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- PDB-9bp2: The death domain (DD) of the human mucosa associated lymphoid tis... -

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Basic information

Entry
Database: PDB / ID: 9bp2
TitleThe death domain (DD) of the human mucosa associated lymphoid tissue lymphoma translocation protein 1 (MALT1)
ComponentsMucosa-associated lymphoid tissue lymphoma translocation protein 1
KeywordsHYDROLASE / Death domain / MALT1
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 / lipopolysaccharide-mediated signaling pathway / 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 / defense response / positive regulation of T cell cytokine production / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / fibrillar center / positive regulation of NF-kappaB transcription factor activity / ubiquitin-protein transferase activity / Downstream TCR signaling / peptidase activity / T cell receptor signaling pathway / protease binding / regulation of apoptotic process / endopeptidase activity / positive regulation of canonical NF-kappaB signal transduction / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / innate immune response / cysteine-type endopeptidase activity / negative regulation of apoptotic process / perinuclear region of cytoplasm / protein-containing complex / proteolysis / identical protein binding / nucleus / cytosol / cytoplasm
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
Mucosa-associated lymphoid tissue lymphoma translocation protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsChen, C.-L. / Tesmer, J.J.G.
Funding support United States, 1items
OrganizationGrant numberCountry
American Heart Association834497 United States
CitationJournal: To Be Published
Title: The death domain (DD) of the human mucosa associated lymphoid tissue lymphoma translocation protein 1 (MALT1)
Authors: Chen, C.-L. / Tesmer, J.J.G.
History
DepositionMay 6, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)12,9871
Polymers12,9871
Non-polymers00
Water34219
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.527, 79.315, 86.389
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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


Mass: 12986.965 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 (E. coli)
References: UniProt: Q9UDY8, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
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: 2.28 Å3/Da / Density % sol: 45.98 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 6 / Details: PEG3350 20% MgCl2 0.2 M MES 0.1 M (pH6)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.01→29.21 Å / Num. obs: 12166 / % possible obs: 78.9 % / Redundancy: 1.6 % / Biso Wilson estimate: 24.39 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.01354 / Rpim(I) all: 0.01354 / Rrim(I) all: 0.01915 / Net I/σ(I): 34.44
Reflection shellResolution: 2.01→2.09 Å / Num. unique obs: 7726 / Rpim(I) all: 0.157

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.21_5207phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→29.21 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2577 1193 9.82 %
Rwork0.2181 --
obs0.2219 12154 78.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.01→29.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms761 0 0 19 780
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.612
X-RAY DIFFRACTIONf_dihedral_angle_d20.081319
X-RAY DIFFRACTIONf_chiral_restr0.027123
X-RAY DIFFRACTIONf_plane_restr0.008140
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.090.5236560.4581465X-RAY DIFFRACTION31
2.09-2.180.3614880.3434725X-RAY DIFFRACTION47
2.18-2.30.36581060.2538990X-RAY DIFFRACTION64
2.3-2.440.27921270.24261249X-RAY DIFFRACTION80
2.44-2.630.29031620.24511427X-RAY DIFFRACTION93
2.63-2.890.30081540.23411515X-RAY DIFFRACTION98
2.89-3.310.27911620.24071512X-RAY DIFFRACTION100
3.31-4.170.2141690.17641538X-RAY DIFFRACTION99
4.17-29.210.20021690.18581540X-RAY DIFFRACTION99

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