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- PDB-4kxf: Crystal structure of NLRC4 reveals its autoinhibition mechanism -

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Basic information

Entry
Database: PDB / ID: 4kxf
TitleCrystal structure of NLRC4 reveals its autoinhibition mechanism
ComponentsNLR family CARD domain-containing protein 4
KeywordsIMMUNE SYSTEM / Auto-inhibition / Muti-domain / Innate Immunity / Phosphorylation / ADP BINDING
Function / homology
Function and homology information


IPAF inflammasome complex / pyroptotic inflammatory response / detection of bacterium / activation of innate immune response / positive regulation of interleukin-1 beta production / protein homooligomerization / regulation of apoptotic process / defense response to bacterium / inflammatory response / innate immune response ...IPAF inflammasome complex / pyroptotic inflammatory response / detection of bacterium / activation of innate immune response / positive regulation of interleukin-1 beta production / protein homooligomerization / regulation of apoptotic process / defense response to bacterium / inflammatory response / innate immune response / apoptotic process / protein homodimerization activity / ATP binding / identical protein binding / cytosol
Similarity search - Function
c-terminal domain of poly(a) binding protein - #50 / NLR family CARD domain-containing protein 4 / NLRC4, helical domain / : / NLRC4 helical domain / Nlrc4-like, winged helix domain / c-terminal domain of poly(a) binding protein / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. ...c-terminal domain of poly(a) binding protein - #50 / NLR family CARD domain-containing protein 4 / NLRC4, helical domain / : / NLRC4 helical domain / Nlrc4-like, winged helix domain / c-terminal domain of poly(a) binding protein / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Death-like domain superfamily / Leucine-rich repeat domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / NLR family CARD domain-containing protein 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.2 Å
AuthorsChai, J. / Hu, Z.
CitationJournal: Science / Year: 2013
Title: Crystal structure of NLRC4 reveals its autoinhibition mechanism
Authors: Hu, Z. / Yan, C. / Liu, P. / Huang, Z. / Ma, R. / Zhang, C. / Wang, R. / Zhang, Y. / Martinon, F. / Miao, D. / Deng, H. / Wang, J. / Chang, J. / Chai, J.
History
DepositionMay 25, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_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
K: NLR family CARD domain-containing protein 4
B: NLR family CARD domain-containing protein 4
D: NLR family CARD domain-containing protein 4
F: NLR family CARD domain-containing protein 4
H: NLR family CARD domain-containing protein 4
L: NLR family CARD domain-containing protein 4
N: NLR family CARD domain-containing protein 4
P: NLR family CARD domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)939,33818
Polymers935,7288
Non-polymers3,61010
Water00
1
K: NLR family CARD domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,3932
Polymers116,9661
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NLR family CARD domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,4893
Polymers116,9661
Non-polymers5232
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: NLR family CARD domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,3932
Polymers116,9661
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
F: NLR family CARD domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,3932
Polymers116,9661
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
H: NLR family CARD domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,3932
Polymers116,9661
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
L: NLR family CARD domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,3932
Polymers116,9661
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
N: NLR family CARD domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,4893
Polymers116,9661
Non-polymers5232
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
P: NLR family CARD domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,3932
Polymers116,9661
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
K: NLR family CARD domain-containing protein 4
hetero molecules

K: NLR family CARD domain-containing protein 4
hetero molecules

P: NLR family CARD domain-containing protein 4
hetero molecules

P: NLR family CARD domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)469,5738
Polymers467,8644
Non-polymers1,7094
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
crystal symmetry operation4_444y-1/2,-x-1/2,z-1/41
crystal symmetry operation6_555x+1/2,-y+1/2,-z+3/41
Buried area14970 Å2
ΔGint-51 kcal/mol
Surface area138100 Å2
MethodPISA
10
B: NLR family CARD domain-containing protein 4
F: NLR family CARD domain-containing protein 4
H: NLR family CARD domain-containing protein 4
L: NLR family CARD domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)469,6699
Polymers467,8644
Non-polymers1,8055
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15890 Å2
ΔGint-71 kcal/mol
Surface area136190 Å2
MethodPISA
11
D: NLR family CARD domain-containing protein 4
N: NLR family CARD domain-containing protein 4
hetero molecules

D: NLR family CARD domain-containing protein 4
N: NLR family CARD domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)469,76510
Polymers467,8644
Non-polymers1,9016
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556-y,-x,-z+3/21
Buried area15480 Å2
ΔGint-63 kcal/mol
Surface area135860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)334.052, 334.052, 177.567
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
11K-433-

GLN

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Components

#1: Protein
NLR family CARD domain-containing protein 4 / Caspase recruitment domain-containing protein 12 / Ice protease-activating factor / Ipaf


Mass: 116965.984 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nlrc4, Card12, Ipaf / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q3UP24
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
Has protein modificationY

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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: 2.65 Å3/Da / Density % sol: 53.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 1.65M sodium phosphate monobasic monohydrate/potassium phosphate dibasic, 1% n-propyl formate., pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1.0, 1.008, 1.06, 1.225
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 10, 2012
RadiationMonochromator: double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.0081
31.061
41.2251
ReflectionResolution: 3.2→99 Å / Num. all: 165225 / Num. obs: 150190 / % possible obs: 90.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Rsym value: 0.114
Reflection shellResolution: 3.2→3.31 Å / Num. unique all: 15039 / Rsym value: 0.585 / % possible all: 92.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 3.2→39.326 Å / SU ML: 0.45 / σ(F): 0 / Phase error: 27.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2656 7517 5.04 %RANDOM
Rwork0.226 ---
obs0.228 149279 90.91 %-
all-150190 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→39.326 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms56855 0 226 0 57081
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00458211
X-RAY DIFFRACTIONf_angle_d1.10878677
X-RAY DIFFRACTIONf_dihedral_angle_d19.70621551
X-RAY DIFFRACTIONf_chiral_restr0.0728998
X-RAY DIFFRACTIONf_plane_restr0.0049962
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.2-3.23630.38022310.3341477592
3.2363-3.27440.37672710.3172471393
3.2744-3.31430.34792470.307475793
3.3143-3.35620.32832590.3052477693
3.3562-3.40040.33682440.2967477693
3.4004-3.44690.31542560.2984477793
3.4469-3.49620.33752650.2909478293
3.4962-3.54830.31762550.2817478893
3.5483-3.60370.31272560.2636482593
3.6037-3.66280.29682510.2521477793
3.6628-3.72590.31012440.2475478793
3.7259-3.79360.27382690.2439479793
3.7936-3.86650.28052510.2394478193
3.8665-3.94530.27382850.2213473592
3.9453-4.0310.2782540.2239474992
4.031-4.12470.24872420.2192474092
4.1247-4.22770.24232380.2124475192
4.2277-4.34190.24812410.2008475291
4.3419-4.46950.26512370.2083474992
4.4695-4.61350.2452780.1991470391
4.6135-4.77820.21762280.2004476791
4.7782-4.96910.24032610.2006473191
4.9691-5.19480.24532610.2078470390
5.1948-5.4680.27672410.2157469490
5.468-5.80960.28592470.2327466989
5.8096-6.25650.30582590.2312464289
6.2565-6.88310.27432410.226469089
6.8831-7.87210.23982430.1997464288
7.8721-9.89190.18432230.1729458185
9.8919-39.32860.22072390.2031435378
Refinement TLS params.Method: refined / Origin x: -81.1018 Å / Origin y: 120.3768 Å / Origin z: 89.7651 Å
111213212223313233
T0.0269 Å2-0.0079 Å20.0008 Å2-0.0245 Å2-0.0024 Å2--0.035 Å2
L0.0111 °20.0189 °2-0.004 °2-0.0295 °2-0.003 °2--0.0185 °2
S-0.0135 Å °-0.0052 Å °0.0103 Å °-0.0136 Å °-0.028 Å °-0.009 Å °0.0046 Å °-0.0164 Å °-0.0592 Å °
Refinement TLS groupSelection details: all

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