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- PDB-6kea: crystal structure of MBP-tagged REV7-IpaB complex -

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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 / zeta DNA polymerase complex / positive regulation of isotype switching / negative regulation of transcription by competitive promoter binding / negative regulation of cell-cell adhesion mediated by cadherin / JUN kinase binding / negative regulation of epithelial to mesenchymal transition / negative regulation of ubiquitin protein ligase activity / positive regulation of double-strand break repair via nonhomologous end joining ...somatic diversification of immunoglobulins involved in immune response / DNA damage response, signal transduction resulting in transcription / zeta DNA polymerase complex / positive regulation of isotype switching / negative regulation of transcription by competitive promoter binding / negative regulation of cell-cell adhesion mediated by cadherin / JUN kinase binding / negative regulation of epithelial to mesenchymal transition / negative regulation of ubiquitin protein ligase activity / positive regulation of double-strand break repair via nonhomologous end joining / mitotic spindle assembly checkpoint signaling / detection of maltose stimulus / maltose transport complex / carbohydrate transport / telomere maintenance in response to DNA damage / host cell membrane / carbohydrate transmembrane transporter activity / positive regulation of peptidyl-serine phosphorylation / maltose binding / maltose transport / maltodextrin transmembrane transport / error-prone translesion synthesis / negative regulation of double-strand break repair via homologous recombination / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / actin filament organization / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / cell chemotaxis / regulation of cell growth / negative regulation of canonical Wnt signaling pathway / double-strand break repair via homologous recombination / negative regulation of protein catabolic process / DNA-templated DNA replication / spindle / transcription corepressor activity / double-strand break repair / host cell / site of double-strand break / chromosome / outer membrane-bounded periplasmic space / 4 iron, 4 sulfur cluster binding / DNA-directed DNA polymerase / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-directed DNA polymerase activity / periplasmic space / cell division / nucleotide binding / DNA damage response / chromatin / positive regulation of DNA-templated transcription / nucleolus / host cell nucleus / negative regulation of transcription by RNA polymerase II / DNA binding / extracellular region / zinc ion binding / nucleoplasm / nucleus / membrane / 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 / : / DNA polymerase zeta catalytic subunit, N-terminal ...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 / : / DNA polymerase zeta catalytic subunit, N-terminal / Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A / HORMA domain / C4-type zinc-finger of DNA polymerase delta / : / C4-type zinc-finger of DNA polymerase delta / DNA polymerase delta catalytic subunit-like, N-terminal domain / Mad2-like / HORMA domain / HORMA domain / HORMA domain profile. / HORMA domain superfamily / DNA polymerase family B, thumb domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B signature. / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease 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 / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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


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

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Experimental details

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Experiment

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

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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

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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

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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 %

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