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- PDB-4xib: Crystal structure of the MZM-REP domains of Mind bomb 1 in comple... -

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Basic information

Entry
Database: PDB / ID: 4xib
TitleCrystal structure of the MZM-REP domains of Mind bomb 1 in complex with fly Delta N-box peptide
Components
  • Delta N-box peptide
  • E3 ubiquitin-protein ligase MIB1
KeywordsLIGASE / E3 ligase / Notch signaling
Function / homology
Function and homology information


compound eye photoreceptor development / R7 cell differentiation / R3/R4 cell differentiation / apposition of dorsal and ventral imaginal disc-derived wing surfaces / oocyte localization involved in germarium-derived egg chamber formation / compound eye retinal cell programmed cell death / regulation of establishment of planar polarity / lateral inhibition / second mitotic wave involved in compound eye morphogenesis / imaginal disc-derived wing margin morphogenesis ...compound eye photoreceptor development / R7 cell differentiation / R3/R4 cell differentiation / apposition of dorsal and ventral imaginal disc-derived wing surfaces / oocyte localization involved in germarium-derived egg chamber formation / compound eye retinal cell programmed cell death / regulation of establishment of planar polarity / lateral inhibition / second mitotic wave involved in compound eye morphogenesis / imaginal disc-derived wing margin morphogenesis / imaginal disc-derived leg segmentation / wing disc dorsal/ventral pattern formation / antennal morphogenesis / follicle cell of egg chamber stalk formation / imaginal disc-derived leg morphogenesis / chaeta morphogenesis / follicle cell of egg chamber development / wing disc anterior/posterior pattern formation / neuroblast fate determination / border follicle cell migration / neural tube formation / asymmetric cell division / imaginal disc-derived wing morphogenesis / neuron fate specification / glycosphingolipid binding / glial cell migration / sensory organ development / germ-line stem cell population maintenance / apical cortex / peripheral nervous system development / Notch binding / cell fate specification / oogenesis / heart looping / blood vessel development / positive regulation of endocytosis / mesoderm development / centriolar satellite / endocytic vesicle / negative regulation of neuron differentiation / somitogenesis / Notch signaling pathway / Constitutive Signaling by NOTCH1 HD Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / positive regulation of mitotic cell cycle / actin filament organization / NOTCH3 Activation and Transmission of Signal to the Nucleus / stem cell differentiation / RING-type E3 ubiquitin transferase / neuron differentiation / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / endocytosis / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process / cytoplasmic vesicle / in utero embryonic development / receptor ligand activity / protein ubiquitination / early endosome / endosome / centrosome / calcium ion binding / positive regulation of cell population proliferation / cell surface / zinc ion binding / membrane / plasma membrane / cytosol
Similarity search - Function
Mind bomb, SH3 repeat domain / E3 ubiquitin-protein ligase MIB1/2, zinc finger, ZZ-type / Mind bomb SH3 repeat domain / Delta/Serrate/lag-2 (DSL) protein / Notch ligand, N-terminal domain / Delta serrate ligand / N terminus of Notch ligand C2-like domain / DSL domain profile. / delta serrate ligand / Mib-herc2 ...Mind bomb, SH3 repeat domain / E3 ubiquitin-protein ligase MIB1/2, zinc finger, ZZ-type / Mind bomb SH3 repeat domain / Delta/Serrate/lag-2 (DSL) protein / Notch ligand, N-terminal domain / Delta serrate ligand / N terminus of Notch ligand C2-like domain / DSL domain profile. / delta serrate ligand / Mib-herc2 / Mib/herc2 domain superfamily / Mib_herc2 / MIB/HERC2 domain profile. / EGF-like, conserved site / Human growth factor-like EGF / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Ankyrin repeats (many copies) / Zinc finger, C3HC4 type (RING finger) / EGF-type aspartate/asparagine hydroxylation site / EGF-like domain / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / Ring finger / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Zinc finger RING-type profile. / Zinc finger, RING-type / Ankyrin repeat-containing domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Neurogenic locus protein delta / E3 ubiquitin-protein ligase MIB1
Similarity search - Component
Biological speciesHomo sapiens (human)
Drosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.147 Å
AuthorsMcMillan, B.J. / Blacklow, S.C.
Funding support United States, Germany, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P01 CA119070 United States
American Cancer Society120246-PF-11-044-01-DMC United States
German Research Foundation (DFG)KL 1028/3-1 Germany
CitationJournal: Mol.Cell / Year: 2015
Title: A tail of two sites: a bipartite mechanism for recognition of notch ligands by mind bomb e3 ligases.
Authors: McMillan, B.J. / Schnute, B. / Ohlenhard, N. / Zimmerman, B. / Miles, L. / Beglova, N. / Klein, T. / Blacklow, S.C.
History
DepositionJan 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software / struct_keywords
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _struct_keywords.text
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase MIB1
C: Delta N-box peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7916
Polymers43,4682
Non-polymers3234
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-22 kcal/mol
Surface area17670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.131, 74.131, 170.174
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein E3 ubiquitin-protein ligase MIB1 / DAPK-interacting protein 1 / DIP-1 / Mind bomb homolog 1 / Zinc finger ZZ type with ankyrin repeat ...DAPK-interacting protein 1 / DIP-1 / Mind bomb homolog 1 / Zinc finger ZZ type with ankyrin repeat domain protein 2


Mass: 42148.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MIB1, DIP1, KIAA1323, ZZANK2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q86YT6, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide Delta N-box peptide


Mass: 1319.506 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly) / References: UniProt: P10041*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.69 Å3/Da / Density % sol: 54.26 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: Protein at 6 mg/mL in 25 mM HEPES 7.4, 500 mM NaCl, 10% w/v glucose, 100 mM Arg, 2 mM TCEP Precipitant: 1.5 M (NH4)2SO4, 20% v/v glycerol, HEPES pH 7.6 1:1 drop volume

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.147→50 Å / Num. obs: 24766 / % possible obs: 100 % / Redundancy: 7 % / Net I/σ(I): 17.6
Reflection shellResolution: 2.147→2.19 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.993 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.147→45.049 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 4.61 / Phase error: 24.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2444 1995 7.45 %
Rwork0.209 24766 -
obs0.2117 26761 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 188.73 Å2 / Biso mean: 58.6979 Å2 / Biso min: 18.33 Å2
Refinement stepCycle: final / Resolution: 2.147→45.049 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2888 0 12 108 3008
Biso mean--41.6 38 -
Num. residues----369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042970
X-RAY DIFFRACTIONf_angle_d0.784014
X-RAY DIFFRACTIONf_chiral_restr0.031425
X-RAY DIFFRACTIONf_plane_restr0.003519
X-RAY DIFFRACTIONf_dihedral_angle_d12.5021060
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1471-2.20080.30291380.26891715185399
2.2008-2.26030.30611400.258717381878100
2.2603-2.32680.25651380.236117341872100
2.3268-2.40190.27951390.231917261865100
2.4019-2.48770.29691400.227817281868100
2.4877-2.58730.30051400.223317401880100
2.5873-2.70510.27831420.219217531895100
2.7051-2.84770.3081420.224317581900100
2.8477-3.0260.26431400.21417421882100
3.026-3.25960.2531430.211717851928100
3.2596-3.58750.24591440.204117671911100
3.5875-4.10630.19791450.185818021947100
4.1063-5.17240.18931460.165818261972100
5.1724-45.05890.24221580.227419522110100
Refinement TLS params.Method: refined / Origin x: -7.0908 Å / Origin y: -36.3738 Å / Origin z: -19.2379 Å
111213212223313233
T0.1963 Å20.0407 Å2-0.0389 Å2-0.3151 Å2-0.0533 Å2--0.2523 Å2
L1.0518 °20.0668 °2-0.2468 °2-0.2097 °20.0504 °2--0.7988 °2
S0.061 Å °-0.1841 Å °-0.0817 Å °0.0498 Å °0.0963 Å °-0.065 Å °0.0462 Å °0.3048 Å °0.0362 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA7 - 384
2X-RAY DIFFRACTION1allB1 - 2
3X-RAY DIFFRACTION1allC1 - 7
4X-RAY DIFFRACTION1allD2 - 3
5X-RAY DIFFRACTION1allE1 - 185

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