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- PDB-3k0w: Crystal structure of the tandem IG-like C2-type 2 domains of the ... -

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Basic information

Entry
Database: PDB / ID: 3k0w
TitleCrystal structure of the tandem IG-like C2-type 2 domains 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 / CHROMOSOMAL TRANSLOCATION / LYMPHOMA / UBL CONJUGATION PATHWAY / STRUCTURAL GENOMICS CONSORTIUM / SGC / Alternative splicing / Chromosomal rearrangement / Cytoplasm / Disulfide bond / Phosphoprotein / Polymorphism
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 / stimulatory C-type lectin receptor signaling pathway / Fc-epsilon receptor signaling pathway / 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 / Mucosa-associated lymphoid tissue lymphoma translocation protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWalker, J.R. / Qiu, L. / Butler-Cole, C. / Weigelt, J. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Structure of the Tandem Ig-Like C2-Type 2 Domains of the Human Mucosa-Associated Lymphoid Tissue Lymphoma Translocation Protein 1.
Authors: Walker, J.R. / Qiu, L. / Butler-Cole, C. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S.
History
DepositionSep 25, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9252
Polymers24,8901
Non-polymers351
Water25214
1
A: Mucosa-associated lymphoid tissue lymphoma translocation protein 1, isoform 2
hetero molecules

A: Mucosa-associated lymphoid tissue lymphoma translocation protein 1, isoform 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8514
Polymers49,7802
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
Buried area2250 Å2
ΔGint-7.3 kcal/mol
Surface area18570 Å2
MethodPISA
2
A: Mucosa-associated lymphoid tissue lymphoma translocation protein 1, isoform 2
hetero molecules

A: Mucosa-associated lymphoid tissue lymphoma translocation protein 1, isoform 2
hetero molecules

A: Mucosa-associated lymphoid tissue lymphoma translocation protein 1, isoform 2
hetero molecules

A: Mucosa-associated lymphoid tissue lymphoma translocation protein 1, isoform 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,7028
Polymers99,5604
Non-polymers1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
crystal symmetry operation9_555-x,-x+y,-z+1/31
crystal symmetry operation12_565x,x-y+1,-z+1/31
Buried area7190 Å2
ΔGint-35.6 kcal/mol
Surface area34460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.355, 90.355, 182.173
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, isoform 2 / MALT lymphoma-associated translocation / Paracaspase


Mass: 24890.014 Da / Num. of mol.: 1
Fragment: Tandem IG-like C2-type 2 domain: UNP residues 128-326
Source method: isolated from a genetically manipulated source
Details: THE SEQUENCE MGSSHHHHHHSSGLVPRGS BELONGS TO THE VECTOR.
Source: (gene. exp.) Homo sapiens (human) / Gene: MALT1, MLT / Plasmid: pET28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9UDY8-2, UniProt: Q9UDY8*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 4.31 Å3/Da / Density % sol: 71.48 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 1:1 VOLUME RATIO OF PROTEIN SOLUTION (10 mg/mL) AND RESERVOIR SOLUTION (1.5 M MAGNESIUM CHLORIDE, 0.1 M BICINE pH 9.0), VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 9, 2009 / Details: Mirrors
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.8→40.47 Å / Num. all: 11498 / Num. obs: 11498 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 18.8 % / Biso Wilson estimate: 96.13 Å2 / Rsym value: 0.082 / Net I/σ(I): 43.44
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 17.9 % / Mean I/σ(I) obs: 2.82 / Num. unique all: 1104 / Rsym value: 0.791 / % possible all: 91.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
BUSTER2.8.0refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3BFO

3bfo


Resolution: 2.8→40.47 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2489 549 4.8 %RANDOM
Rwork0.2183 ---
all0.2196 11447 --
obs0.2196 11447 --
Displacement parametersBiso mean: 87.14 Å2
Baniso -1Baniso -2Baniso -3
1--1.0991 Å20 Å20 Å2
2---1.0991 Å20 Å2
3---2.1982 Å2
Refinement stepCycle: LAST / Resolution: 2.8→40.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1457 0 1 14 1472
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.01
X-RAY DIFFRACTIONo_angle_deg1.32
LS refinement shellResolution: 2.8→3.07 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3238 138 5.22 %
Rwork0.2674 2506 -
obs-2644 -

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