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- PDB-3v4o: Human MALT1 (caspase domain) in complex with an irreversible pept... -

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Basic information

Entry
Database: PDB / ID: 3v4o
TitleHuman MALT1 (caspase domain) in complex with an irreversible peptidic inhibitor
Components
  • MALT1 Inhibitor
  • Mucosa-associated lymphoid tissue lymphoma translocation protein 1
KeywordsHYDROLASE/INHIBITOR / Caspase / Hydrolase / TRAF6 / BCL10 / Cytosolic / HYDROLASE-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 / Rossmann fold - #1460 / Immunoglobulin domain / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : ...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 / Rossmann fold / 3-Layer(aba) Sandwich / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _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
Revision 1.5Nov 29, 2023Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_name
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: MALT1 Inhibitor


Theoretical massNumber of molelcules
Total (without water)28,4072
Polymers28,4072
Non-polymers00
Water2,702150
1
A: Mucosa-associated lymphoid tissue lymphoma translocation protein 1
B: MALT1 Inhibitor

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


Theoretical massNumber of molelcules
Total (without water)56,8144
Polymers56,8144
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area5850 Å2
ΔGint-23 kcal/mol
Surface area19290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.500, 77.500, 180.493
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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


Mass: 27709.799 Da / Num. of mol.: 1 / Fragment: UNP residues 329-569
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MALT1, MLT / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9UDY8, 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: PDB-3v4l, 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.76 Å3/Da / Density % sol: 55.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: 20% PeG3550, 0.4 Ammonium nitrate, 0.1M Bis-tris propane, VAPOR DIFFUSION, temperature 298K, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 26, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
ReflectionResolution: 2.1→67.11 Å / Num. obs: 19456 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 13.2
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.536 / Mean I/σ(I) obs: 3.6 / % possible all: 99.7

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Processing

Software
NameVersionClassification
Adxvdata processing
PHASERphasing
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2PYO

2pyo


Resolution: 2.1→53.86 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.22827 973 FREE R VALUE TEST SET SIZE (%) : 5.0
Rwork0.17598 --
obs0.17856 18482 -
Refinement stepCycle: LAST / Resolution: 2.1→53.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1910 0 0 150 2060

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