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- PDB-3uo8: Crystal structure of the MALT1 paracaspase (P1 form) -

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Basic information

Entry
Database: PDB / ID: 3uo8
TitleCrystal structure of the MALT1 paracaspase (P1 form)
Components
  • Mucosa-associated lymphoid tissue lymphoma translocation protein 1
  • Z-Val-Arg-Pro-DL-Arg-fluoromethylketone
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Paracaspase / Lymphoma / NF-KB Signalling / Caspase fold / Immunoglobulin Fold / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


polkadots / B-1 B cell differentiation / positive regulation of T-helper 17 cell differentiation / regulation of T cell receptor signaling pathway / CBM complex / 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 / regulation of T cell receptor signaling pathway / CBM complex / response to fungus / activation of NF-kappaB-inducing kinase activity / CLEC7A/inflammasome pathway / nuclear export / B cell activation / small molecule binding / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / T cell proliferation / lipopolysaccharide-mediated signaling pathway / positive regulation of interleukin-2 production / proteolysis involved in protein catabolic process / positive regulation of protein ubiquitination / positive regulation of interleukin-1 beta production / Activation of NF-kappaB in B cells / defense response / fibrillar center / CLEC7A (Dectin-1) signaling / positive regulation of T cell cytokine production / FCERI mediated NF-kB activation / ubiquitin-protein transferase activity / : / Downstream TCR signaling / positive regulation of NF-kappaB transcription factor activity / peptidase activity / T cell receptor signaling pathway / positive regulation of canonical NF-kappaB signal transduction / regulation of apoptotic process / endopeptidase activity / protease binding / 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 / 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. / : ...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
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: 1.9 Å
AuthorsJeffrey, P.D. / Yu, J.W. / Shi, Y.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Crystal structure of the mucosa-associated lymphoid tissue lymphoma translocation 1 (MALT1) paracaspase region.
Authors: Yu, J.W. / Jeffrey, P.D. / Ha, J.Y. / Yang, X. / Shi, Y.
History
DepositionNov 16, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2012Group: Database references
Revision 1.2Dec 12, 2012Group: Other
Revision 1.3Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Mucosa-associated lymphoid tissue lymphoma translocation protein 1
C: Mucosa-associated lymphoid tissue lymphoma translocation protein 1
L: Z-Val-Arg-Pro-DL-Arg-fluoromethylketone
M: Z-Val-Arg-Pro-DL-Arg-fluoromethylketone


Theoretical massNumber of molelcules
Total (without water)90,2594
Polymers90,2594
Non-polymers00
Water3,999222
1
B: Mucosa-associated lymphoid tissue lymphoma translocation protein 1
L: Z-Val-Arg-Pro-DL-Arg-fluoromethylketone


Theoretical massNumber of molelcules
Total (without water)45,1292
Polymers45,1292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint0 kcal/mol
Surface area16810 Å2
MethodPISA
2
C: Mucosa-associated lymphoid tissue lymphoma translocation protein 1
M: Z-Val-Arg-Pro-DL-Arg-fluoromethylketone


Theoretical massNumber of molelcules
Total (without water)45,1292
Polymers45,1292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint0 kcal/mol
Surface area16720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.235, 61.158, 71.126
Angle α, β, γ (deg.)108.590, 97.230, 117.230
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 44432.090 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 339-719
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: Protein/peptide Z-Val-Arg-Pro-DL-Arg-fluoromethylketone / MALT1 Inhibitor / Z-VRPR-FMK


Type: Oligopeptide / Class: Inhibitor / Mass: 697.244 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: The peptide was chemically synthesized.
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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.36 Å3/Da / Density % sol: 47.78 % / Mosaicity: 0.475 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M MES (pH 6.0), 0.2M calcium acetate, 2% benzamidine, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.97891 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 28, 2009
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97891 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 63071 / Num. obs: 63071 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Rmerge(I) obs: 0.051 / Χ2: 0.996 / Net I/σ(I): 9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.972.70.49262881.161196.7
1.97-2.052.70.34662771.103196.9
2.05-2.142.70.24762821.084197
2.14-2.252.70.17463101.073197.3
2.25-2.392.70.12562831.031197.7
2.39-2.582.70.09563780.987197.9
2.58-2.842.70.06663780.953198.1
2.84-3.252.70.04463940.887198.6
3.25-4.092.70.03163670.847198.3
4.09-502.60.02961140.82194.3

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→34.262 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8035 / SU ML: 0.27 / σ(F): 0.05 / Phase error: 27.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2497 3036 5.07 %Random
Rwork0.2066 ---
all0.2089 59902 --
obs0.2089 59902 92.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.499 Å2 / ksol: 0.436 e/Å3
Displacement parametersBiso max: 213.44 Å2 / Biso mean: 48.7393 Å2 / Biso min: 12.87 Å2
Baniso -1Baniso -2Baniso -3
1-7.0401 Å26.3817 Å2-2.0965 Å2
2---4.0201 Å25.8794 Å2
3----3.02 Å2
Refinement stepCycle: LAST / Resolution: 1.9→34.262 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5782 0 0 222 6004
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065883
X-RAY DIFFRACTIONf_angle_d0.9917950
X-RAY DIFFRACTIONf_chiral_restr0.06918
X-RAY DIFFRACTIONf_plane_restr0.0041012
X-RAY DIFFRACTIONf_dihedral_angle_d13.1262208
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.92970.39721110.27462179229078
1.9297-1.96130.26891240.24152315243983
1.9613-1.99510.29351370.22322395253285
1.9951-2.03140.24171190.21892429254887
2.0314-2.07050.27361380.22422433257187
2.0705-2.11270.2891380.2132502264089
2.1127-2.15870.24211340.20122533266791
2.1587-2.20890.2651240.19742551267591
2.2089-2.26410.25261380.18452618275692
2.2641-2.32530.21811450.18262579272493
2.3253-2.39370.24411340.19232616275094
2.3937-2.4710.29941420.20212682282495
2.471-2.55920.26481520.21342677282996
2.5592-2.66170.26891470.21232721286896
2.6617-2.78280.27411180.2032727284597
2.7828-2.92940.27951420.21842701284397
2.9294-3.11280.2611240.21972752287698
3.1128-3.3530.25981610.22172751291298
3.353-3.690.26041410.20672743288498
3.69-4.22320.18871710.18352711288298
4.2232-5.31750.20271490.1742684283396
5.3175-34.2680.2951470.24662567271492
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)
10.644-0.49380.37441.1553-0.78561.6917-0.08830.04560.1285-0.03070.0013-0.18090.0672-0.11750.0840.1365-0.00620.02010.1543-0.02070.1932-29.47174.8808-16.8053
21.1639-0.55380.96452.4398-1.38271.1532-0.3904-0.19730.0893-0.27860.1711-0.1962-0.198-0.15340.19150.38170.0319-0.04180.23250.0430.2235-42.645228.3451-38.4258
31.2429-0.84920.58131.1848-1.08251.2113-0.0532-0.02810.07970.0352-0.018-0.14480.0983-0.03120.06660.1773-0.01470.01220.166-0.0210.1735-20.2302-13.6832.3274
41.89620.25180.38641.2524-0.94961.09090.0405-0.4117-0.2007-0.2625-0.2008-0.13410.1316-0.17640.12560.26810.0062-0.0130.29530.05650.1973-10.7341-35.22725.7806
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN L OR (CHAIN B AND RESID 338:565)L0
2X-RAY DIFFRACTION2CHAIN B AND RESID 580:715B580 - 715
3X-RAY DIFFRACTION3CHAIN M OR (CHAIN C AND RESID 338:565)M0
4X-RAY DIFFRACTION4CHAIN C AND RESID 577:718C577 - 718

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