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- PDB-7a41: MALT1 in complex with a NVS-MALT1 chemical probe -

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Basic information

Entry
Database: PDB / ID: 7a41
TitleMALT1 in complex with a NVS-MALT1 chemical probe
ComponentsMucosa-associated lymphoid tissue lymphoma translocation protein 1
KeywordsHYDROLASE / Allosteric Inhibitor / complex
Function / homology
Function and homology information


polkadots / B-1 B cell differentiation / positive regulation of T-helper 17 cell differentiation / CBM complex / regulation of T cell receptor signaling pathway / response to fungus / CLEC7A/inflammasome pathway / nuclear export / small molecule binding / B cell activation ...polkadots / B-1 B cell differentiation / positive regulation of T-helper 17 cell differentiation / CBM complex / regulation of T cell receptor signaling pathway / response to fungus / CLEC7A/inflammasome pathway / nuclear export / small molecule binding / B cell activation / endopeptidase activator activity / T cell proliferation / positive regulation of interleukin-2 production / proteolysis involved in protein catabolic process / lipopolysaccharide-mediated signaling pathway / positive regulation of interleukin-1 beta production / positive regulation of protein ubiquitination / Activation of NF-kappaB in B cells / defense response / positive regulation of T cell cytokine production / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / fibrillar center / ubiquitin-protein transferase activity / Downstream TCR signaling / peptidase activity / T cell receptor signaling pathway / protease binding / regulation of apoptotic process / endopeptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / positive regulation of canonical NF-kappaB signal transduction / innate immune response / cysteine-type endopeptidase activity / negative regulation of apoptotic process / perinuclear region of cytoplasm / protein-containing complex / proteolysis / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Mucosa-associated lymphoid tissue lymphoma translocation protein 1 / MALT1, death domain / MALT1 immunoglobulin-like domain / : / MALT1 Ig-like domain / Immunoglobulin domain / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : / Caspase domain ...Mucosa-associated lymphoid tissue lymphoma translocation protein 1 / MALT1, death domain / MALT1 immunoglobulin-like domain / : / MALT1 Ig-like domain / Immunoglobulin domain / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : / Caspase domain / Caspase-like domain superfamily / Immunoglobulin domain / Death-like domain superfamily / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Chem-QYQ / Mucosa-associated lymphoid tissue lymphoma translocation protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.13 Å
AuthorsRenatus, M.
CitationJournal: Not Published
Title: MALT1 in complex with a NVS-MALT1 chemical probe
Authors: Renatus, M.
History
DepositionAug 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mucosa-associated lymphoid tissue lymphoma translocation protein 1
B: Mucosa-associated lymphoid tissue lymphoma translocation protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,5855
Polymers91,3592
Non-polymers1,2263
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint2 kcal/mol
Surface area33210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.21, 106.57, 73.68
Angle α, β, γ (deg.)90, 111.84, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Mucosa-associated lymphoid tissue lymphoma translocation protein 1 / MALT lymphoma-associated translocation / Paracaspase


Mass: 45679.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MALT1, MLT / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9UDY8, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-QYQ / ~{N}-[(1~{S})-1-[4-[[2-chloranyl-7-[(1~{S})-1-methoxyethyl]pyrazolo[1,5-a]pyrimidin-6-yl]amino]phenyl]-2,2,2-tris(fluoranyl)ethyl]-~{N}-methyl-1,1-bis(oxidanylidene)thiane-4-carboxamide


Mass: 574.015 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H27ClF3N5O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.7 Å3/Da / Density % sol: 54.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Magnesium formate dehydrate 15% w/v PEG3550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99996 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99996 Å / Relative weight: 1
ReflectionResolution: 2.13→68.391 Å / Num. obs: 51061 / % possible obs: 99.3 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.026 / Rrim(I) all: 0.049 / Net I/σ(I): 16.9 / Num. measured all: 171768
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.5 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.13-2.1380.53518305220.8650.3370.634299.2
9.879-68.3910.018189753910.0110.02247.298.4

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XDS1.1.5data reduction
Aimless0.3.3data scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6yn8

6yn8


Resolution: 2.13→57.56 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.93 / SU R Cruickshank DPI: 0.199 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.192 / SU Rfree Blow DPI: 0.163 / SU Rfree Cruickshank DPI: 0.167
RfactorNum. reflection% reflectionSelection details
Rfree0.2298 2566 -RANDOM
Rwork0.2001 ---
obs0.2016 51036 99.1 %-
Displacement parametersBiso mean: 50.06 Å2
Baniso -1Baniso -2Baniso -3
1--0.0559 Å20 Å22.8061 Å2
2---11.7778 Å20 Å2
3---11.8337 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.13→57.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5680 0 80 162 5922
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0085890HARMONIC2
X-RAY DIFFRACTIONt_angle_deg17979HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2087SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes987HARMONIC5
X-RAY DIFFRACTIONt_it5890HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion747SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4481SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.2
X-RAY DIFFRACTIONt_other_torsion16.68
LS refinement shellResolution: 2.13→2.15 Å
RfactorNum. reflection% reflection
Rfree0.2383 50 -
Rwork0.2183 --
obs0.2193 1021 95.26 %

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