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- PDB-7wbt: Crystal structure of bovine NLRP9 -

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Basic information

Entry
Database: PDB / ID: 7wbt
TitleCrystal structure of bovine NLRP9
ComponentsNACHT, LRR and PYD domains-containing protein 9
KeywordsIMMUNE SYSTEM / NLR / NOD-like receptor / NLRP9 / Inflammasome
Function / homology
Function and homology information


canonical inflammasome complex / regulation of inflammatory response / inflammatory response / innate immune response / ATP binding / cytoplasm
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 / DAPIN domain / NACHT nucleoside triphosphatase / NACHT domain / DAPIN domain profile. / NACHT-NTPase domain profile. ...: / NACHT, LRR and PYD domains-containing protein, helical domain HD2 / NLRC4 helical domain HD2 / NOD2, winged helix domain / NOD2 winged helix domain / DAPIN domain / NACHT nucleoside triphosphatase / NACHT domain / DAPIN domain profile. / NACHT-NTPase domain profile. / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / Leucine rich repeat, ribonuclease inhibitor type / Leucine Rich repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Death-like domain superfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / NACHT, LRR and PYD domains-containing protein 9
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsKamitsukasa, Y. / Shimizu, T. / Ohto, U.
Funding support Japan, 2items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)19H03164 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)19H00976 Japan
CitationJournal: FEBS Lett / Year: 2022
Title: The structure of NLRP9 reveals a unique C-terminal region with putative regulatory function.
Authors: Yukie Kamitsukasa / Kenji Nakano / Karin Murakami / Kunio Hirata / Masaki Yamamoto / Toshiyuki Shimizu / Umeharu Ohto /
Abstract: Nucleotide-binding and oligomerisation domain-like receptors (NLRs) can form inflammasomes that activate caspase-1 and pro-interleukin-1β and induce pyroptosis. NLR family pyrin domain-containing 9 ...Nucleotide-binding and oligomerisation domain-like receptors (NLRs) can form inflammasomes that activate caspase-1 and pro-interleukin-1β and induce pyroptosis. NLR family pyrin domain-containing 9 (NLRP9) forms an inflammasome and activates innate immune responses during virus infection, but little is known about this process. Here, we report the crystal and cryo-electron microscopy structures of NLRP9 in an ADP-bound state, revealing inactive and closed conformations of NLRP9 and its similarities to other structurally characterised NLRs. Moreover, we found a C-terminal region interacting with the concave surface of the leucine-rich repeat domain of NLRP9. This region is unique among NLRs and might be involved in the specific function of NLRP9. These data provide the structural basis for understanding the mechanism of NLRP9 regulation and activation.
History
DepositionDec 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 30, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id ..._pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NACHT, LRR and PYD domains-containing protein 9
B: NACHT, LRR and PYD domains-containing protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,9974
Polymers208,1432
Non-polymers8542
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint-42 kcal/mol
Surface area75410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.260, 169.120, 177.840
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 94 through 541 or resid 543 through 803 or resid 805 through 996))
21(chain B and (resid 94 through 541 or resid 543 through 803 or resid 805 through 996))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNASNASN(chain A and (resid 94 through 541 or resid 543 through 803 or resid 805 through 996))AA94 - 54110 - 457
12METMETASNASN(chain A and (resid 94 through 541 or resid 543 through 803 or resid 805 through 996))AA543 - 803459 - 719
13SERSERVALVAL(chain A and (resid 94 through 541 or resid 543 through 803 or resid 805 through 996))AA805 - 996721 - 912
21GLNGLNASNASN(chain B and (resid 94 through 541 or resid 543 through 803 or resid 805 through 996))BB94 - 54110 - 457
22METMETASNASN(chain B and (resid 94 through 541 or resid 543 through 803 or resid 805 through 996))BB543 - 803459 - 719
23SERSERVALVAL(chain B and (resid 94 through 541 or resid 543 through 803 or resid 805 through 996))BB805 - 996721 - 912

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Components

#1: Protein NACHT, LRR and PYD domains-containing protein 9


Mass: 104071.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: NLRP9, NALP9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q288C4
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
Has ligand of interestY
Has protein modificationY

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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: 3.69 Å3/Da / Density % sol: 66.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 6.25-7.50% PEG20000, 100 mM MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.67→177.84 Å / Num. obs: 88250 / % possible obs: 100 % / Redundancy: 427.6 % / CC1/2: 0.999 / Net I/σ(I): 27.9
Reflection shellResolution: 2.67→2.83 Å / Num. unique obs: 13957 / CC1/2: 0.774

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→49.14 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 33.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2615 4021 5.19 %
Rwork0.2316 73408 -
obs0.2332 77429 96.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 283.41 Å2 / Biso mean: 116.1425 Å2 / Biso min: 43.71 Å2
Refinement stepCycle: final / Resolution: 2.75→49.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14312 0 54 0 14366
Biso mean--86.94 --
Num. residues----1798
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8647X-RAY DIFFRACTION9.732TORSIONAL
12B8647X-RAY DIFFRACTION9.732TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.75-2.781.0023520.773377382530
2.78-2.820.7651940.64281786188068
2.82-2.850.57231350.52572377251291
2.85-2.890.50381390.43122512265197
2.89-2.930.36561410.342526032744100
2.93-2.970.37531460.322925662712100
2.97-3.020.38381260.328526622788100
3.02-3.060.34931170.333825992716100
3.06-3.110.39071350.348126232758100
3.11-3.170.38821310.348326132744100
3.17-3.230.38051490.311426102759100
3.23-3.290.33451290.27626252754100
3.29-3.350.28631380.255326302768100
3.35-3.430.27411270.239826232750100
3.43-3.510.29921520.241826262778100
3.51-3.60.26181500.244426082758100
3.6-3.690.27681500.239125992749100
3.69-3.80.25461390.245126592798100
3.8-3.920.28061570.229725832740100
3.92-4.060.27961560.214226212777100
4.06-4.230.23811740.201126142788100
4.23-4.420.21191430.192326362779100
4.42-4.650.23161500.193126452795100
4.65-4.940.22481380.191626612799100
4.94-5.320.26541690.203226432812100
5.32-5.860.28221260.234626782804100
5.86-6.70.26881420.239226972839100
6.71-8.440.23321500.222827372887100
8.44-49.140.17661660.18432799296599
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)
11.96470.3759-0.51624.3411-1.92953.2617-0.2826-0.2388-0.05380.12680.30750.6180.4063-0.40190.0060.42090.0470.03760.95540.17150.5749-28.106-8.1273-37.0055
25.5395-0.40792.88232.6949-0.55433.8863-0.2550.07860.2360.50940.3333-0.3226-0.18430.27-0.04630.37150.0624-0.13340.6214-0.04660.4393-1.45828.2486-40.7241
30.67640.2410.37190.88250.01341.06650.109-0.0367-0.07721.59810.13-0.284-0.75850.1431-0.01122.49960.0867-0.52890.9518-0.08510.56388.925528.5276-7.7458
42.0550.2811-0.22723.64780.70252.2445-0.4146-0.44040.2649-0.55270.4083-1.69140.12680.5726-0.02940.85070.07620.22381.0213-0.2941.24627.6007-14.3166-51.2861
53.5817-0.179-2.67883.8811-0.69057.9815-0.342-0.307-0.1641-0.22060.38480.05270.5527-0.0664-0.05760.55160.03040.12520.66680.0470.37482.6739-30.3844-42.2234
60.5863-0.10360.20542.7591-0.35332.5294-0.2637-0.42740.02741.27440.8162-0.0902-0.4687-0.4219-0.44311.08390.318-0.10511.20520.01730.452210.2961-50.7847-8.2378
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 94:475)A94 - 475
2X-RAY DIFFRACTION2(chain A and resid 476:672)A476 - 672
3X-RAY DIFFRACTION3(chain A and resid 673:996)A673 - 996
4X-RAY DIFFRACTION4(chain B and resid 94:475)B94 - 475
5X-RAY DIFFRACTION5(chain B and resid 476:672)B476 - 672
6X-RAY DIFFRACTION6(chain B and resid 673:996)B673 - 996

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