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- PDB-9me8: Co-crystal structure of maltose binding protein (MBP)-human SENP3... -

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Basic information

Entry
Database: PDB / ID: 9me8
TitleCo-crystal structure of maltose binding protein (MBP)-human SENP3 fusion protein in complex with PELP1 peptide
Components
  • Maltose/maltodextrin-binding periplasmic protein,Sentrin-specific protease 3
  • Proline-, glutamic acid- and leucine-rich protein 1
KeywordsHYDROLASE / cysteine protease / SUMO maturation / rixosome / ribosome biogenesis
Function / homology
Function and homology information


deSUMOylase activity / protein desumoylation / PTK6 Expression / SUMO binding / MLL1 complex / carbohydrate transmembrane transporter activity / maltose binding / cellular response to estrogen stimulus / maltose transport / maltodextrin transmembrane transport ...deSUMOylase activity / protein desumoylation / PTK6 Expression / SUMO binding / MLL1 complex / carbohydrate transmembrane transporter activity / maltose binding / cellular response to estrogen stimulus / maltose transport / maltodextrin transmembrane transport / negative regulation of double-strand break repair via homologous recombination / Major pathway of rRNA processing in the nucleolus and cytosol / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / cysteine-type peptidase activity / euchromatin / rRNA processing / outer membrane-bounded periplasmic space / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / nuclear body / intracellular membrane-bounded organelle / chromatin binding / nucleolus / positive regulation of transcription by RNA polymerase II / proteolysis / RNA binding / nucleoplasm / nucleus / membrane / cytoplasm
Similarity search - Function
Sentrin-specific protease 3/5, conserved domain / Sentrin-specific protease 3/5 N-terminal / Uncharacterised domain NUC202 / PELP1, middle domain / Pre-rRNA-processing protein RIX1, N-terminal / rRNA processing/ribosome biogenesis / Ulp1 protease family, C-terminal catalytic domain / Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein ...Sentrin-specific protease 3/5, conserved domain / Sentrin-specific protease 3/5 N-terminal / Uncharacterised domain NUC202 / PELP1, middle domain / Pre-rRNA-processing protein RIX1, N-terminal / rRNA processing/ribosome biogenesis / Ulp1 protease family, C-terminal catalytic domain / Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Papain-like cysteine peptidase superfamily / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
alpha-maltotetraose / Maltose/maltodextrin-binding periplasmic protein / Proline-, glutamic acid- and leucine-rich protein 1 / Sentrin-specific protease 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.93 Å
AuthorsKaminski, A.M. / Gordon, J. / Pedersen, L.C. / Stanley, R.E.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ZIA ES103247 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ZIC ES102645 United States
Department of Energy (DOE, United States)DE-SC0012704 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30M133893 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)KP1605010 United States
CitationJournal: Sci Adv / Year: 2025
Title: PELP1 coordinates the modular assembly and enzymatic activity of the rixosome complex.
Authors: Gordon, J. / Kaminski, A.M. / Bommu, S.R. / Skrajna, A. / Petrovich, R.M. / Pedersen, L.C. / McGinty, R.K. / Warren, A.J. / Stanley, R.E.
History
DepositionDec 6, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltose/maltodextrin-binding periplasmic protein,Sentrin-specific protease 3
B: Proline-, glutamic acid- and leucine-rich protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5114
Polymers73,8222
Non-polymers6902
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint1 kcal/mol
Surface area28670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.970, 140.970, 119.633
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Maltose/maltodextrin-binding periplasmic protein,Sentrin-specific protease 3 / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / SUMO-1-specific protease 3 / ...MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / SUMO-1-specific protease 3 / Sentrin/SUMO-specific protease SENP3


Mass: 71738.672 Da / Num. of mol.: 1 / Mutation: C532S
Source method: isolated from a genetically manipulated source
Details: fixed-arm fusion MBP-SENP3 / Source: (gene. exp.) Homo sapiens (human) / Gene: malE, Z5632, ECs5017, SENP3, SSP3, SUSP3 / Plasmid: pMALX / Production host: Escherichia coli (E. coli) / Strain (production host): LOBSTR
References: UniProt: P0AEY0, UniProt: Q9H4L4, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Protein/peptide Proline-, glutamic acid- and leucine-rich protein 1 / Modulator of non-genomic activity of estrogen receptor / Transcription factor HMX3


Mass: 2083.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q8IZL8
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotetraose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1a_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}LINUCSPDB-CARE
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 4.8 Å3/Da / Density % sol: 74.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.085M HEPES pH 7.5, 17-20% (v/v) PEG8000

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9202 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 25, 2024
RadiationMonochromator: double crystal Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9202 Å / Relative weight: 1
ReflectionResolution: 2.93→34.71 Å / Num. obs: 28983 / % possible obs: 96.6 % / Redundancy: 11.4 % / Biso Wilson estimate: 65.73 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.296 / Rpim(I) all: 0.091 / Rrim(I) all: 0.31 / Net I/σ(I): 8.6
Reflection shellResolution: 2.93→2.98 Å / Redundancy: 12.1 % / Rmerge(I) obs: 3.518 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1468 / CC1/2: 0.35 / Rpim(I) all: 1.051 / Rrim(I) all: 3.673 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.93→34.71 Å / SU ML: 0.4015 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.5116
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2322 1475 5.09 %random selection
Rwork0.2019 27503 --
obs0.2035 28978 96.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.76 Å2
Refinement stepCycle: LAST / Resolution: 2.93→34.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5098 0 46 5 5149
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00585275
X-RAY DIFFRACTIONf_angle_d0.75227169
X-RAY DIFFRACTIONf_chiral_restr0.0448799
X-RAY DIFFRACTIONf_plane_restr0.0056922
X-RAY DIFFRACTIONf_dihedral_angle_d13.43841961
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.93-3.020.38661510.34582520X-RAY DIFFRACTION99.78
3.02-3.130.33911050.31992598X-RAY DIFFRACTION99.93
3.13-3.250.38071240.3012540X-RAY DIFFRACTION99.85
3.25-3.40.29861300.26242574X-RAY DIFFRACTION99.96
3.4-3.580.27991500.24782114X-RAY DIFFRACTION83.67
3.58-3.80.26311290.21872210X-RAY DIFFRACTION85.96
3.8-4.10.23281250.19392412X-RAY DIFFRACTION93.34
4.1-4.510.18611430.16482581X-RAY DIFFRACTION99.96
4.51-5.160.19091190.15582622X-RAY DIFFRACTION100
5.16-6.490.20441390.1882616X-RAY DIFFRACTION100
6.49-34.710.17121600.15272716X-RAY DIFFRACTION99.79
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)
11.908740900280.167001301833-0.3270563753793.27257370266-0.4928376452521.40227001266-0.02158711768380.02255815579110.009374264759610.5475571055070.09054813827890.240345522651-0.0172409298702-0.106587203656.24866416697E-90.7051114865240.1265517617710.1334790941630.7210262301320.02771489517130.60988703899251.00807957511.02949587848.9607933977
20.31187241772-0.524477070777-0.4338588753041.639321654921.255130360672.95302481827-0.036342724828-0.01668447808840.05231780616110.1002557433790.0852662857650.1882598447250.0366376965517-0.120658087348-2.84104354595E-50.567369616046-0.0653206717354-0.03799892860410.7300839403610.04341001504140.68575000477557.3241597062-32.865894636521.2407730879
30.0910771255768-0.0192461458510.05678507646310.0873071525885-0.04290755744980.0477779497990.2660832550770.187583465992-0.632963850401-0.01530168446350.00531326334321-0.06439728518040.75016686953-0.139998742855-1.38383124767E-60.912488140208-0.0285450527675-0.1156174559890.7760055055560.01601616105630.77745365899664.3972830439-55.663186346314.8784546758
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain A and resid 1:370AA1 - 3701 - 370
22chain A and resid 1311:1574AA1311 - 1574371 - 634
33chain B and resid 764:781BB764 - 7811 - 18

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