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- PDB-7w75: Crystal structure of the K. lactis Bre1 RBD in complex with Rad6,... -

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Basic information

Entry
Database: PDB / ID: 7w75
TitleCrystal structure of the K. lactis Bre1 RBD in complex with Rad6, crystal form I
Components
  • E3 ubiquitin-protein ligase BRE1
  • Ubiquitin-conjugating enzyme E2 2
KeywordsGENE REGULATION / Complex / ubiquitin / ubiquitin ligase
Function / homology
Function and homology information


HULC complex / E2 ubiquitin-conjugating enzyme / sporulation resulting in formation of a cellular spore / ubiquitin conjugating enzyme activity / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / chromatin organization / protein ubiquitination / DNA repair / ATP binding ...HULC complex / E2 ubiquitin-conjugating enzyme / sporulation resulting in formation of a cellular spore / ubiquitin conjugating enzyme activity / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / chromatin organization / protein ubiquitination / DNA repair / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
E3 ubiquitin ligase Bre1 / BRE1 E3 ubiquitin ligase / : / Zinc finger, C3HC4 RING-type / 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. ...E3 ubiquitin ligase Bre1 / BRE1 E3 ubiquitin ligase / : / Zinc finger, C3HC4 RING-type / 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 / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 2 / E3 ubiquitin-protein ligase BRE1
Similarity search - Component
Biological speciesKluyveromyces lactis NRRL Y-1140 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsShi, M. / Zhao, J. / Xiang, S.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071205 China
National Natural Science Foundation of China (NSFC)31870769 China
CitationJournal: Elife / Year: 2023
Title: Structural basis for the Rad6 activation by the Bre1 N-terminal domain.
Authors: Shi, M. / Zhao, J. / Zhang, S. / Huang, W. / Li, M. / Bai, X. / Zhang, W. / Zhang, K. / Chen, X. / Xiang, S.
History
DepositionDec 3, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 2
B: Ubiquitin-conjugating enzyme E2 2
C: E3 ubiquitin-protein ligase BRE1
D: E3 ubiquitin-protein ligase BRE1
E: E3 ubiquitin-protein ligase BRE1
F: E3 ubiquitin-protein ligase BRE1


Theoretical massNumber of molelcules
Total (without water)130,9966
Polymers130,9966
Non-polymers00
Water00
1
A: Ubiquitin-conjugating enzyme E2 2
C: E3 ubiquitin-protein ligase BRE1
D: E3 ubiquitin-protein ligase BRE1


Theoretical massNumber of molelcules
Total (without water)65,4983
Polymers65,4983
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10790 Å2
ΔGint-91 kcal/mol
Surface area23640 Å2
MethodPISA
2
B: Ubiquitin-conjugating enzyme E2 2
E: E3 ubiquitin-protein ligase BRE1
F: E3 ubiquitin-protein ligase BRE1


Theoretical massNumber of molelcules
Total (without water)65,4983
Polymers65,4983
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10170 Å2
ΔGint-91 kcal/mol
Surface area24030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.441, 94.441, 534.644
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 3 through 157)
21chain B
12(chain C and (resid 18 through 121 or resid 130 through 170))
22(chain D and (resid 18 through 121 or resid 130 through 170))
32(chain E and (resid 18 through 121 or resid 130 through 170))
42(chain F and resid 18 through 170)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111THRTHRALAALA(chain A and resid 3 through 157)AA3 - 1576 - 160
211THRTHRALAALAchain BBB3 - 1576 - 160
112GLUGLULYSLYS(chain C and (resid 18 through 121 or resid 130 through 170))CC18 - 12118 - 121
122ASNASNASPASP(chain C and (resid 18 through 121 or resid 130 through 170))CC130 - 170130 - 170
212GLUGLULYSLYS(chain D and (resid 18 through 121 or resid 130 through 170))DD18 - 12118 - 121
222ASNASNASPASP(chain D and (resid 18 through 121 or resid 130 through 170))DD130 - 170130 - 170
312GLUGLULYSLYS(chain E and (resid 18 through 121 or resid 130 through 170))EE18 - 12118 - 121
322ASNASNASPASP(chain E and (resid 18 through 121 or resid 130 through 170))EE130 - 170130 - 170
412GLUGLUASPASP(chain F and resid 18 through 170)FF18 - 17018 - 170

NCS ensembles :
ID
1
2

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 2 / E2 ubiquitin-conjugating enzyme 2 / Ubiquitin carrier protein UBC2 / Ubiquitin-protein ligase UBC2


Mass: 19172.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis NRRL Y-1140 (yeast)
Strain: NRRL Y-1140 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6CUD9, E2 ubiquitin-conjugating enzyme
#2: Protein
E3 ubiquitin-protein ligase BRE1 / RING-type E3 ubiquitin transferase BRE1


Mass: 23162.822 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis NRRL Y-1140 (yeast)
Strain: NRRL Y-1140 / Gene: BRE1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6CWM4, RING-type E3 ubiquitin transferase
Has protein modificationY

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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: 2.46 Å3/Da / Density % sol: 50.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: sodium acetrate, PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 24184 / % possible obs: 100 % / Redundancy: 18 % / CC1/2: 0.985 / Net I/σ(I): 17
Reflection shellResolution: 3.2→3.26 Å / Num. unique obs: 1206 / CC1/2: 0.623

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ayz

1ayz


Resolution: 3.2→40.89 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2633 1066 4.7 %
Rwork0.2132 21610 -
obs0.2156 22676 91.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 261.3 Å2 / Biso mean: 107.631 Å2 / Biso min: 43.4 Å2
Refinement stepCycle: final / Resolution: 3.2→40.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7563 0 0 0 7563
Num. residues----950
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1462X-RAY DIFFRACTION10.622TORSIONAL
12B1462X-RAY DIFFRACTION10.622TORSIONAL
21C2735X-RAY DIFFRACTION10.622TORSIONAL
22D2735X-RAY DIFFRACTION10.622TORSIONAL
23E2735X-RAY DIFFRACTION10.622TORSIONAL
24F2735X-RAY DIFFRACTION10.622TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2-3.350.39341160.32572349246583
3.35-3.520.38841150.28922478259386
3.52-3.740.3231270.25622651277893
3.74-4.030.3141410.22762745288696
4.03-4.440.25261330.19962804293796
4.44-5.080.21221460.18652862300898
5.08-6.390.26551340.23972754288892
6.39-40.890.22571540.1762967312192
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)
12.0964-0.250.16061.51160.57492.8039-0.1157-0.06410.7702-0.29630.121-0.6003-0.01230.209600.6233-0.1052-0.03780.72620.09381.111614.1688-20.857-8.16
22.84940.11833.19440.0249-0.14975.8623-0.3830.78261.647-0.4914-1.7217-0.6149-2.2676-0.61090.71571.04740.2813-0.27680.9119-0.13931.75130.5362-10.914-11.3809
31.460.2083-0.18320.83221.32452.0191-0.5716-0.39760.53190.28630.47410.4177-0.0074-0.6586-0.44280.7217-0.0667-0.17180.74940.11881.0882-4.7798-21.0494-5.1048
40.46840.841-0.36971.5261-0.79960.48890.41270.3071-0.43230.5309-0.8389-0.81640.6410.4959-0.18890.84530.4637-0.11371.1063-0.28790.4664-15.0995-38.2334-51.2176
51.0630.9332-0.11840.6380.10621.2051-0.5909-0.2083-0.92820.6241-0.18350.66360.504-0.2816-0.39390.72390.0862-0.28531.0427-0.3650.544-15.5892-47.1386-41.6446
61.7665-0.5240.31091.0559-0.07320.0508-0.6636-0.37720.16320.6065-0.16961.5887-1.0238-1.29860.01751.04250.0484-0.10061.3212-0.4470.8221-22.1795-46.5662-36.6609
70.18120.05350.07590.29140.0550.3362-0.2358-0.1304-0.36040.39590.0932-0.40430.9045-0.58-0.00281.0895-0.16010.0091.20720.00910.6571-9.4174-54.6492-26.2852
81.85510.2731-0.95270.1539-0.41851.5959-0.01430.178-0.8455-0.7757-0.2696-0.5767-0.1481-0.72490.12941.1040.3288-0.05550.7377-0.26951.1269-1.5542-46.8739-47.8369
90.0696-0.3693-0.22721.4130.22460.1976-0.0916-0.14011.00350.27670.3017-0.6016-0.0260.02330.13920.50290.1187-0.13150.7793-0.00270.661-21.607-19.821412.7147
100.21920.2013-0.26051.2916-0.61410.3183-0.24020.2245-0.894-0.5353-0.06170.72220.6803-0.3457-0.04660.5284-0.08250.07970.65290.04540.4709-62.9502-11.93185.1204
113.90140.14360.85680.79440.40770.6982-0.2062-0.35440.10040.08770.3590.13470.1413-0.0634-0.23650.56630.11580.11420.51210.08390.5631-40.822-3.392512.3596
120.46990.21440.13673.8774-0.8830.30430.0626-0.72670.32150.83920.89860.4659-0.5331-0.18581.10420.9050.39450.01791.593-0.37651.4297-9.019-30.191817.9352
130.07980.0657-0.0580.0426-0.04020.03480.92890.5171.08310.1191-0.9998-1.16610.9933-0.4135-0.00021.41070.3067-0.00841.4882-0.00641.1654-2.5479-33.018816.1836
140.5791-0.1152-0.58620.528-0.54380.4735-0.2026-0.21750.07110.24770.2523-0.24380.13150.09270.15260.520.1277-0.02940.555-0.13010.6866-34.0434-14.95468.6482
150.37290.43940.12891.1910.64651.54210.1222-0.081-0.0330.3562-0.0930.1796-0.6249-0.47380.00010.80580.23740.13170.74910.02890.5559-55.54251.163522.7939
161.9821-1.13013.14940.8889-2.00515.21620.4291-1.6402-0.34270.07731.4963-0.5987-0.62560.07081.46320.70250.18350.33651.0011-0.35991.7872-61.805511.970212.8719
170.92140.48830.44290.99840.2906-0.0823-0.05210.9644-0.2560.271-0.138-0.21560.08480.2746-0.00070.65850.12290.03580.7285-0.06060.7039-25.8407-1.17679.9716
181.0275-0.6181-0.26310.8559-0.62161.5487-1.2757-1.21710.46981.5621-0.240.555-1.88310.3884-0.00681.0668-0.0719-0.24811.1718-0.10571.63686.9231-19.400613.2477
190.96910.3252-0.51231.59791.34381.8279-0.25790.07850.3823-0.4147-0.23230.1281-1.52530.1785-1.19611.1860.0104-0.03160.62681.23760.5367-1.2681-32.0657-46.2074
20-0.0151-0.0020.2213-0.0377-0.48710.3503-0.17640.06770.07510.1486-0.3152-0.2449-0.76280.4729-0.00010.73290.0057-0.13470.64210.21680.653812.939-51.8409-9.7475
210.1082-0.02380.03530.1254-0.05250.030.09970.11470.0934-0.3210.3823-1.15250.7855-0.54150.00073.2753-0.0170.41281.5894-0.14141.657218.039-76.060531.854
222.2437-1.5526-1.34952.95762.46422.6359-0.5215-2.0172-0.95570.93050.4887-0.2441.00210.1958-0.10111.11650.11730.02431.1230.17041.107316.6965-77.241422.6887
235.05753.57826.11742.51484.33657.46780.56920.6361-1.2596-0.63230.1946-0.5930.20241.83380.42011.36330.14070.14090.64890.28040.787917.5169-68.653211.8387
242.9171.6556-0.11421.0338-0.05690.02250.3332-0.9432-2.18520.3857-0.06930.09610.8121-1.73510.09681.63220.28650.18551.12240.25320.688610.5728-66.557927.2235
252.456-0.0384-0.10340.64740.65010.6009-0.02750.24150.40190.68190.0613-0.3508-1.0658-0.33990.0010.75510.1083-0.06840.4697-0.04210.59599.3218-44.8420.4781
260.73520.5511-0.6730.4717-0.61321.17530.0918-0.240.10920.24660.04270.0711-0.25960.2391-0.01010.8465-0.0262-0.03210.78970.01450.596312.0808-53.1144-4.9452
272.90730.95430.10920.39710.09780.05661.2837-0.69580.30880.7659-0.223-0.28281.04010.30280.17221.0618-0.0823-0.47960.54180.07811.572318.5488-48.4920.7929
282.1863-0.5563-0.17070.3175-0.33770.66850.6211-0.88620.5140.8053-0.2094-0.7545-0.32130.19281.75631.4665-0.126-0.48971.1671-0.51330.997521.2348-56.327928.9224
290.3836-1.5215-0.41271.0226-1.11292.7456-0.3980.2590.00870.05150.01620.2779-0.017-0.50930.2140.7296-0.0536-0.0230.6423-0.0070.82240.6117-41.219-7.3167
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 112 )A2 - 112
2X-RAY DIFFRACTION2chain 'A' and (resid 113 through 123 )A113 - 123
3X-RAY DIFFRACTION3chain 'A' and (resid 124 through 157 )A124 - 157
4X-RAY DIFFRACTION4chain 'B' and (resid 3 through 41 )B3 - 41
5X-RAY DIFFRACTION5chain 'B' and (resid 42 through 77 )B42 - 77
6X-RAY DIFFRACTION6chain 'B' and (resid 78 through 123 )B78 - 123
7X-RAY DIFFRACTION7chain 'B' and (resid 124 through 150 )B124 - 150
8X-RAY DIFFRACTION8chain 'B' and (resid 151 through 157 )B151 - 157
9X-RAY DIFFRACTION9chain 'C' and (resid 12 through 80 )C12 - 80
10X-RAY DIFFRACTION10chain 'C' and (resid 81 through 111 )C81 - 111
11X-RAY DIFFRACTION11chain 'C' and (resid 112 through 170 )C112 - 170
12X-RAY DIFFRACTION12chain 'D' and (resid 16 through 22 )D16 - 22
13X-RAY DIFFRACTION13chain 'D' and (resid 23 through 29 )D23 - 29
14X-RAY DIFFRACTION14chain 'D' and (resid 30 through 82 )D30 - 82
15X-RAY DIFFRACTION15chain 'D' and (resid 83 through 121 )D83 - 121
16X-RAY DIFFRACTION16chain 'D' and (resid 122 through 129 )D122 - 129
17X-RAY DIFFRACTION17chain 'D' and (resid 130 through 172 )D130 - 172
18X-RAY DIFFRACTION18chain 'D' and (resid 173 through 182 )D173 - 182
19X-RAY DIFFRACTION19chain 'E' and (resid 13 through 21 )E13 - 21
20X-RAY DIFFRACTION20chain 'E' and (resid 22 through 80 )E22 - 80
21X-RAY DIFFRACTION21chain 'E' and (resid 81 through 85 )E81 - 85
22X-RAY DIFFRACTION22chain 'E' and (resid 86 through 96 )E86 - 96
23X-RAY DIFFRACTION23chain 'E' and (resid 97 through 110 )E97 - 110
24X-RAY DIFFRACTION24chain 'E' and (resid 111 through 129 )E111 - 129
25X-RAY DIFFRACTION25chain 'E' and (resid 130 through 173 )E130 - 173
26X-RAY DIFFRACTION26chain 'F' and (resid 18 through 88 )F18 - 88
27X-RAY DIFFRACTION27chain 'F' and (resid 89 through 110 )F89 - 110
28X-RAY DIFFRACTION28chain 'F' and (resid 111 through 131 )F111 - 131
29X-RAY DIFFRACTION29chain 'F' and (resid 132 through 182 )F132 - 182

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