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- PDB-6gfj: Structure of RIP2 CARD domain fused to crystallisable MBP tag -

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Basic information

Entry
Database: PDB / ID: 6gfj
TitleStructure of RIP2 CARD domain fused to crystallisable MBP tag
ComponentsSugar ABC transporter substrate-binding protein,Receptor-interacting serine/threonine-protein kinase 2
KeywordsTRANSFERASE / CARD / crystallographic MBP / RIP2 / Death Domain
Function / homology
Function and homology information


toll-like receptor 2 signaling pathway / nucleotide-binding oligomerization domain containing 1 signaling pathway / caspase binding / LIM domain binding / positive regulation of protein K63-linked ubiquitination / cellular response to muramyl dipeptide / CARD domain binding / JUN kinase kinase kinase activity / nucleotide-binding oligomerization domain containing 2 signaling pathway / positive regulation of interferon-alpha production ...toll-like receptor 2 signaling pathway / nucleotide-binding oligomerization domain containing 1 signaling pathway / caspase binding / LIM domain binding / positive regulation of protein K63-linked ubiquitination / cellular response to muramyl dipeptide / CARD domain binding / JUN kinase kinase kinase activity / nucleotide-binding oligomerization domain containing 2 signaling pathway / positive regulation of interferon-alpha production / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / positive regulation of interleukin-12 production / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / canonical NF-kappaB signal transduction / signaling adaptor activity / positive regulation of interferon-beta production / positive regulation of protein ubiquitination / p75NTR recruits signalling complexes / positive regulation of interleukin-1 beta production / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / non-specific protein-tyrosine kinase / activated TAK1 mediates p38 MAPK activation / non-membrane spanning protein tyrosine kinase activity / NOD1/2 Signaling Pathway / TAK1-dependent IKK and NF-kappa-B activation / protein homooligomerization / positive regulation of interleukin-6 production / T cell receptor signaling pathway / Interleukin-1 signaling / positive regulation of tumor necrosis factor production / Ovarian tumor domain proteases / Downstream TCR signaling / vesicle / adaptive immune response / cytoskeleton / positive regulation of canonical NF-kappaB signal transduction / periplasmic space / non-specific serine/threonine protein kinase / defense response to bacterium / positive regulation of apoptotic process / inflammatory response / signaling receptor binding / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / SARS-CoV-2 activates/modulates innate and adaptive immune responses / signal transduction / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / protein-containing complex / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Receptor-interacting serine/threonine-protein kinase 2 / RIP2, CARD domain / Death Domain, Fas / Death Domain, Fas / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / : / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site ...Receptor-interacting serine/threonine-protein kinase 2 / RIP2, CARD domain / Death Domain, Fas / Death Domain, Fas / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / : / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Death-like domain superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
alpha-maltose / Maltodextrin-binding protein / Receptor-interacting serine/threonine-protein kinase 2
Similarity search - Component
Biological speciesMethanosarcina mazei (archaea)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsPellegrini, E. / Cusack, S.
CitationJournal: Nat Commun / Year: 2018
Title: RIP2 filament formation is required for NOD2 dependent NF-κB signalling.
Authors: Erika Pellegrini / Ambroise Desfosses / Arndt Wallmann / Wiebke Manuela Schulze / Kristina Rehbein / Philippe Mas / Luca Signor / Stephanie Gaudon / Grasilda Zenkeviciute / Michael Hons / ...Authors: Erika Pellegrini / Ambroise Desfosses / Arndt Wallmann / Wiebke Manuela Schulze / Kristina Rehbein / Philippe Mas / Luca Signor / Stephanie Gaudon / Grasilda Zenkeviciute / Michael Hons / Helene Malet / Irina Gutsche / Carsten Sachse / Guy Schoehn / Hartmut Oschkinat / Stephen Cusack /
Abstract: Activation of the innate immune pattern recognition receptor NOD2 by the bacterial muramyl-dipeptide peptidoglycan fragment triggers recruitment of the downstream adaptor kinase RIP2, eventually ...Activation of the innate immune pattern recognition receptor NOD2 by the bacterial muramyl-dipeptide peptidoglycan fragment triggers recruitment of the downstream adaptor kinase RIP2, eventually leading to NF-κB activation and proinflammatory cytokine production. Here we show that full-length RIP2 can form long filaments mediated by its caspase recruitment domain (CARD), in common with other innate immune adaptor proteins. We further show that the NOD2 tandem CARDs bind to one end of the RIP2 CARD filament, suggesting a mechanism for polar filament nucleation by activated NOD2. We combine X-ray crystallography, solid-state NMR and high-resolution cryo-electron microscopy to determine the atomic structure of the helical RIP2 CARD filament, which reveals the intermolecular interactions that stabilize the assembly. Using structure-guided mutagenesis, we demonstrate the importance of RIP2 polymerization for the activation of NF-κB signalling by NOD2. Our results could be of use to develop new pharmacological strategies to treat inflammatory diseases characterised by aberrant NOD2 signalling.
History
DepositionApr 30, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sugar ABC transporter substrate-binding protein,Receptor-interacting serine/threonine-protein kinase 2
B: Sugar ABC transporter substrate-binding protein,Receptor-interacting serine/threonine-protein kinase 2
C: Sugar ABC transporter substrate-binding protein,Receptor-interacting serine/threonine-protein kinase 2
D: Sugar ABC transporter substrate-binding protein,Receptor-interacting serine/threonine-protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,0328
Polymers210,6634
Non-polymers1,3694
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint2 kcal/mol
Surface area77140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.460, 121.570, 123.160
Angle α, β, γ (deg.)90.00, 109.04, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21B
12A
22C
13A
23D
14S
24T
15S
25X
16S
26Y
17B
27C
18B
28D
19T
29X
110T
210Y
111C
211D
112X
212Y

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A2 - 370
2010B2 - 370
1020A2 - 370
2020C2 - 370
1030A7 - 369
2030D7 - 369
1040S434 - 521
2040T434 - 521
1050S434 - 519
2050X434 - 519
1060S434 - 521
2060Y434 - 521
1070B2 - 370
2070C2 - 370
1080B7 - 369
2080D7 - 369
1090T434 - 519
2090X434 - 519
10100T434 - 521
20100Y434 - 521
10110C7 - 369
20110D7 - 369
10120X434 - 519
20120Y434 - 519

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

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Components

#1: Protein
Sugar ABC transporter substrate-binding protein,Receptor-interacting serine/threonine-protein kinase 2 / CARD-containing interleukin-1 beta-converting enzyme-associated kinase / CARD-containing IL-1 beta ...CARD-containing interleukin-1 beta-converting enzyme-associated kinase / CARD-containing IL-1 beta ICE-kinase / RIP-like-interacting CLARP kinase / Receptor-interacting protein 2 / RIP-2 / Tyrosine-protein kinase RIPK2


Mass: 52665.781 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei (archaea), (gene. exp.) Homo sapiens (human)
Strain: K12
Gene: malE, DU74_04045, RIPK2, CARDIAK, RICK, RIP2, UNQ277/PRO314/PRO34092
Production host: Escherichia coli (E. coli)
References: UniProt: A0A0F8NYV9, UniProt: O43353, non-specific serine/threonine protein kinase, non-specific protein-tyrosine kinase
#2: Polysaccharide
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-6-deoxy-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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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: 3.05 Å3/Da / Density % sol: 59.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.25 M NaNO3, and 22% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 3.29→46.98 Å / Num. obs: 37320 / % possible obs: 98.5 % / Redundancy: 3.8 % / Biso Wilson estimate: 131.5 Å2 / Rrim(I) all: 0.19 / Net I/σ(I): 5.45
Reflection shellResolution: 3.29→3.38 Å / Rrim(I) all: 1.37

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IFP

4ifp


Resolution: 3.3→46.98 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.899 / SU B: 105.632 / SU ML: 0.645 / Cross valid method: THROUGHOUT / ESU R Free: 0.563 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26569 1540 4.1 %RANDOM
Rwork0.23489 ---
obs0.23613 35780 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 129.1 Å2
Baniso -1Baniso -2Baniso -3
1-7.36 Å20 Å24.79 Å2
2---7.39 Å20 Å2
3----2.65 Å2
Refinement stepCycle: 1 / Resolution: 3.3→46.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14164 0 88 0 14252
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0214580
X-RAY DIFFRACTIONr_bond_other_d0.0010.0213575
X-RAY DIFFRACTIONr_angle_refined_deg1.0531.97219797
X-RAY DIFFRACTIONr_angle_other_deg0.872331700
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.12151818
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.34826.069641
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.17152508
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8361536
X-RAY DIFFRACTIONr_chiral_restr0.060.22210
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02116126
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022698
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2539.0357284
X-RAY DIFFRACTIONr_mcbond_other1.2539.0357283
X-RAY DIFFRACTIONr_mcangle_it2.22613.5539098
X-RAY DIFFRACTIONr_mcangle_other2.22613.5539099
X-RAY DIFFRACTIONr_scbond_it0.9539.1127296
X-RAY DIFFRACTIONr_scbond_other0.9539.1117294
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7713.61910699
X-RAY DIFFRACTIONr_long_range_B_refined3.96517195
X-RAY DIFFRACTIONr_long_range_B_other3.96517196
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A235180.03
12B235180.03
21A234860.03
22C234860.03
31A231700.03
32D231700.03
71B235220.02
72C235220.02
81B231960.03
82D231960.03
111C231580.03
112D231580.03
LS refinement shellResolution: 3.3→3.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.432 111 -
Rwork0.417 2477 -
obs--93.73 %
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)
11.9977-0.15-0.79462.19760.13154.0980.04350.1174-0.1546-0.40940.1787-0.26220.2401-0.0651-0.22220.4677-0.13810.14150.054-0.05330.147952.0078-18.2035165.0759
21.78440.2725-1.00164.0930.79352.2642-0.0027-0.04150.09210.1264-0.08670.068-0.0551-0.09760.08950.5166-0.0142-0.03450.3482-0.0140.44551.8244-44.6377187.3928
32.09280.3669-0.872.2137-1.00684.3544-0.12360.06030.1332-0.1828-0.0384-0.5086-0.17210.37730.1620.4518-0.0650.08640.0781-0.08140.418729.2741-31.1376123.0702
44.30630.49620.15056.015-0.28835.56080.0872-0.1187-0.00340.4433-0.0547-0.1629-0.0690.0497-0.03250.58460.0691-0.00250.2183-0.04120.361815.3717-4.7147140.4014
54.6523-0.4794-2.05373.93660.33482.8607-0.44710.0793-0.09930.65110.17360.24690.3559-0.17410.27350.53220.06840.1410.02930.00480.057710.1065-20.4271176.3985
60.7749-0.4916-0.7513.145-0.22253.71470.0161-0.01290.0329-0.0479-0.1183-0.2840.49150.02150.10210.5697-0.0710.12970.5450.03010.5623-2.4134-41.8524202.5518
72.8196-0.05570.23723.7503-0.832.87-0.039-0.0237-0.01430.04620.18410.76990.0196-0.3527-0.14510.51360.02730.09890.08950.08330.218232.4321-28.5407217.7951
81.7681-0.6529-1.48383.3045-0.52894.48780.13060.12370.2235-0.2002-0.08040.1392-0.07790.1968-0.05020.5756-0.03850.06680.4969-0.06370.4527.3318-7.2471246.9771
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 370
2X-RAY DIFFRACTION1A501
4X-RAY DIFFRACTION3B2 - 370
5X-RAY DIFFRACTION3B501
7X-RAY DIFFRACTION5C2 - 370
8X-RAY DIFFRACTION5C501
10X-RAY DIFFRACTION7D7 - 370
11X-RAY DIFFRACTION7D501

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