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- PDB-8v0d: Ubch5B-RING3 of MIB1 fusion structure -

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Basic information

Entry
Database: PDB / ID: 8v0d
TitleUbch5B-RING3 of MIB1 fusion structure
ComponentsUbch5B-RING3 of MIB1 fusion protein
KeywordsLIGASE / E3 ligase
Function / homology
Function and homology information


neural tube formation / (E3-independent) E2 ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme / blood vessel development / heart looping / positive regulation of endocytosis / ubiquitin conjugating enzyme activity / centriolar satellite / negative regulation of neuron differentiation / somitogenesis ...neural tube formation / (E3-independent) E2 ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme / blood vessel development / heart looping / positive regulation of endocytosis / ubiquitin conjugating enzyme activity / centriolar satellite / negative regulation of neuron differentiation / somitogenesis / protein K48-linked ubiquitination / protein autoubiquitination / 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 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / Peroxisomal protein import / Regulation of TNFR1 signaling / protein modification process / RING-type E3 ubiquitin transferase / Inactivation of CSF3 (G-CSF) signaling / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / neuron differentiation / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / endocytosis / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / E3 ubiquitin ligases ubiquitinate target proteins / Neddylation / ubiquitin-dependent protein catabolic process / cytoplasmic vesicle / in utero embryonic development / postsynaptic density / protein ubiquitination / centrosome / glutamatergic synapse / protein-containing complex / extracellular exosome / zinc ion binding / nucleoplasm / ATP binding / nucleus / 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) / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / 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 / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 D2 / E3 ubiquitin-protein ligase MIB1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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: To Be Published
Title: Ubch5b-RING3 fusion structure
Authors: Cao, R. / Blacklow, S.C.
History
DepositionNov 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Ubch5B-RING3 of MIB1 fusion protein
A: Ubch5B-RING3 of MIB1 fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7517
Polymers52,4242
Non-polymers3275
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-31 kcal/mol
Surface area22630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.985, 65.119, 135.931
Angle α, β, γ (deg.)90.000, 93.030, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 0 through 99 or resid 101 through 104 or resid 106 through 148))
d_2ens_1(chain "B" and (resid 0 through 99 or resid 101 through 104 or resid 106 through 148))
d_1ens_2(chain "C" and resid 945 through 1006)
d_2ens_2chain "D"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1SERSERILEILEAB0 - 991 - 100
d_12ens_1LYSLYSLEULEUAB101 - 104102 - 105
d_13ens_1ILEILEGLYGLYAB106 - 148107 - 149
d_21ens_1SERSERILEILEBA0 - 991 - 100
d_22ens_1LYSLYSLEULEUBA101 - 104102 - 105
d_23ens_1ILEILEGLYGLYBA106 - 148107 - 149
d_11ens_2ALAALATYRTYRBA945 - 1006176 - 237
d_21ens_2ALAALATYRTYRAB945 - 1006176 - 237

NCS ensembles :
ID
ens_1
ens_2

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Components

#1: Protein Ubch5B-RING3 of MIB1 fusion protein


Mass: 26212.041 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B, MIB1, DIP1, KIAA1323, ZZANK2
Production host: Escherichia coli (E. coli)
References: UniProt: P62837, UniProt: Q86YT6, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme, RING-type E3 ubiquitin transferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.44 Å3/Da / Density % sol: 49.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 4% v/v TacsimateTM pH 6.0, 12% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→37.16 Å / Num. obs: 18194 / % possible obs: 91.35 % / Redundancy: 3 % / Biso Wilson estimate: 45.79 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.057 / Net I/σ(I): 16.86
Reflection shellResolution: 2.4→2.44 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 932 / CC1/2: 0.903 / Rpim(I) all: 0.288

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.20.1_4487refinement
HKL-2000data reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→37.16 Å / SU ML: 0.3252 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 29.003
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2434 938 5.16 %
Rwork0.2127 17242 -
obs0.2142 18180 91.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.45 Å2
Refinement stepCycle: LAST / Resolution: 2.4→37.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3379 0 5 39 3423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00723475
X-RAY DIFFRACTIONf_angle_d0.95464717
X-RAY DIFFRACTIONf_chiral_restr0.0552517
X-RAY DIFFRACTIONf_plane_restr0.0092615
X-RAY DIFFRACTIONf_dihedral_angle_d14.00711341
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CBX-RAY DIFFRACTIONTorsion NCS1.12392001655
ens_2d_2BAX-RAY DIFFRACTIONTorsion NCS3.00079986885
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.530.31031140.30742292X-RAY DIFFRACTION86.24
2.53-2.690.32761230.27122465X-RAY DIFFRACTION91.58
2.69-2.890.2811530.28212476X-RAY DIFFRACTION91.86
2.89-3.180.27791320.26682470X-RAY DIFFRACTION92.33
3.18-3.650.28281720.23662529X-RAY DIFFRACTION94.71
3.65-4.590.23541280.18072447X-RAY DIFFRACTION90.93
4.59-37.160.16721160.16682563X-RAY DIFFRACTION91.84
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)
10.353690267145-0.304758251409-0.2710832637921.264245712750.2588218054860.6300655958660.01002938370050.0181256649879-0.06350649481040.0378208477521-0.1638875993630.2129273457390.385408288974-0.00364065306385-8.04948279E-50.555322490810.006285184010510.04778878874660.419143814099-0.01876586765390.5590423393950.516-7.99555.299
20.366114621980.506959967651-0.1157360767532.679803555531.736117104491.56597121408-0.100393378522-0.001450141499330.1044601296350.0390428972127-0.0660286189276-0.0949485692329-0.0970194989778-0.175280531123-0.00143255543950.478436220650.03342211414320.02994434396730.3136181089980.02456424507120.506587394716.2053.90663.961
30.566918643588-0.0582012486810.1876029339630.182846757399-0.1962371138590.224223591663-0.42028755177-0.08681334179070.0916170682886-0.07616009493930.274133471424-0.218223772459-0.2515395547910.2908541985450.0006112746481740.625918013356-0.09791774268540.004563571777240.434076223345-0.02752139971060.5606743385558.7817.05651.343
40.2860532642730.1010734386230.1331095470010.3021287710310.02926801149810.302032468827-0.1126875754720.209873489965-0.133535287625-0.3384684939970.336179013582-0.420629330311-0.214539868740.386988063120.0001020575069380.515888017025-0.008832591836160.02177238141710.362582221476-0.05510948773710.53207378007216.47510.51663.999
50.1859653004990.350313248457-0.3649068300160.6689001809430.1282005568260.501874696233-0.0255172013114-0.3338708649660.1988841366280.699404258296-0.266619921249-0.2242986071460.07355680603890.04132768504870.0001752436382930.861824427760.08536830416460.04105402207460.440881623410.01180711089450.64221868987317.0447.51177.494
60.0503341864644-0.1575573553340.008108277433130.150048288843-0.05839103431690.0225400633428-0.3550041856960.1804657044260.2588401033710.5723884641030.358901435874-0.743576205632-0.4287542210260.0502374659752-0.000740080802051.50936032460.1309326008460.02304195829490.6896312092090.001333071255750.66831790217811.358-23.45743.59
71.15794175703-0.0717762245570.6340659147080.120616785836-0.5545161360771.120078489790.3030814948820.2378158586440.1493038076720.014125300383-0.09255778675590.189617433923-0.0254614053789-0.09324071042610.00019935903870.8044414887180.03187187237220.1172245253040.588564930977-0.02822086876310.576062124467.213-0.68834.917
80.989932978866-0.861724545812-0.4475795484681.345659716970.03410279554151.37067246560.16943893671-0.500272093912-0.5185002791230.4118214192740.0185558150692-0.1896013303520.244115666221-0.365177382803-4.12878307879E-50.4609015703770.0564320209288-0.02423597517970.7792147516090.1031602557690.58711109175218.493-34.06818.692
91.03586146398-0.0009432574750560.2653203842520.88748638507-0.174106244572.700738020990.0562402747549-0.1469512177130.159896202154-0.133485468846-0.03047510922-0.163702977946-0.330973684781-0.5296726729830.0003903364150.3090459640980.0727849429121-0.02954805681810.678085320508-0.01614863868070.50437295446913.265-30.2196.195
100.1209157111240.179606474590.149531109520.6614293745040.2522043562570.144672983477-0.1470384806720.2752433155520.8338274041540.02861639286250.176507725731-0.327015329606-1.3426553805-0.7853026600020.001371851309440.9175355801050.328150560008-0.001886591717250.7335375490030.02490378417280.6745539743897.003-24.913-4.348
110.808105101031-0.57613265884-0.5237218409190.748989722660.6025033320811.89504644954-0.1169238698360.761693684464-0.6944795446140.0873928095693-0.1097703484941.044395265340.675931844897-2.00129324177-0.3384200050990.303733559841-0.0376504481428-0.248630255331.341270537320.01170697619570.4899898179053.224-37.516-7.862
120.1512142405980.1108865215640.0933716584680.04621522326120.03956150622620.0186439227796-0.03599363411820.358903526209-0.463864097808-0.1711537274590.4007835873660.5637130354210.0883605916762-0.210166858217-0.000670057252221.15692004202-0.01141087277710.1663406003020.7645383987480.03647786861050.8706037953855.221-26.33535.859
130.9674592573850.2556085149310.3453730594120.9217893462350.01279363492070.2993134711560.2686279276130.078954777198-0.0531312564929-0.184011007289-0.255057055992-0.0488941838289-0.3053855006150.3865760742040.0002226637205020.6484235776070.15942009647-0.01262694699880.778910113781-0.01337557996680.46880062851917.414-10.36523.058
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 0:31 )B0 - 31
2X-RAY DIFFRACTION2( CHAIN B AND RESID 32:84 )B32 - 84
3X-RAY DIFFRACTION3( CHAIN B AND RESID 85:98 )B85 - 98
4X-RAY DIFFRACTION4( CHAIN B AND RESID 99:130 )B99 - 130
5X-RAY DIFFRACTION5( CHAIN B AND RESID 131:148 )B131 - 148
6X-RAY DIFFRACTION6( CHAIN B AND RESID 943:961 )B943 - 961
7X-RAY DIFFRACTION7( CHAIN B AND RESID 962:1006 )B962 - 1006
8X-RAY DIFFRACTION8( CHAIN A AND RESID 0:38 )A0 - 38
9X-RAY DIFFRACTION9( CHAIN A AND RESID 39:111 )A39 - 111
10X-RAY DIFFRACTION10( CHAIN A AND RESID 112:120 )A112 - 120
11X-RAY DIFFRACTION11( CHAIN A AND RESID 121:148 )A121 - 148
12X-RAY DIFFRACTION12( CHAIN A AND RESID 945:961 )A945 - 961
13X-RAY DIFFRACTION13( CHAIN A AND RESID 962:1006 )A962 - 1006

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