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- PDB-8u38: Structure of a bacterial multi-ubiquitin domain protein -

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Basic information

Entry
Database: PDB / ID: 8u38
TitleStructure of a bacterial multi-ubiquitin domain protein
ComponentsMethylobacterium brachiatum Ubl-BilA
KeywordsPROTEIN BINDING / antiviral / anti-phage / ubiquitin
Function / homologyPHOSPHATE ION
Function and homology information
Biological speciesMethylobacterium brachiatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.04 Å
AuthorsYe, Q. / Gong, M. / Corbett, K.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM144121 United States
CitationJournal: Structure / Year: 2025
Title: Structural diversity and oligomerization of bacterial ubiquitin-like proteins.
Authors: Minheng Gong / Qiaozhen Ye / Yajie Gu / Lydia R Chambers / Andrey A Bobkov / Neal K Arakawa / Mariusz Matyszewski / Kevin D Corbett /
Abstract: Bacteria possess a variety of operons with homology to eukaryotic ubiquitination pathways that encode predicted E1, E2, E3, deubiquitinase, and ubiquitin-like proteins. Some of these pathways have ...Bacteria possess a variety of operons with homology to eukaryotic ubiquitination pathways that encode predicted E1, E2, E3, deubiquitinase, and ubiquitin-like proteins. Some of these pathways have recently been shown to function in anti-bacteriophage immunity, but the biological functions of others remain unknown. Here, we show that ubiquitin-like proteins in two bacterial operon families show surprising architectural diversity, possessing one to three β-grasp domains preceded by diverse N-terminal domains. We find that a large group of bacterial ubiquitin-like proteins possess three β-grasp domains and form homodimers and helical filaments mediated by conserved Ca ion binding sites. Our findings highlight a distinctive mode of self-assembly for ubiquitin-like proteins and suggest that Ca-mediated ubiquitin-like protein filament assembly and/or disassembly enables cells to sense and respond to stress conditions that alter intracellular metal ion concentration.
History
DepositionSep 7, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methylobacterium brachiatum Ubl-BilA
B: Methylobacterium brachiatum Ubl-BilA
C: Methylobacterium brachiatum Ubl-BilA
D: Methylobacterium brachiatum Ubl-BilA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,76515
Polymers108,0494
Non-polymers71511
Water95553
1
A: Methylobacterium brachiatum Ubl-BilA
B: Methylobacterium brachiatum Ubl-BilA
C: Methylobacterium brachiatum Ubl-BilA
D: Methylobacterium brachiatum Ubl-BilA
hetero molecules

A: Methylobacterium brachiatum Ubl-BilA
B: Methylobacterium brachiatum Ubl-BilA
C: Methylobacterium brachiatum Ubl-BilA
D: Methylobacterium brachiatum Ubl-BilA
hetero molecules

A: Methylobacterium brachiatum Ubl-BilA
B: Methylobacterium brachiatum Ubl-BilA
C: Methylobacterium brachiatum Ubl-BilA
D: Methylobacterium brachiatum Ubl-BilA
hetero molecules

A: Methylobacterium brachiatum Ubl-BilA
B: Methylobacterium brachiatum Ubl-BilA
C: Methylobacterium brachiatum Ubl-BilA
D: Methylobacterium brachiatum Ubl-BilA
hetero molecules

A: Methylobacterium brachiatum Ubl-BilA
B: Methylobacterium brachiatum Ubl-BilA
C: Methylobacterium brachiatum Ubl-BilA
D: Methylobacterium brachiatum Ubl-BilA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)543,82375
Polymers540,24620
Non-polymers3,57755
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z+1/31
crystal symmetry operation2_564-y,x-y+1,z-2/31
crystal symmetry operation3_454-x+y-1,-x,z-1/31
crystal symmetry operation3_455-x+y-1,-x,z+2/31
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.024, 136.024, 105.807
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 10 through 154 or (resid 155...
d_2ens_1(chain "B" and (resid 10 through 154 or (resid 155...
d_3ens_1(chain "C" and ((resid 10 and (name N or name...
d_4ens_1chain "D"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 10 - 156 / Label seq-ID: 10 - 156

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB
d_3CC
d_4DD

NCS oper:
IDCodeMatrixVector
1given(-0.96534400337, 0.260980081133, -0.000593641077868), (0.260917178747, 0.965056133499, -0.0242669534756), (-0.00576029452364, -0.023580849173, -0.999705337867)-143.871001909, 18.0067914075, -87.1406030364
2given(0.507026519023, 0.861862161742, -0.0108500306134), (-0.861928578015, 0.507011511421, -0.00429577549976), (0.00179872406167, 0.0115300235561, 0.999931909256)-67.9933658631, -39.3126837726, -17.7627620064
3given(-0.714946319787, -0.699140982506, 0.00732437053109), (-0.699134619155, 0.714742864085, -0.0187995356046), (0.00790848422227, -0.018561379796, -0.999796444811)-88.4698505414, -36.8318890257, -68.778883735

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Components

#1: Protein
Methylobacterium brachiatum Ubl-BilA


Mass: 27012.311 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylobacterium brachiatum (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN
Sequence detailsThe sequence was obtained from NCBI WP_230366735.1.

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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: 2.62 Å3/Da / Density % sol: 52.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 100 mM CAPS pH 10.5, 0.2 M Li2SO4, 1.2 M NaH2PO4, and 0.8 M K2HPO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97911 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 3.04→117.8 Å / Num. obs: 22162 / % possible obs: 100 % / Redundancy: 10 % / Biso Wilson estimate: 110.85 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.204 / Net I/σ(I): 14
Reflection shellResolution: 3.04→3.22 Å / Rmerge(I) obs: 3.416 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3521 / CC1/2: 0.433

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.04→117.8 Å / SU ML: 0.5013 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 35.29
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2751 1056 4.8 %
Rwork0.2356 20958 -
obs0.2376 22014 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 117.6 Å2
Refinement stepCycle: LAST / Resolution: 3.04→117.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4695 0 31 53 4779
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00264828
X-RAY DIFFRACTIONf_angle_d0.56176589
X-RAY DIFFRACTIONf_chiral_restr0.0489742
X-RAY DIFFRACTIONf_plane_restr0.0041872
X-RAY DIFFRACTIONf_dihedral_angle_d10.64791743
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.46805567802
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.432039738495
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.408567181728
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.04-3.180.41081120.34862532X-RAY DIFFRACTION96.89
3.18-3.340.35371130.30892597X-RAY DIFFRACTION99.71
3.34-3.550.3191420.31792595X-RAY DIFFRACTION99.82
3.55-3.830.28681550.25752589X-RAY DIFFRACTION99.75
3.83-4.210.29391200.23122638X-RAY DIFFRACTION100
4.22-4.820.2561440.19782603X-RAY DIFFRACTION99.85
4.82-6.080.25431160.24442668X-RAY DIFFRACTION99.82
6.08-117.80.25921540.20992736X-RAY DIFFRACTION99.45
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)
14.924144425883.402660144311.738281774934.636272563591.597195351794.450973907310.112883061202-0.118982271555-0.0141679983724-0.0676437965111-0.001859704767330.05796273779380.1299390810680.0974628256017-0.08149131284310.9438211971470.0722093249343-0.03950440528880.7081752179630.02466280777740.925154536976-64.42428629018.35335720041-27.4898511236
24.97836460959-2.90541008091.090786819126.4032557964-2.338888111543.956535608670.2478978029820.432774157509-0.1891049043170.0328326665062-0.221034118688-0.1443977697020.2106773120050.219445686817-0.1127864429961.10521591592-0.0367448102455-0.05301116216690.900880121997-0.1103165068690.821714987699-79.58985517449.92596722982-59.4249830829
35.03622690498-1.601947894051.626028140083.36389771385-0.2643842914644.17992356063-0.327005413775-0.0830162500506-0.03751466060270.3291559706270.3924281210760.3286438632070.126548241061-0.293065061885-0.1525917157221.153268553590.1010872402540.06444853547280.8149686915370.09305737210770.919550549042-93.226729617420.7125604635-45.0982939401
46.453583029390.2162387698192.705977273742.343905976-0.7792877449882.51143120247-0.2504162421810.6100996916820.17350261311-0.4178010351280.278378738857-0.2753740934560.006576452058190.354986637256-0.04220595648221.30174573812-0.07905532331090.1105432538871.12780541264-0.05467949397531.02010966352-48.615361199514.5989827754-41.8936092896
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain AAA9 - 1571 - 149
22chain BBB10 - 1561 - 147
33chain CCC9 - 1591 - 151
44chain DDD10 - 1561 - 147

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