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- PDB-3v4l: Mouse MALT1(caspase-IG3 domains) in complex with a irreversible p... -

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Basic information

Entry
Database: PDB / ID: 3v4l
TitleMouse MALT1(caspase-IG3 domains) in complex with a irreversible peptidic inhibitor
Components
  • MALT1 Inhibitor
  • Mucosa-associated lymphoid tissue lymphoma translocation protein 1 homolog
KeywordsHYDROLASE/INHIBITOR / Caspase / IG like / Hydrolyse / TRAF6 / Cytosol / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


CLEC7A/inflammasome pathway / polkadots / B-1 B cell differentiation / positive regulation of T-helper 17 cell differentiation / regulation of T cell receptor signaling pathway / CBM complex / Activation of NF-kappaB in B cells / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / response to fungus ...CLEC7A/inflammasome pathway / polkadots / B-1 B cell differentiation / positive regulation of T-helper 17 cell differentiation / regulation of T cell receptor signaling pathway / CBM complex / Activation of NF-kappaB in B cells / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / response to fungus / Downstream TCR signaling / activation of NF-kappaB-inducing kinase activity / kinase activator activity / nuclear export / B cell activation / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / T cell proliferation / lipopolysaccharide-mediated signaling pathway / positive regulation of interleukin-2 production / positive regulation of interleukin-1 beta production / fibrillar center / positive regulation of T cell cytokine production / ubiquitin-protein transferase activity / : / positive regulation of T cell activation / positive regulation of NF-kappaB transcription factor activity / peptidase activity / T cell receptor signaling pathway / regulation of apoptotic process / cellular response to lipopolysaccharide / protease binding / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cysteine-type endopeptidase activity / innate immune response / perinuclear region of cytoplasm / protein-containing complex / proteolysis / identical protein binding / nucleus / cytosol / cytoplasm
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. / Caspase domain ...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 / 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
N-[(benzyloxy)carbonyl]-L-valyl-N~5~-[amino(iminio)methyl]-L-ornithyl-N-[(3R)-6-{[amino(iminio)methyl]amino}-1-fluoro-2-oxohexan-3-yl]-L-prolinamide / Mucosa-associated lymphoid tissue lymphoma translocation protein 1 homolog
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsRenatus, M. / Wiesmann, C.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Structural Determinants of MALT1 Protease Activity.
Authors: Wiesmann, C. / Leder, L. / Blank, J. / Bernardi, A. / Melkko, S. / Decock, A. / D'Arcy, A. / Villard, F. / Erbel, P. / Hughes, N. / Freuler, F. / Nikolay, R. / Alves, J. / Bornancin, F. / Renatus, M.
History
DepositionDec 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1May 9, 2012Group: Database references
Revision 1.2Dec 12, 2012Group: Other
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Nov 29, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_related / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.db_name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mucosa-associated lymphoid tissue lymphoma translocation protein 1 homolog
B: MALT1 Inhibitor


Theoretical massNumber of molelcules
Total (without water)45,2682
Polymers45,2682
Non-polymers00
Water0
1
A: Mucosa-associated lymphoid tissue lymphoma translocation protein 1 homolog
B: MALT1 Inhibitor

A: Mucosa-associated lymphoid tissue lymphoma translocation protein 1 homolog
B: MALT1 Inhibitor


Theoretical massNumber of molelcules
Total (without water)90,5354
Polymers90,5354
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z1
Buried area5160 Å2
ΔGint-19 kcal/mol
Surface area32940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.861, 150.861, 91.822
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

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


Mass: 44570.285 Da / Num. of mol.: 1 / Fragment: UNP residues 338-832
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Malt1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q2TBA3, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Protein/peptide MALT1 Inhibitor / Z-VRPR-FMK


Type: Oligopeptide / Class: Inhibitor / Mass: 697.244 Da / Num. of mol.: 1 / Source method: obtained synthetically
References: N-[(benzyloxy)carbonyl]-L-valyl-N~5~-[amino(iminio)methyl]-L-ornithyl-N-[(3R)-6-{[amino(iminio)methyl]amino}-1-fluoro-2-oxohexan-3-yl]-L-prolinamide
Compound detailsA LARGE SECTION OF THE C-TERMINAL RESIDUES 730-832 WAS CLEAVED DUE TO PROTEASE ACITIVITY DURING ...A LARGE SECTION OF THE C-TERMINAL RESIDUES 730-832 WAS CLEAVED DUE TO PROTEASE ACITIVITY DURING CRYSTALLIZATION

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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: 3.33 Å3/Da / Density % sol: 63.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: 0.2 M Li2SO4, 0.1M Bis-tris propane pH7, pH 7.0, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 8, 2010
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.15→60 Å / Num. obs: 10950 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 80.75 Å2 / Rsym value: 0.149
Reflection shellResolution: 3.15→3.28 Å / Redundancy: 13 % / Mean I/σ(I) obs: 3.8 / Rsym value: 0.0803 / % possible all: 97.5

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Processing

Software
NameVersionClassification
Adxvdata processing
PHASERphasing
BUSTER2.11.2refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.15→58.29 Å / Cor.coef. Fo:Fc: 0.9028 / Cor.coef. Fo:Fc free: 0.8753 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2311 548 5 %RANDOM
Rwork0.1782 ---
obs0.1808 10950 98.53 %-
Displacement parametersBiso mean: 69.9 Å2
Baniso -1Baniso -2Baniso -3
1--15.6168 Å20 Å20 Å2
2---15.6168 Å20 Å2
3---31.2336 Å2
Refine analyzeLuzzati coordinate error obs: 0.53 Å
Refinement stepCycle: LAST / Resolution: 3.15→58.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3097 0 0 0 3097
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013165HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.324282HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1104SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes83HARMONIC2
X-RAY DIFFRACTIONt_gen_planes449HARMONIC5
X-RAY DIFFRACTIONt_it3165HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3
X-RAY DIFFRACTIONt_other_torsion23.98
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion403SEMIHARMONIC5
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_contact3589SEMIHARMONIC4
LS refinement shellResolution: 3.15→3.45 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2956 127 5.01 %
Rwork0.2205 2406 -
all0.2241 2533 -
obs--98.53 %

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