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- PDB-8v0e: ANK repeat of MIB1 -

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Basic information

Entry
Database: PDB / ID: 8v0e
TitleANK repeat of MIB1
Components
  • E3 ubiquitin-protein ligase MIB1
  • Unidentified MIB1 peptide
KeywordsLIGASE / E3 ligase
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 / 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. / Zinc finger, C3HC4 type (RING finger) / Ankyrin repeat / 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 / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsCao, R. / Blacklow, S.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R35 CA220340 United States
CitationJournal: Structure / Year: 2024
Title: Structural requirements for activity of Mind bomb1 in Notch signaling.
Authors: Cao, R. / Gozlan, O. / Airich, A. / Tveriakhina, L. / Zhou, H. / Jiang, H. / Cole, P.A. / Aster, J.C. / Klein, T. / Sprinzak, D. / Blacklow, S.C.
History
DepositionNov 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Database references / Structure summary / Category: citation / pdbx_entry_details
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_entry_details.has_protein_modification

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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
D: Unidentified MIB1 peptide


Theoretical massNumber of molelcules
Total (without water)84,2903
Polymers84,2903
Non-polymers00
Water2,720151
1
A: E3 ubiquitin-protein ligase MIB1
D: Unidentified MIB1 peptide


Theoretical massNumber of molelcules
Total (without water)42,3672
Polymers42,3672
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: E3 ubiquitin-protein ligase MIB1


Theoretical massNumber of molelcules
Total (without water)41,9231
Polymers41,9231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.997, 137.470, 96.248
Angle α, β, γ (deg.)90.000, 108.140, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-844-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 438 through 447 or resid 452...
d_2ens_1(chain "B" and (resid 438 through 447 or resid 452...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ALAALAVALVALAA438 - 44730 - 39
d_12LYSLYSASPASPAA452 - 45544 - 47
d_13ASPASPASPASPAA45749
d_14ASNASNGLYGLYAA459 - 46051 - 52
d_15CYSCYSCYSCYSAA46254
d_16THRTHRASPASPAA466 - 47858 - 70
d_17LYSLYSLYSLYSAA48173
d_18VALVALHISHISAA488 - 51780 - 109
d_19GLYGLYLYSLYSAA519 - 528111 - 120
d_110ARGARGPROPROAA530 - 620122 - 212
d_111PROPROLEULEUAA622 - 715214 - 307
d_112GLNGLNVALVALAA717 - 724309 - 316
d_113LYSLYSLYSLYSAA749341
d_114SERSERLYSLYSAA751 - 794343 - 386
d_21ALAALAVALVALBB438 - 44730 - 39
d_22LYSLYSASPASPBB452 - 45544 - 47
d_23ASPASPASPASPBB45749
d_24ASNASNGLYGLYBB459 - 46051 - 52
d_25CYSCYSASPASPBB462 - 47854 - 70
d_26LYSLYSLYSLYSBB48173
d_27VALVALHISHISBB488 - 51780 - 109
d_28GLYGLYLYSLYSBB519 - 528111 - 120
d_29ARGARGPROPROBB530 - 620122 - 212
d_210PROPROLEULEUBB622 - 715214 - 307
d_211GLNGLNVALVALBB717 - 724309 - 316
d_212LYSLYSLYSLYSBB749341
d_213SERSERLYSLYSBB751 - 794343 - 386

NCS oper: (Code: givenMatrix: (-0.999999272908, 9.16693003375E-5, 0.0012024057755), (-9.92469810117E-5, -0.999980127479, -0.00630355439657), (0.00120180403824, -0.00630366914845, 0.999979409499) ...NCS oper: (Code: given
Matrix: (-0.999999272908, 9.16693003375E-5, 0.0012024057755), (-9.92469810117E-5, -0.999980127479, -0.00630355439657), (0.00120180403824, -0.00630366914845, 0.999979409499)
Vector: 79.0038798246, 130.568098992, 0.552363727212)

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Components

#1: Protein E3 ubiquitin-protein ligase MIB1


Mass: 41923.336 Da / Num. of mol.: 2 / Fragment: ANK repeat
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MIB1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q86YT6, RING-type E3 ubiquitin transferase
#2: Protein/peptide Unidentified MIB1 peptide


Mass: 443.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MIB1 / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN
Sequence detailsChain D is fragment of MIB1 that cannot be registered to the sample sequence due to weak density.

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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: 2.95 Å3/Da / Density % sol: 58.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1M Ammonium tartrate dibasic, 0.1M Sodium acetate trihydrate pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.39→47.74 Å / Num. obs: 37769 / % possible obs: 99 % / Redundancy: 4.6 % / Biso Wilson estimate: 45.29 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.062 / Net I/σ(I): 14.29
Reflection shellResolution: 2.39→2.44 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 1.12 / Num. unique obs: 1868 / CC1/2: 0.528 / CC star: 0.831 / Rpim(I) all: 0.568 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-20001.20.1_4487data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.39→47.64 Å / SU ML: 0.3004 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.3302
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2443 1843 4.89 %
Rwork0.2066 35871 -
obs0.2083 37714 97.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.58 Å2
Refinement stepCycle: LAST / Resolution: 2.39→47.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5190 0 0 156 5346
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075259
X-RAY DIFFRACTIONf_angle_d0.94297120
X-RAY DIFFRACTIONf_chiral_restr0.0521827
X-RAY DIFFRACTIONf_plane_restr0.0096959
X-RAY DIFFRACTIONf_dihedral_angle_d15.20011934
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.581683503596 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.450.3031260.25252467X-RAY DIFFRACTION88.41
2.45-2.530.3051290.25352636X-RAY DIFFRACTION93.19
2.53-2.610.28781610.24152709X-RAY DIFFRACTION97.12
2.61-2.70.27081500.24712766X-RAY DIFFRACTION99.12
2.7-2.810.27351570.22472791X-RAY DIFFRACTION98.79
2.81-2.940.26781410.22012806X-RAY DIFFRACTION99.33
2.94-3.090.27371510.20662760X-RAY DIFFRACTION99.08
3.09-3.290.25661570.22162824X-RAY DIFFRACTION99.7
3.29-3.540.25281410.21052789X-RAY DIFFRACTION99.66
3.54-3.90.23281210.18682850X-RAY DIFFRACTION99.6
3.9-4.460.19821260.17442840X-RAY DIFFRACTION99.36
4.46-5.620.24291520.20362755X-RAY DIFFRACTION97.58
5.62-47.640.21631310.20532878X-RAY DIFFRACTION99.57
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.03608060822580.0511754541435-0.007509146025480.469316217051-0.2053935083560.0811538080491-0.453361125702-0.104147045632-0.300366027089-0.1589420362470.2473811044820.2949597526590.771903382533-0.154992105089-0.008452521634860.9316138687960.004445519079620.1074726083270.9192459357680.01506841067720.37471984158139.745833877875.592483178845.1545222656
20.0352723387382-0.0116985885124-0.06826876898850.375615952676-0.2119913121070.207537765841-0.296318495038-0.4252147617010.134955068747-0.1586028504880.161708408205-0.0658732663128-0.1196805987120.126301588536-0.003615761223030.8290347189330.1115175489640.09246820021050.9919098400660.01969951381470.34476589843441.742284388181.702669655840.8902400998
30.2247500809120.0736413732735-0.1382385398150.310578937056-0.292736722930.2609011347390.1699079878650.00902763304340.2774614675960.283527939112-0.1840285622690.04490355211630.2993662873220.3643522681770.001681276690510.680834958789-0.0861414793923-0.0375696280080.850710858741-0.0974185418480.31796202443944.597327226686.365197218331.6129922995
40.904567508810.430248010841-0.8697499829120.393184750878-0.2622649257131.43841544120.0273857101693-0.2772389532130.1672886789130.131112938553-0.0874871600531-0.001961568609860.07404720824570.115033221626-0.0001516662085790.3455867643660.042074087829-0.03767387506470.333965211884-0.02789535774180.26290549736848.742150171487.584522236212.6271339816
50.455658436497-0.182062711097-0.6184492284320.3064182193770.3189020582230.94880121546-0.0359711646438-0.08444252741870.0736432714782-0.04089854577250.0842668999575-0.181137594230.04633327805050.0437190928199-5.29908028226E-50.2695550394710.073877745435-0.0004860262184870.2113950580720.05909866773770.32175823980456.517622515989.0732943562-7.24363668354
60.10455457987-0.048863992165-0.08950532157430.334218054087-0.1980479633120.607363066227-0.152230009489-0.0982082201474-0.2248221165370.02377901110280.0568570609178-0.229065769110.853936742213-0.146583275698-0.009485055562590.5248940740450.131525215427-0.002364096838580.2791715826410.05352629842670.32986463459157.904053457279.5116336538-15.8465751015
70.1800506693460.0987169976329-0.07010056694180.234191877155-0.0199254433584-0.0496029431232-0.192836873472-0.1249263357650.02944017702790.04984533049670.231112434318-0.09069547664740.04892938191820.2218675979540.0001388414349330.4015765005990.199963218961-0.007477156855710.4853275670030.03434600964670.38298633446270.127967663175.9350590759-20.2373469582
80.38925945835-0.135926996898-0.400996555434-0.0182600274320.06923884045760.373571463158-0.0225712922770.6695427086-0.2429509283650.0384448847251-0.310767409160.4161105223670.134230521576-0.456286488376-0.07090147222440.532140676840.04952146870080.05615149402310.265718423207-0.07240743674450.31602682321264.894800911369.3199581995-22.7214405316
90.5276681492440.268683868548-0.1236582849820.2718825387460.1352028086720.159619429441-0.2940947951820.5212243502340.0504529830893-0.5929209656960.339546661753-0.350072439913-0.001088208470720.519622943049-0.008342630966180.624622198750.2062641950030.06444105457820.680362025187-0.05122189453930.41921838482869.078969018279.3499103739-29.9470381182
100.687292007724-0.2842803432830.0719230983451.01282827182-0.3393272532650.4137911446960.0676938246003-0.5410212994040.2793300359260.379704611288-0.0530047254246-0.121422908453-0.344027295559-0.474207879512-0.786876743490.899610523024-0.1076781943660.02793222870211.31839199111-0.2252433636510.64715013898436.903419240448.021127748637.829100175
112.43047621142-0.4753912749221.326232298730.40434943788-0.1400239351941.552980372560.0685367472717-0.3680746598060.3532132743090.0246979722142-0.09212840881020.196202459525-0.0494231141532-0.173942790562-0.0008799838463750.2902286148490.02265198380810.05367343945620.235109088692-0.04562515122520.53522157696826.815234553443.5370157643.20314471931
120.122446695433-0.1989279835980.3878075438960.0932186791571-0.09166383306420.555465416120.1066489400520.1255174957350.0888655412612-0.38228051411-0.304072089523-0.0337689164541-0.1659365759820.1415831785530.0002510034150450.5035574271530.167548178375-0.02855793579080.4464671502790.2070352023150.77338026712310.779346971256.8818801741-20.9986050473
130.01042173943540.0020883183819-0.07370152351330.0241208785968-0.05438197064710.2237159024570.02247528972841.024123982950.151231459302-0.4424792115230.4920742474050.2902483511370.586837999157-0.4425144086850.01199391659520.8317937108380.284597292786-0.1476985010460.7781754850310.22179325430.9300918265769.4109860289751.4729749147-29.905289095
140.248485083020.300594472089-0.02567746743620.371646527145-0.0270367380450.00750643369353-0.492578124060.1475229150720.2027666489120.172467190868-0.362432008764-0.200102085982-0.0059740920353-0.1472541816310.00333683935851.25218494429-0.144023055496-0.2210428779280.729254566175-0.04768697506070.80176560652850.495761967966.772894686860.4962063483
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 428 through 451 )AA428 - 4511 - 24
22chain 'A' and (resid 452 through 485 )AA452 - 48525 - 58
33chain 'A' and (resid 486 through 518 )AA486 - 51859 - 91
44chain 'A' and (resid 519 through 618 )AA519 - 61892 - 191
55chain 'A' and (resid 619 through 668 )AA619 - 668192 - 241
66chain 'A' and (resid 669 through 688 )AA669 - 688242 - 261
77chain 'A' and (resid 689 through 721 )AA689 - 721262 - 294
88chain 'A' and (resid 722 through 761 )AA722 - 761295 - 311
99chain 'A' and (resid 762 through 794 )AA762 - 794312 - 344
1010chain 'B' and (resid 429 through 518 )BB429 - 5181 - 87
1111chain 'B' and (resid 519 through 688 )BB519 - 68888 - 257
1212chain 'B' and (resid 689 through 762 )BB689 - 762258 - 310
1313chain 'B' and (resid 763 through 794 )BB763 - 794311 - 342
1414chain 'D' and (resid 1 through 5 )DC1 - 51 - 5

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