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- PDB-4xi6: Crystal structure of the MZM-REP domains of Mind bomb 1 -

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Basic information

Entry
Database: PDB / ID: 4xi6
TitleCrystal structure of the MZM-REP domains of Mind bomb 1
ComponentsE3 ubiquitin-protein ligase MIB1
KeywordsLIGASE / E3 ligase / Notch signaling
Function / homology
Function and homology information


neural tube formation / blood vessel development / heart looping / positive regulation of endocytosis / centriolar satellite / 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 ...neural tube formation / blood vessel development / heart looping / positive regulation of endocytosis / centriolar satellite / 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 / NOTCH3 Activation and Transmission of Signal to the Nucleus / 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 / postsynaptic density / protein ubiquitination / centrosome / glutamatergic synapse / zinc ion binding / 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 / Mib-herc2 / Mib/herc2 domain superfamily / Mib_herc2 / MIB/HERC2 domain profile. / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type ...Mind bomb, SH3 repeat domain / E3 ubiquitin-protein ligase MIB1/2, zinc finger, ZZ-type / Mind bomb SH3 repeat domain / Mib-herc2 / Mib/herc2 domain superfamily / Mib_herc2 / MIB/HERC2 domain profile. / 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. / Zinc finger, C3HC4 type (RING finger) / SH3 Domains / Ankyrin repeat / Ring finger / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / SH3 type barrels. / Zinc finger, RING/FYVE/PHD-type / Roll / Mainly Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase MIB1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.04 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
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list / software
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_struct_oper_list.symmetry_operation / _software.classification
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 1.5Dec 27, 2023Group: 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

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase MIB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4715
Polymers42,1481
Non-polymers3234
Water3,351186
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area330 Å2
ΔGint-24 kcal/mol
Surface area17360 Å2
2
A: E3 ubiquitin-protein ligase MIB1
hetero molecules

A: E3 ubiquitin-protein ligase MIB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,94210
Polymers84,2962
Non-polymers6468
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_544x,-y-1,-z-1/21
Buried area2750 Å2
ΔGint-58 kcal/mol
Surface area32630 Å2
MethodPISA
3
A: E3 ubiquitin-protein ligase MIB1
hetero molecules

A: E3 ubiquitin-protein ligase MIB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,94210
Polymers84,2962
Non-polymers6468
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_644y+1,x-1,-z-1/41
Buried area3220 Å2
ΔGint-62 kcal/mol
Surface area32150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.083, 73.083, 170.959
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-264-

LEU

21A-663-

HOH

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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: Chemical ChemComp-ZN / ZINC ION


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


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


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.61 Å3/Da / Density % sol: 52.92 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.6 / Details: 1.5 M (NH4)2SO4, 20% v/v glycerol, HEPES pH 7.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.2562, 1.2822, 1.283
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 17, 2013
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.25621
21.28221
31.2831
ReflectionRedundancy: 8.1 % / Number: 235966 / Rmerge(I) obs: 0.067 / Χ2: 0.99 / D res high: 2.04 Å / D res low: 50 Å / Num. obs: 29269 / % possible obs: 95.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
5.545010.0381.4338.2
4.395.5410.0411.1238.1
3.844.3910.0441.0468.9
3.493.8410.0520.9768.1
3.243.4910.0631.028.5
3.053.2410.0741.0268.8
2.893.0510.0941.0068.8
2.772.8910.1181.0497.8
2.662.7710.141.0018.4
2.572.6610.1720.9738.7
2.492.5710.1890.9518.8
2.422.4910.2120.9368.9
2.352.4210.2540.9118.1
2.32.3510.2940.9058.2
2.252.310.2910.8918.2
2.22.2510.3320.8937.9
2.152.210.3740.8747.3
2.112.1510.3560.8246.6
2.082.1110.3660.876.2
2.042.0810.4040.8634.6
ReflectionResolution: 2.04→50 Å / Num. obs: 29269 / % possible obs: 95.2 % / Redundancy: 8.1 % / Biso Wilson estimate: 19.79 Å2 / Rmerge(I) obs: 0.067 / Χ2: 0.992 / Net I/av σ(I): 28.7 / Net I/σ(I): 6.5 / Num. measured all: 235966
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.04-2.084.60.4048080.86353.6
2.08-2.116.20.36612110.8780.7
2.11-2.156.60.35613600.82490.3
2.15-2.27.30.37414450.87496.9
2.2-2.257.90.33214740.89398.1
2.25-2.38.20.29115000.89199.3
2.3-2.358.20.29415030.90599.5
2.35-2.428.10.25414820.91199.1
2.42-2.498.90.21215160.93699.3
2.49-2.578.80.18914890.95199.5
2.57-2.668.70.17215220.97399.7
2.66-2.778.40.1415151.00199.7
2.77-2.897.80.11815381.04999.6
2.89-3.058.80.09415411.00699.5
3.05-3.248.80.07415211.02699.5
3.24-3.498.50.06315461.0299.5
3.49-3.848.10.05215230.97698.1
3.84-4.398.90.04415481.04698.7
4.39-5.548.10.04115651.12397.3
5.54-508.20.03816621.43395.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.14data extraction
HKL-2000data scaling
Cootmodel building
PHENIXphasing
RefinementResolution: 2.04→44.939 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2481 2000 6.58 %
Rwork0.2085 28375 -
obs0.2111 30375 93.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 143.96 Å2 / Biso mean: 39.8021 Å2 / Biso min: 0 Å2
Refinement stepCycle: final / Resolution: 2.04→44.939 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2836 0 12 186 3034
Biso mean--21.66 31.91 -
Num. residues----363
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052918
X-RAY DIFFRACTIONf_angle_d0.9673941
X-RAY DIFFRACTIONf_chiral_restr0.036416
X-RAY DIFFRACTIONf_plane_restr0.004512
X-RAY DIFFRACTIONf_dihedral_angle_d14.2841043
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 (%)
1.9947-2.04460.3725850.31141197128257
2.0446-2.09990.36721100.30331554166474
2.0999-2.16170.3161340.28151910204490
2.1617-2.23150.27351460.25312076222298
2.2315-2.31120.24311480.22292093224199
2.3112-2.40380.2311490.21572132228199
2.4038-2.51320.22181520.199621452297100
2.5132-2.64560.24621500.20621232273100
2.6456-2.81140.2371520.202721602312100
2.8114-3.02840.25481520.200621512303100
3.0284-3.33310.25451530.186221812334100
3.3331-3.81510.20131520.1812156230899
3.8151-4.80580.18951550.16192200235599
4.8058-44.95070.30231620.23392297245997
Refinement TLS params.Method: refined / Origin x: 6.93 Å / Origin y: -37.7679 Å / Origin z: -19.8573 Å
111213212223313233
T0.0242 Å20.0596 Å20.0597 Å2-0.2741 Å20.081 Å2--0.142 Å2
L0.148 °20.0335 °2-0.0894 °2-0.1146 °20.0007 °2--0.2114 °2
S0.1204 Å °-0.0669 Å °0.0848 Å °0.1142 Å °0.1133 Å °0.042 Å °-0.0361 Å °-0.2672 Å °0.3042 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA7 - 400
2X-RAY DIFFRACTION1allB1 - 2
3X-RAY DIFFRACTION1allE1 - 2
4X-RAY DIFFRACTION1allS1 - 310

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