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- PDB-6nif: crystal structure of human REV7-RAN complex -

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Basic information

Entry
Database: PDB / ID: 6nif
Titlecrystal structure of human REV7-RAN complex
ComponentshREV7, GTP-binding nuclear protein Ran, hREV3 fusion
KeywordsCELL CYCLE / small GTPase / MAD2L2
Function / homology
Function and homology information


somatic diversification of immunoglobulins involved in immune response / DNA damage response, signal transduction resulting in transcription / 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 / JUN kinase binding / nucleocytoplasmic transport ...somatic diversification of immunoglobulins involved in immune response / DNA damage response, signal transduction resulting in transcription / 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 / JUN kinase binding / nucleocytoplasmic transport / 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 / telomere maintenance in response to DNA damage / 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 / 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 DNA-binding transcription factor activity / negative regulation of protein catabolic process / DNA-templated DNA replication / spindle / protein transport / double-strand break repair / positive regulation of peptidyl-serine phosphorylation / nuclear envelope / chromosome / site of double-strand break / 4 iron, 4 sulfur cluster binding / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / cell division / GTPase activity / nucleotide binding / chromatin / nucleolus / GTP binding / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
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 ...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 / small GTPase Ran family profile. / Ran GTPase / small GTPase Rab1 family profile. / DNA polymerase family B, thumb domain / DNA-directed DNA polymerase, family B, multifunctional 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 polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / small GTPase Ras family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GTP-binding nuclear protein Ran / DNA polymerase zeta catalytic subunit / Mitotic spindle assembly checkpoint protein MAD2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.002 Å
AuthorsWang, X. / Pertz, L. / Hua, D.P. / Zhang, T.Q. / Listovsky, T. / Xie, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31600605 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
DepositionDec 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
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 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hREV7, GTP-binding nuclear protein Ran, hREV3 fusion


Theoretical massNumber of molelcules
Total (without water)28,7281
Polymers28,7281
Non-polymers00
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.571, 64.571, 113.775
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-607-

HOH

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Components

#1: Protein hREV7, GTP-binding nuclear protein Ran, hREV3 fusion / Mitotic spindle assembly checkpoint protein MAD2B / Mitotic arrest deficient 2-like protein 2 / ...Mitotic spindle assembly checkpoint protein MAD2B / Mitotic arrest deficient 2-like protein 2 / MAD2-like protein 2 / REV7 homolog / Protein reversionless 3-like / hREV3


Mass: 28728.141 Da / Num. of mol.: 1 / Mutation: R124A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAD2L2, MAD2B, REV7, RAN, REV3L, POLZ, REV3
Production host: Escherichia coli str. K-12 substr. DH10B (bacteria)
References: UniProt: Q9UI95, UniProt: F5H018, UniProt: O60673, DNA-directed DNA polymerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O

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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: 2.38 Å3/Da / Density % sol: 48.39 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 100 mM HEPES, pH 7.0, 1.1 M sodium malonate, 0.5% Jeffamine ED-2001

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.002→32.285 Å / Num. obs: 18976 / % possible obs: 99.23 % / Redundancy: 19.2 % / Biso Wilson estimate: 34.5 Å2 / Rpim(I) all: 0.02 / Rrim(I) all: 0.086 / Χ2: 1.855 / Net I/σ(I): 41.7
Reflection shellResolution: 2.002→2.03 Å / Redundancy: 18.3 % / Num. unique obs: 934 / CC1/2: 0.984 / Rpim(I) all: 0.076 / Rrim(I) all: 0.325 / Χ2: 0.524 / % possible all: 97.16

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ABD

3abd


Resolution: 2.002→32.285 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.14
RfactorNum. reflection% reflection
Rfree0.2658 974 5.13 %
Rwork0.2264 --
obs0.2285 18968 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.002→32.285 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1702 0 0 147 1849
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071753
X-RAY DIFFRACTIONf_angle_d0.8382386
X-RAY DIFFRACTIONf_dihedral_angle_d13.6341077
X-RAY DIFFRACTIONf_chiral_restr0.053281
X-RAY DIFFRACTIONf_plane_restr0.006304
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.002-2.10750.40691360.28562489X-RAY DIFFRACTION98
2.1075-2.23950.40361300.28292552X-RAY DIFFRACTION100
2.2395-2.41240.33971230.28312570X-RAY DIFFRACTION100
2.4124-2.6550.31831430.27942539X-RAY DIFFRACTION100
2.655-3.0390.3171330.25152589X-RAY DIFFRACTION100
3.039-3.82780.22891480.21992590X-RAY DIFFRACTION99
3.8278-32.28970.2181610.18142665X-RAY DIFFRACTION98

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