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- PDB-4tse: Crystal Structure of the Mib Repeat Domain of Mind bomb 1 -

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Basic information

Entry
Database: PDB / ID: 4tse
TitleCrystal Structure of the Mib Repeat Domain of Mind bomb 1
ComponentsE3 ubiquitin-protein ligase MIB1
KeywordsLIGASE / E3 ubiquitin ligase / Notch pathway
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 / cytoplasmic vesicle / ubiquitin-dependent protein catabolic process / in utero embryonic development / protein ubiquitination / centrosome / 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. / Ankyrin repeats (many copies) / Zinc finger, C3HC4 type (RING finger) / Ring finger / 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
E3 ubiquitin-protein ligase MIB1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.057 Å
AuthorsMcMillan, B.J. / Blacklow, S.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P01 CA119070 United States
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
DepositionJun 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list / pdbx_validate_close_contact / 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_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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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
B: E3 ubiquitin-protein ligase MIB1


Theoretical massNumber of molelcules
Total (without water)37,0012
Polymers37,0012
Non-polymers00
Water4,324240
1
A: E3 ubiquitin-protein ligase MIB1


Theoretical massNumber of molelcules
Total (without water)18,5011
Polymers18,5011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E3 ubiquitin-protein ligase MIB1


Theoretical massNumber of molelcules
Total (without water)18,5011
Polymers18,5011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-8 kcal/mol
Surface area15870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.320, 86.420, 86.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid A
21chain B and segid B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segid AA0
211chain B and segid BB0
Detailsbiological unit is the same as asym.

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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: 18500.529 Da / Num. of mol.: 2 / Fragment: UNP residues 239-409
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MIB1, DIP1, KIAA1323, ZZANK2 / Plasmid: pTD68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q86YT6, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.6 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 24% v/v PEK2K MME, 0.8M HCOONa using 6 mg/ml protein

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.988 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.988 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 24570 / % possible obs: 99.7 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.113 / Χ2: 1.079 / Net I/av σ(I): 14.6 / Net I/σ(I): 6.2 / Num. measured all: 149146
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.05-2.0960.6442.611871.19399.8
2.09-2.126.10.48912101.05399.9
2.12-2.166.10.45912190.988100
2.16-2.216.20.39511961.042100
2.21-2.266.10.3912061.20599.9
2.26-2.316.20.3412211.049100
2.31-2.376.20.32612081.082100
2.37-2.436.20.28712201.09100
2.43-2.56.20.27112141.17699.9
2.5-2.586.20.21112271.105100
2.58-2.686.10.20512251.175100
2.68-2.786.10.17212241.04199.9
2.78-2.916.20.14912201.14299.9
2.91-3.066.10.12812401.04699.9
3.06-3.256.10.10812181.03799.8
3.25-3.5160.0912381.03699.6
3.51-3.865.70.07612441.0399.5
3.86-4.4260.05612511.06199.3
4.42-5.566.10.05212711.01499.1
5.56-505.80.04413311.02497.2

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.2_1309)refinement
RefinementResolution: 2.057→44.15 Å / FOM work R set: 0.7569 / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29.22 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2293 1061 5.14 %Random selection
Rwork0.1897 19572 --
obs0.1918 20633 83.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.98 Å2 / Biso mean: 18.72 Å2 / Biso min: 6.19 Å2
Refinement stepCycle: final / Resolution: 2.057→44.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 0 240 2609
Biso mean---28.95 -
Num. residues----313
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122415
X-RAY DIFFRACTIONf_angle_d1.3113286
X-RAY DIFFRACTIONf_chiral_restr0.083373
X-RAY DIFFRACTIONf_plane_restr0.006428
X-RAY DIFFRACTIONf_dihedral_angle_d14.713852
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1432X-RAY DIFFRACTION5.396TORSIONAL
12B1432X-RAY DIFFRACTION5.396TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.057-2.15020.2319440.196491796132
2.1502-2.26360.2489880.1991675176359
2.2636-2.40540.24121320.20562345247781
2.4054-2.59110.28451700.22852837300799
2.5911-2.85180.25121620.216629153077100
2.8518-3.26440.25431700.196928683038100
3.2644-4.11230.19241630.16162937310099
4.1123-44.160.18631320.16823078321098
Refinement TLS params.Method: refined / Origin x: -4.6607 Å / Origin y: -14.1102 Å / Origin z: 21.5636 Å
111213212223313233
T0.0925 Å20.0079 Å2-0.0017 Å2-0.1206 Å20.0399 Å2--0.1141 Å2
L0.1191 °2-0.0224 °2-0.1888 °2-0.204 °20.0429 °2--0.3156 °2
S0.0134 Å °-0.0404 Å °0.0614 Å °-0.0089 Å °0.0179 Å °-0.0028 Å °-0.0113 Å °0.0987 Å °-0.0059 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 409
2X-RAY DIFFRACTION1allB1 - 409
3X-RAY DIFFRACTION1allS1 - 240

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