
Total (without water)68,9641
Polymers68,9641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Maltose-binding periplasmic protein,LINKER,hREV7,LINKER,Invasin IpaB,hREV3


Theoretical massNumber of molelcules
Total (without water)68,9641
Polymers68,9641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Maltose-binding periplasmic protein,LINKER,hREV7,LINKER,Invasin IpaB,hREV3


Theoretical massNumber of molelcules
Total (without water)68,9641
Polymers68,9641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.829, 146.707, 102.468
Angle α, β, γ (deg.)90.00, 116.58, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein
Maltose-binding periplasmic protein,LINKER,hREV7,LINKER,Invasin IpaB,hREV3 / MBP


Mass: 68963.570 Da / Num. of mol.: 4 / Mutation: D83A/K84A/E173A/N174A/K240A/R485A
Source method: isolated from a genetically manipulated source
Details: MBP-tagged human REV7 and Shigella Invasin IpaB fusion protein
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) synthetic construct (others), (gene. exp.) Homo sapiens (human), (gene. exp.) Shigella flexneri (bacteria)
Strain: K12 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P0AEX9, UniProt: Q9UI95, UniProt: P18011, UniProt: O60673
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 331 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsresidues 360-373 and 573-596 are LINKER

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 100 mM Bistris, pH 5.6, 25% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.35→29.91 Å / Num. obs: 98435 / % possible obs: 97.5 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.1366 / Net I/σ(I): 14.22
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.8728 / % possible all: 97.8

-
Processing

Software
NameVersionClassification
PHENIX1.14-3260refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VD8, 3ABD

3vd8

3abd


Resolution: 2.35→29.91 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2263 4849 -
Rwork0.1919 --
obs-98287 99.85 %
Refinement stepCycle: LAST / Resolution: 2.35→29.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18061 0 0 335 18396
LS refinement shellResolution: 2.35→2.434 Å
RfactorNum. reflection% reflection
Rfree0.2905 449 -
Rwork0.2721 --
obs-9819 97.83 %

+
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