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- PDB-6yn8: Human MALT1(334-719) in complex with a tetrazole containing compound -

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Basic information

Entry
Database: PDB / ID: 6yn8
TitleHuman MALT1(334-719) in complex with a tetrazole containing compound
ComponentsMucosa-associated lymphoid tissue lymphoma translocation protein 1
KeywordsHYDROLASE / DIMER / Active Site inhibitor
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 / activation of NF-kappaB-inducing kinase activity / CLEC7A/inflammasome pathway / nuclear export / 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 / activation of NF-kappaB-inducing kinase activity / CLEC7A/inflammasome pathway / nuclear export / B cell activation / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / small molecule binding / T cell proliferation / lipopolysaccharide-mediated signaling pathway / positive regulation of interleukin-2 production / proteolysis involved in protein catabolic process / positive regulation of interleukin-1 beta production / positive regulation of protein ubiquitination / Activation of NF-kappaB in B cells / positive regulation of T cell cytokine production / CLEC7A (Dectin-1) signaling / fibrillar center / defense response / FCERI mediated NF-kB activation / ubiquitin-protein transferase activity / : / Downstream TCR signaling / peptidase activity / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / protease binding / endopeptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cysteine-type endopeptidase activity / innate immune response / negative regulation of apoptotic process / perinuclear region of cytoplasm / protein-containing complex / proteolysis / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Immunoglobulin-like - #3360 / Mucosa-associated lymphoid tissue lymphoma translocation protein 1 / MALT1, death domain / MALT1 immunoglobulin-like domain / MALT1 Ig-like domain / Rossmann fold - #1460 / Immunoglobulin domain / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : ...Immunoglobulin-like - #3360 / Mucosa-associated lymphoid tissue lymphoma translocation protein 1 / MALT1, death domain / MALT1 immunoglobulin-like domain / MALT1 Ig-like domain / Rossmann fold - #1460 / 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 / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-OZK / Mucosa-associated lymphoid tissue lymphoma translocation protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.052 Å
AuthorsRenatus, M.
CitationJournal: Advanced Therapeutics / Year: 2020
Title: Stabilizing Inactive Conformations of MALT1 as an Effective Approach to Inhibit Its Protease Activity
Authors: Hughes, N. / Erbel, P. / Bornancin, F. / Wiesmann, C. / Schiering, N. / Villard, F. / Decock, A. / Rubi, B. / Melkko, S. / Spanka, C. / Buschmann, N. / Pissot-Soldermann, C. / Simic, O. / ...Authors: Hughes, N. / Erbel, P. / Bornancin, F. / Wiesmann, C. / Schiering, N. / Villard, F. / Decock, A. / Rubi, B. / Melkko, S. / Spanka, C. / Buschmann, N. / Pissot-Soldermann, C. / Simic, O. / Beerli, R. / Sorge, M. / Tintelnot-Blomley, M. / Beltz, K. / Regnier, C.H. / Quancard, J. / Schlapbach, A. / Langlois, J. / Renatus, M.
History
DepositionApr 11, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4952
Polymers43,9841
Non-polymers5121
Water724
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.293, 106.356, 106.455
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-901-

HOH

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Components

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


Mass: 43983.512 Da / Num. of mol.: 1
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-OZK / 3-azanyl-3-methyl-~{N}-[(3~{R})-4-oxidanylidene-5-[[4-[2-(1~{H}-1,2,3,4-tetrazol-5-yl)phenyl]phenyl]methyl]-2,3-dihydro-1,5-benzoxazepin-3-yl]butanamide


Mass: 511.575 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H29N7O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.26 Å3/Da / Density % sol: 62.26 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 1.8 M Sodium/Potassium phosphate pH 6.9 10mg/ml protein in 25mM HEPES pH7.5, 50mM NaCl, 1mM TCEP. Mixed with compound (final concentration at 1mM)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 3.052→60.4 Å / Num. obs: 11243 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 105.64 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.033 / Rrim(I) all: 0.085 / Net I/σ(I): 15.8 / Num. measured all: 72615
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.052-3.0626.60.9357621160.8510.3941.0152.2100
14.105-60.45.10.0287131400.9990.0140.03240.498.6

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Processing

Software
NameVersionClassification
Aimless0.7.4 (13-Dec-2018)data scaling
BUSTER2.11.7 (6-FEB-2020)refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3v55

3v55


Resolution: 3.052→60.4 Å / Cor.coef. Fo:Fc: 0.871 / Cor.coef. Fo:Fc free: 0.868 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.373
RfactorNum. reflection% reflectionSelection details
Rfree0.244 547 4.87 %RANDOM
Rwork0.2128 ---
obs0.2143 11243 99.8 %-
Displacement parametersBiso max: 178.46 Å2 / Biso mean: 109.53 Å2 / Biso min: 49.96 Å2
Baniso -1Baniso -2Baniso -3
1--59.1364 Å20 Å20 Å2
2--14.081 Å20 Å2
3---45.0555 Å2
Refine analyzeLuzzati coordinate error obs: 0.47 Å
Refinement stepCycle: final / Resolution: 3.052→60.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2892 0 38 4 2934
Biso mean--78.41 77.96 -
Num. residues----365
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1063SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes528HARMONIC5
X-RAY DIFFRACTIONt_it2987HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion378SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1956SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2987HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg4042HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion2.92
X-RAY DIFFRACTIONt_other_torsion18.73
LS refinement shellResolution: 3.052→3.09 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.4104 26 6.24 %
Rwork0.3002 391 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -19.9235 Å / Origin y: -5.7631 Å / Origin z: -26.9817 Å
111213212223313233
T0.0371 Å2-0.1069 Å2-0.022 Å2--0.1684 Å20.0316 Å2---0.0506 Å2
L0.5473 °20.0048 °2-0.1739 °2-2.2228 °20.3716 °2--4.5903 °2
S-0.0229 Å °-0.0455 Å °0.0698 Å °-0.5442 Å °-0.0065 Å °0.0049 Å °-0.0327 Å °-0.0806 Å °0.0294 Å °
Refinement TLS groupSelection details: { A|* }

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