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- PDB-8j5i: MALT1 death domain -

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Basic information

Entry
Database: PDB / ID: 8j5i
TitleMALT1 death domain
ComponentsMucosa-associated lymphoid tissue lymphoma translocation protein 1
KeywordsSIGNALING PROTEIN / CARMAs-BCL10-MALT1 complex / MALT lymphoma
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
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 ...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: 2.1 Å
AuthorsLo, Y.C. / Kuo, B.J.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)MOST 111-2311-B-006 -005 -MY3 Taiwan
CitationJournal: To Be Published
Title: MALT1 death domain
Authors: Lo, Y.C. / Kuo, B.J.
History
DepositionApr 22, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2024Provider: 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)10,8711
Polymers10,8711
Non-polymers00
Water1267
1
B: Mucosa-associated lymphoid tissue lymphoma translocation protein 1

B: Mucosa-associated lymphoid tissue lymphoma translocation protein 1


Theoretical massNumber of molelcules
Total (without water)21,7412
Polymers21,7412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
Buried area630 Å2
ΔGint-8 kcal/mol
Surface area12410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.232, 83.229, 85.403
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: 10870.658 Da / Num. of mol.: 1 / Fragment: death domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MALT1, MLT / Plasmid: pET28a / 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.: 7 / Source method: isolated from a natural source / Formula: H2O

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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: 2.88 Å3/Da / Density % sol: 57.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: PEG 3350, Tacsimate pH 6

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Data collection

DiffractionMean temperature: 103 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 10, 2019 / Details: Molecular Replacement
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 7761 / % possible obs: 99.24 % / Redundancy: 3.6 % / Biso Wilson estimate: 41.32 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.028 / Rrim(I) all: 0.054 / Χ2: 1.061 / Net I/av σ(I): 14.8 / Net I/σ(I): 14.8
Reflection shellResolution: 2.1→2.16 Å / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 2.98 / Num. unique obs: 728 / CC1/2: 1 / Rpim(I) all: 0.289 / Rrim(I) all: 0.568 / Χ2: 1.059

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→21.35 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 31.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2407 387 5.1 %
Rwork0.2179 --
obs0.2191 7594 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→21.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms756 0 0 7 763
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005764
X-RAY DIFFRACTIONf_angle_d0.8671028
X-RAY DIFFRACTIONf_dihedral_angle_d5.012106
X-RAY DIFFRACTIONf_chiral_restr0.034121
X-RAY DIFFRACTIONf_plane_restr0.008133
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.40.27421310.22362350X-RAY DIFFRACTION99
2.4-3.030.27881260.24772382X-RAY DIFFRACTION99
3.03-21.350.22231300.20562475X-RAY DIFFRACTION99
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)
17.84281.0221-1.10493.7757-2.03346.41520.18590.37860.6895-0.12840.27260.2813-0.5517-0.4963-0.33250.35130.04780.03660.28280.09020.37268.471333.29246.2253
22.4366-1.84821.89892.2555-0.66242.21180.0125-0.4828-0.7165-0.19570.19830.51950.42090.1208-0.19420.3715-0.01150.02590.46380.26170.519914.808517.809717.575
35.8876-0.52840.66158.41290.90039.34910.2487-0.15530.98630.4289-0.02510.5377-1.3624-0.3929-0.21440.4815-0.00220.10920.29750.11410.44062.141532.949316.326
43.34582.84182.07632.4212.02189.42710.45240.7725-0.77540.7206-0.2838-1.07851.11220.7391-0.09810.45150.10070.02230.57350.14510.584515.249224.257611.3463
55.4714-5.5163-0.86176.1766-0.21912.37090.2367-0.4689-1.62920.16750.83312.90641.40611.0653-1.07150.7187-0.1018-0.10040.73840.03510.93717.877119.31331.9883
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 71 through 102 )
2X-RAY DIFFRACTION2chain 'B' and (resid 103 through 124 )
3X-RAY DIFFRACTION3chain 'B' and (resid 28 through 47 )
4X-RAY DIFFRACTION4chain 'B' and (resid 48 through 64 )
5X-RAY DIFFRACTION5chain 'B' and (resid 65 through 70 )

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