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- PDB-2g7r: X-ray structure of the death domain of the human mucosa associate... -

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Basic information

Entry
Database: PDB / ID: 2g7r
TitleX-ray structure of the death domain of the human mucosa associated lymphoid tissue lymphoma translocation protein 1
ComponentsMucosa-associated lymphoid tissue lymphoma translocation protein 1
KeywordsHYDROLASE / DEATH DOMAIN / CHROMOSOMAL TRANSLOCATION / PROTEASE / STRUCTURAL GENOMICS CONSORTIUM / SGC
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 / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / 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
Mucosa-associated lymphoid tissue lymphoma translocation protein 1 / MALT1, death domain / MALT1 immunoglobulin-like domain / MALT1 Ig-like domain / Death Domain, Fas / Death Domain, Fas / 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 / Death Domain, Fas / Death Domain, Fas / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Mucosa-associated lymphoid tissue lymphoma translocation protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsWalker, J.R. / Wybenga-Groot, L. / Newman, E.M. / Finerty Jr., P.J. / Butler-Cole, C. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Bochkarev, A. ...Walker, J.R. / Wybenga-Groot, L. / Newman, E.M. / Finerty Jr., P.J. / Butler-Cole, C. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: X-ray structure of the death domain of the human mucosa associated lymphoid tissue lymphoma translocation protein 1
Authors: Wybenga-Groot, L. / Walker, J.R. / Newman, E.M. / Finerty Jr., P.J. / Butler-Cole, C. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Bochkarev, A. / Dhe-Paganon, S.
History
DepositionFeb 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance

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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
B: Mucosa-associated lymphoid tissue lymphoma translocation protein 1


Theoretical massNumber of molelcules
Total (without water)25,9742
Polymers25,9742
Non-polymers00
Water543
1
A: Mucosa-associated lymphoid tissue lymphoma translocation protein 1


Theoretical massNumber of molelcules
Total (without water)12,9871
Polymers12,9871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mucosa-associated lymphoid tissue lymphoma translocation protein 1


Theoretical massNumber of molelcules
Total (without water)12,9871
Polymers12,9871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.937, 88.910, 34.598
Angle α, β, γ (deg.)90.00, 113.45, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: THR / End label comp-ID: PRO / Refine code: 1 / Auth seq-ID: 29 - 124 / Label seq-ID: 20 - 115

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 12986.965 Da / Num. of mol.: 2 / Fragment: DEATH DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MALT1, MLT / Plasmid: PET28-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q9UDY8, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979 Å
DetectorType: SBC-3 / Detector: CCD / Date: Nov 30, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→19.791 Å / Num. all: 6654 / Num. obs: 6562 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 1.8 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 18
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 4 / Num. unique all: 643 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→19.8 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.892 / SU B: 29.556 / SU ML: 0.279 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.775 / ESU R Free: 0.361 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28417 292 4.4 %RANDOM
Rwork0.23605 ---
obs0.23807 6270 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.603 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å20.18 Å2
2--0.31 Å20 Å2
3----0.68 Å2
Refinement stepCycle: LAST / Resolution: 2.7→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1330 0 0 3 1333
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221342
X-RAY DIFFRACTIONr_angle_refined_deg1.5652.0461804
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5435166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.47724.23152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.85615268
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3941512
X-RAY DIFFRACTIONr_chiral_restr0.0940.2220
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02938
X-RAY DIFFRACTIONr_nbd_refined0.2560.2598
X-RAY DIFFRACTIONr_nbtor_refined0.310.2904
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1060.239
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2890.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1270.26
X-RAY DIFFRACTIONr_mcbond_it1.3123876
X-RAY DIFFRACTIONr_mcangle_it1.9941352
X-RAY DIFFRACTIONr_scbond_it2.7285508
X-RAY DIFFRACTIONr_scangle_it4.2127452
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 665 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.040.05
tight thermal0.150.5
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 26 -
Rwork0.213 428 -
obs--99.56 %
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)
12.51044.006-2.07336.3924-3.30841.71220.8368-1.40170.59160.937-0.70260.66861.03660.372-0.13420.3330.02130.05890.4990.02820.2195-17.807113.023915.4074
230.91058.89171.708911.7431-9.77562.75540.2467-1.2844-1.35930.2171-0.1946-0.80591.42560.0147-0.05210.22510.02780.05570.34080.03840.4808-23.06696.948710.1614
324.3216-31.536.381946.172311.954478.91120.14670.4975-3.1255-1.6899-1.79024.25731.07-1.35331.64350.27260.0176-0.020.1767-0.10310.5742-22.16138.09063.1151
421.20891.2216-1.59053.1938-6.132411.80220.82562.09970.3951-1.3732-1.4169-0.449-0.046-1.10770.59130.40020.25420.03750.575-0.03980.2503-17.850910.4735-3.9839
58.1611.3114-3.292627.0175-25.951625.4382-0.5680.96360.3864-1.1722-0.4181-0.7977-0.50340.62880.98620.21230.14180.07260.49480.05840.2645-9.537414.0312-2.2654
645.428928.1294-15.915696.89212.58687.52361.63591.49450.5036-0.3202-0.7031-2.5275-3.6902-1.9017-0.93280.42890.1365-0.05710.53860.17820.1281-9.058619.51810.4231
72.95924.65331.2467.31711.95930.52470.05911.14851.4473-2.0775-0.0316-1.6926-1.24240.353-0.02740.4619-0.03320.06690.4050.04910.3323-3.379617.4285.1376
827.3746-20.02825.266687.135832.898219.64770.65591.76251.83940.10372.3725-1.4035-0.35573.1006-3.02850.22580.09740.04790.4386-0.07060.4172-1.065410.53425.004
952.9615-7.3417-46.14470.346337.900460.9188-0.0499-1.68790.79461.93131.5467-2.05590.5263-0.1449-1.49680.14810.0535-0.11820.1442-0.05330.3642-4.62264.97943.934
1027.96845.5228-1.629216.01038.698111.2152-0.1847-0.2774-1.86931.56210.5422.79390.9833-2.3578-0.35730.4265-0.07830.09480.35410.15990.5624-10.3958-1.70752.1575
1111.0953-13.2466-17.369517.160722.74830.19580.11180.8391-0.78631.1346-0.55220.09530.7278-0.5640.44040.27970.04790.00520.3710.01040.1987-12.43027.04954.6656
121.0728-3.7645-2.226319.3944-4.562929.37980.4881-0.2977-0.39751.0807-0.5601-0.6072-0.13570.31860.0720.28120.024-0.01770.25970.00750.1947-12.162412.547910.2139
1365.368-5.5613-4.46426.2078-4.476530.17551.073-1.92340.50551.2444-0.2334-0.32341.0391-0.0497-0.83960.45430.0032-0.01170.1983-0.09330.1187-11.976517.347713.602
1427.0871-29.93897.875635.7657-2.439216.96660.1768-0.7670.84841.4169-0.2139-0.4027-2.0182-0.23080.03710.48420.10540.11150.35910.08510.187-18.840421.27248.9774
1530.6555-25.5074-11.862226.017926.235360.4549-0.979-0.61272.092-0.46540.8297-1.6612-2.8163-0.26330.14920.44380.16370.12290.26720.07160.3113-17.226222.75453.5352
161.98662.54031.181329.8607-29.218753.1120.07410.1112-0.34510.5541-0.02720.7777-0.516-0.1724-0.04690.30890.15740.04530.36170.08890.2515-15.871125.1807-6.7484
1760.876-11.392641.93372.1321-7.847728.8855-2.43241.92921.33010.4160.523-1.712-2.04563.16511.90950.31780.0459-0.00240.61430.18150.3476-11.413928.5158-16.1468
184.3028-5.3351-1.55187.52941.81470.57281.23350.13581.14291.2964-1.30240.69830.4321-1.83650.06890.3276-0.00730.07610.517-0.04020.253-28.754331.1805-8.1723
1958.28884.674-4.67312.646213.1981.38420.7348-0.89080.24-0.4567-0.23860.7726-2.2631-1.7244-0.49620.44690.1069-0.0880.31910.01440.2327-21.311137.239-7.9597
2070.0667-10.8057-43.653149.7689-23.948246.76520.3238-0.84670.74590.4506-1.9156-4.0825-1.83660.86931.59180.4006-0.0654-0.12080.21310.10360.3157-16.807136.1077-13.471
2129.2518-18.4937-13.914211.69218.79696.61851.83711.0189-0.0306-1.2156-2.4865-0.8490.02522.76550.64940.35250.0683-0.00820.82380.2520.2954-14.618533.702-21.394
2212.3296-7.5065-11.35756.551313.569332.81370.38030.9181-1.0438-2.1878-0.9328-0.3914-0.831-0.58070.55260.40990.18380.00310.44380.04190.2143-21.541330.16-26.297
2320.95-0.054543.549457.7629-22.332899.0747-1.35940.8004-2.127-0.9489-0.7037-0.55333.56753.0292.06310.19140.22930.17880.42390.00920.3904-23.830524.6787-24.8556
243.45354.17691.02155.05171.23550.30220.16460.7055-1.2191-2.61280.2449-0.19880.83980.4338-0.40950.46640.06160.04380.4261-0.01550.4154-31.161526.805-25.7849
2569.249223.96658.3438117.7912-45.145622.0763-0.53432.53981.3535-0.54192.07671.14582.7716-1.6455-1.54240.27540.0586-0.050.40570.11010.1676-32.643133.6618-27.56
267.158913.9271-0.585650.3828-3.391525.62040.3456-0.60950.5161.19290.7361.6451-0.12270.0096-1.08160.27120.0613-0.03550.22190.01160.3027-27.568441.4597-25.3984
2710.311737.359426.8946135.353197.439270.1455-4.2316-11.5315-0.50783.96193.6452-8.5188-2.2531-6.20690.58630.49260.4855-0.34251.26120.02131.2971-22.857847.0879-20.4528
288.76722.1658-12.440328.213-20.733128.92020.7262-0.07510.7340.7216-0.19790.45610.15240.8269-0.52830.19650.0520.00380.3738-0.01250.2034-24.82536.4925-19.4017
2920.75033.1297-12.009627.0833-0.66876.99980.3152-0.06250.5125-0.2275-0.83391.3288-0.3712-0.72180.51870.26670.04240.0470.26150.00850.2813-28.850231.6424-15.8661
3040.6132-0.871410.637618.61371.423426.02360.4135-0.5890.95670.7699-0.2740.9924-0.0691-0.8203-0.13950.3447-0.0410.13890.27590.06020.2893-31.461626.8751-13.6918
3151.1504-17.5693-7.07541.8646-6.708416.7346-0.1462-0.6967-1.64280.6125-0.34590.62232.4803-0.45640.49210.39430.13380.11250.28180.0450.2496-23.395522.9283-11.8354
3237.2366-3.4735-19.467219.9602-24.216844.6905-0.8463-0.2321-2.95080.46411.06710.06691.3171-0.394-0.22080.45640.14290.11340.27510.07650.1936-20.544821.4145-16.7402
3339.5372-25.2266-29.63734.810132.57632.1957-0.32810.0262-0.45570.6598-0.1260.2786-0.14160.48040.45420.38940.17740.06240.27990.05790.2024-13.969818.974-24.7735
3455.6682-176.561511.546-15.861630.99430.40184.1766-2.7942-1.32291.1796-0.24940.7553-0.1104-1.58140.25540.1471-0.03290.5736-0.15750.2915-10.175515.6462-34.4991
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA29 - 3320 - 24
2X-RAY DIFFRACTION2AA34 - 3925 - 30
3X-RAY DIFFRACTION3AA40 - 4331 - 34
4X-RAY DIFFRACTION4AA44 - 4835 - 39
5X-RAY DIFFRACTION5AA53 - 5644 - 47
6X-RAY DIFFRACTION6AA57 - 6048 - 51
7X-RAY DIFFRACTION7AA61 - 7152 - 62
8X-RAY DIFFRACTION8AA72 - 7563 - 66
9X-RAY DIFFRACTION9AA76 - 7967 - 70
10X-RAY DIFFRACTION10AA80 - 8571 - 76
11X-RAY DIFFRACTION11AA86 - 9277 - 83
12X-RAY DIFFRACTION12AA93 - 9784 - 88
13X-RAY DIFFRACTION13AA98 - 10289 - 93
14X-RAY DIFFRACTION14AA103 - 10694 - 97
15X-RAY DIFFRACTION15AA107 - 11098 - 101
16X-RAY DIFFRACTION16AA111 - 120102 - 111
17X-RAY DIFFRACTION17AA121 - 124112 - 115
18X-RAY DIFFRACTION18BB29 - 3320 - 24
19X-RAY DIFFRACTION19BB34 - 3925 - 30
20X-RAY DIFFRACTION20BB40 - 4331 - 34
21X-RAY DIFFRACTION21BB44 - 4835 - 39
22X-RAY DIFFRACTION22BB53 - 5644 - 47
23X-RAY DIFFRACTION23BB57 - 6048 - 51
24X-RAY DIFFRACTION24BB61 - 7152 - 62
25X-RAY DIFFRACTION25BB72 - 7563 - 66
26X-RAY DIFFRACTION26BB76 - 8267 - 73
27X-RAY DIFFRACTION27BB83 - 8674 - 77
28X-RAY DIFFRACTION28BB87 - 9278 - 83
29X-RAY DIFFRACTION29BB93 - 9784 - 88
30X-RAY DIFFRACTION30BB98 - 10289 - 93
31X-RAY DIFFRACTION31BB103 - 10694 - 97
32X-RAY DIFFRACTION32BB107 - 11098 - 101
33X-RAY DIFFRACTION33BB111 - 120102 - 111
34X-RAY DIFFRACTION34BB121 - 124112 - 115

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