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- PDB-4jqw: Crystal Structure of a Complex of NOD1 CARD and Ubiquitin -

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Basic information

Entry
Database: PDB / ID: 4jqw
TitleCrystal Structure of a Complex of NOD1 CARD and Ubiquitin
Components
  • Nucleotide-binding oligomerization domain-containing protein 1
  • Polyubiquitin-C
KeywordsAPOPTOSIS/SIGNALLING PROTEIN / death domain-like fold / innate immunity / RIP2 / ATG16L / S-dimethylarsenic / APOPTOSIS-SIGNALLING PROTEIN complex
Function / homology
Function and homology information


positive regulation of dendritic cell antigen processing and presentation / detection of biotic stimulus / positive regulation of xenophagy / xenophagy / nucleotide-binding oligomerization domain containing 1 signaling pathway / positive regulation of stress-activated MAPK cascade / cellular response to muramyl dipeptide / CARD domain binding / peptidoglycan binding / positive regulation of macrophage cytokine production ...positive regulation of dendritic cell antigen processing and presentation / detection of biotic stimulus / positive regulation of xenophagy / xenophagy / nucleotide-binding oligomerization domain containing 1 signaling pathway / positive regulation of stress-activated MAPK cascade / cellular response to muramyl dipeptide / CARD domain binding / peptidoglycan binding / positive regulation of macrophage cytokine production / pattern recognition receptor signaling pathway / pattern recognition receptor activity / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / cysteine-type endopeptidase activator activity involved in apoptotic process / detection of bacterium / stress-activated MAPK cascade / JNK cascade / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / phagocytic vesicle / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / APC/C:Cdc20 mediated degradation of Cyclin B / ERK1 and ERK2 cascade / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / PINK1-PRKN Mediated Mitophagy / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / Regulation of PTEN localization / NRIF signals cell death from the nucleus / response to endoplasmic reticulum stress / Regulation of BACH1 activity / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / positive regulation of interleukin-1 beta production / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / ubiquitin binding / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / positive regulation of interleukin-8 production / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / NOTCH3 Activation and Transmission of Signal to the Nucleus / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL
Similarity search - Function
: / NACHT, LRR and PYD domains-containing protein, helical domain HD2 / NLRC4 helical domain HD2 / NOD2, winged helix domain / NOD2 winged helix domain / Death Domain, Fas / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / Death Domain, Fas ...: / NACHT, LRR and PYD domains-containing protein, helical domain HD2 / NLRC4 helical domain HD2 / NOD2, winged helix domain / NOD2 winged helix domain / Death Domain, Fas / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / Death Domain, Fas / Leucine rich repeat, ribonuclease inhibitor type / Leucine Rich repeat / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Death-like domain superfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Polyubiquitin-C / Nucleotide-binding oligomerization domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsVer Heul, A.M. / Gakhar, L. / Piper, R.C. / Ramaswamy, S.
CitationJournal: Plos One / Year: 2014
Title: Crystal structure of a complex of NOD1 CARD and ubiquitin
Authors: Ver Heul, A.M. / Gakhar, L. / Piper, R.C. / Ramaswamy, S.
History
DepositionMar 20, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Nov 8, 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 / pdbx_struct_special_symmetry / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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: Nucleotide-binding oligomerization domain-containing protein 1
C: Polyubiquitin-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7133
Polymers20,6182
Non-polymers951
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.688, 61.688, 86.873
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11C-1001-

PO4

21C-1001-

PO4

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Components

#1: Protein Nucleotide-binding oligomerization domain-containing protein 1 / Caspase recruitment domain-containing protein 4


Mass: 12041.616 Da / Num. of mol.: 1 / Fragment: CARD domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CARD4, NOD1 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9Y239
#2: Protein Polyubiquitin-C


Mass: 8576.831 Da / Num. of mol.: 1 / Fragment: Ubiquitin
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Plasmid: pRSUb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P0CG48
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4

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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 Å3/Da / Density % sol: 38.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 100mM PCB, 25% PEG1500, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Apr 23, 2011
RadiationMonochromator: Rosenbaum-Rock monochromator double crystal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→38.982 Å / Num. all: 4052 / Num. obs: 4048 / % possible obs: 99.88 % / Observed criterion σ(I): 5 / Redundancy: 13.35 % / Biso Wilson estimate: 86.06 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 28.4
Reflection shellResolution: 2.9→3 Å / Redundancy: 13.92 % / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 11.4 / Num. unique all: 395

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 2NSN, 1UBQ

2nsn

1ubq


Resolution: 2.9→38.982 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.39 / σ(F): 1.36 / Phase error: 30.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2699 406 10.03 %random
Rwork0.2256 ---
obs0.2302 4046 99.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.84 Å2 / Biso mean: 57.4385 Å2 / Biso min: 27.52 Å2
Refinement stepCycle: LAST / Resolution: 2.9→38.982 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1333 0 5 0 1338
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031357
X-RAY DIFFRACTIONf_angle_d0.7041837
X-RAY DIFFRACTIONf_chiral_restr0.045217
X-RAY DIFFRACTIONf_plane_restr0.002234
X-RAY DIFFRACTIONf_dihedral_angle_d15.393520
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.9001-3.31960.40831310.29811761307
3.3196-4.18160.33921330.266111901323
4.1816-38.98520.21771420.194312741416

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