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- PDB-3bfo: Crystal structure of Ig-like C2-type 2 domain of the human Mucosa... -

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Basic information

Entry
Database: PDB / ID: 3bfo
TitleCrystal structure of Ig-like C2-type 2 domain of the human Mucosa-associated lymphoid tissue lymphoma translocation protein 1
ComponentsMucosa-associated lymphoid tissue lymphoma translocation protein 1 (Isoform 2)
KeywordsHYDROLASE / Immunoglobulin domain / Nucleus / Protease / Ubl conjugation pathway / Structural Genomics Consortium / SGC / Alternative splicing / Chromosomal rearrangement / Cytoplasm
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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
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: 1.15 Å
AuthorsWalker, J.R. / Akutsu, M. / Littler, D.R. / Li, Y. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Structure of the Ig-like C2-type 2 domain of the human Mucosa-associated lymphoid tissue lymphoma translocation protein 1.
Authors: Walker, J.R. / Akutsu, M. / Littler, D.R. / Li, Y. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S.
History
DepositionNov 22, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Assembly

Deposited unit
A: Mucosa-associated lymphoid tissue lymphoma translocation protein 1 (Isoform 2)
B: Mucosa-associated lymphoid tissue lymphoma translocation protein 1 (Isoform 2)
C: Mucosa-associated lymphoid tissue lymphoma translocation protein 1 (Isoform 2)
D: Mucosa-associated lymphoid tissue lymphoma translocation protein 1 (Isoform 2)


Theoretical massNumber of molelcules
Total (without water)42,0604
Polymers42,0604
Non-polymers00
Water7,170398
1
A: Mucosa-associated lymphoid tissue lymphoma translocation protein 1 (Isoform 2)


Theoretical massNumber of molelcules
Total (without water)10,5151
Polymers10,5151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Mucosa-associated lymphoid tissue lymphoma translocation protein 1 (Isoform 2)


Theoretical massNumber of molelcules
Total (without water)10,5151
Polymers10,5151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Mucosa-associated lymphoid tissue lymphoma translocation protein 1 (Isoform 2)


Theoretical massNumber of molelcules
Total (without water)10,5151
Polymers10,5151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Mucosa-associated lymphoid tissue lymphoma translocation protein 1 (Isoform 2)


Theoretical massNumber of molelcules
Total (without water)10,5151
Polymers10,5151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.944, 43.640, 49.595
Angle α, β, γ (deg.)66.50, 90.00, 90.02
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Mucosa-associated lymphoid tissue lymphoma translocation protein 1 (Isoform 2) / MALT lymphoma-associated translocation / Paracaspase


Mass: 10515.014 Da / Num. of mol.: 4
Fragment: Ig-like C2-type 2 domain: Residues 226-314 of Isoform 2 (Q9UDY8-2)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MALT1, MLT / Plasmid: pET28a-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9UDY8, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / 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: 1.88 Å3/Da / Density % sol: 34.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1:1 volume ratio of protein solution (50 mg/mL) and reservoir solution (30% PEG MME 550, 0.2 M Ammonium sulfate, 0.1 M Sodium cacodylate pH 6.5), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9179 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 5, 2007 / Details: Rh coated Si monochromatic mirrors
RadiationMonochromator: Horizontal bent Si(111), asymmetrically cut with water cooled Cu Block
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9179 Å / Relative weight: 1
ReflectionResolution: 1.15→25 Å / Num. all: 103829 / Num. obs: 103829 / % possible obs: 94.6 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Rsym value: 0.06 / Net I/σ(I): 22
Reflection shellResolution: 1.15→1.19 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.48 / Num. unique all: 10043 / Rsym value: 0.651 / % possible all: 91.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1U2H, 2AW2, 1CS6

1u2h

2aw2

1cs6


Resolution: 1.15→25 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.486 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21182 5145 5 %RANDOM
Rwork0.17708 ---
obs0.17882 98073 94.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.976 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å20.17 Å2-0.19 Å2
2---0.67 Å20.63 Å2
3----0.76 Å2
Refinement stepCycle: LAST / Resolution: 1.15→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3040 0 0 401 3441
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223153
X-RAY DIFFRACTIONr_angle_refined_deg1.831.9684343
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.175410
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.07625.161124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.73915579
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.895156
X-RAY DIFFRACTIONr_chiral_restr0.1280.2475
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022438
X-RAY DIFFRACTIONr_nbd_refined0.2260.21408
X-RAY DIFFRACTIONr_nbtor_refined0.3130.22213
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2297
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2320.2102
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.248
X-RAY DIFFRACTIONr_mcbond_it2.5351.51990
X-RAY DIFFRACTIONr_mcangle_it3.33723226
X-RAY DIFFRACTIONr_scbond_it4.00631361
X-RAY DIFFRACTIONr_scangle_it5.094.51117
X-RAY DIFFRACTIONr_rigid_bond_restr2.79233351
X-RAY DIFFRACTIONr_sphericity_free9.7063401
X-RAY DIFFRACTIONr_sphericity_bonded6.54333040
LS refinement shellResolution: 1.15→1.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 379 -
Rwork0.265 7040 -
obs--91.66 %

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