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- PDB-7jwp: Fab CJ11 in complex IL-18 peptide liberated by Caspase cleavage -

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Basic information

Entry
Database: PDB / ID: 7jwp
TitleFab CJ11 in complex IL-18 peptide liberated by Caspase cleavage
Components
  • Fab CJ11 Heavy chain
  • Fab CJ11 Light chain
  • IL-18 peptide
KeywordsIMMUNE SYSTEM / IL-18 / caspase
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsPayandeh, J. / Ho, H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Discovery of a caspase cleavage motif antibody reveals insights into noncanonical inflammasome function.
Authors: Davies, C.W. / Stowe, I. / Phung, Q.T. / Ho, H. / Bakalarski, C.E. / Gupta, A. / Zhang, Y. / Lill, J.R. / Payandeh, J. / Kayagaki, N. / Koerber, J.T.
History
DepositionAug 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI ..._citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Fab CJ11 Heavy chain
B: Fab CJ11 Light chain
C: Fab CJ11 Heavy chain
D: Fab CJ11 Light chain
E: Fab CJ11 Heavy chain
F: Fab CJ11 Light chain
G: Fab CJ11 Heavy chain
H: Fab CJ11 Light chain
I: Fab CJ11 Heavy chain
J: Fab CJ11 Light chain
K: Fab CJ11 Heavy chain
L: Fab CJ11 Light chain
M: Fab CJ11 Heavy chain
N: Fab CJ11 Light chain
O: Fab CJ11 Heavy chain
P: Fab CJ11 Light chain
Q: IL-18 peptide
R: IL-18 peptide
S: IL-18 peptide
T: IL-18 peptide
U: IL-18 peptide
V: IL-18 peptide
W: IL-18 peptide
X: IL-18 peptide


Theoretical massNumber of molelcules
Total (without water)376,27524
Polymers376,27524
Non-polymers00
Water00
1
A: Fab CJ11 Heavy chain
B: Fab CJ11 Light chain
Q: IL-18 peptide


Theoretical massNumber of molelcules
Total (without water)47,0343
Polymers47,0343
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-28 kcal/mol
Surface area18880 Å2
MethodPISA
2
C: Fab CJ11 Heavy chain
D: Fab CJ11 Light chain
R: IL-18 peptide


Theoretical massNumber of molelcules
Total (without water)47,0343
Polymers47,0343
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-28 kcal/mol
Surface area18780 Å2
MethodPISA
3
E: Fab CJ11 Heavy chain
F: Fab CJ11 Light chain
S: IL-18 peptide


Theoretical massNumber of molelcules
Total (without water)47,0343
Polymers47,0343
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-27 kcal/mol
Surface area18790 Å2
MethodPISA
4
G: Fab CJ11 Heavy chain
H: Fab CJ11 Light chain
T: IL-18 peptide


Theoretical massNumber of molelcules
Total (without water)47,0343
Polymers47,0343
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-27 kcal/mol
Surface area19020 Å2
MethodPISA
5
I: Fab CJ11 Heavy chain
J: Fab CJ11 Light chain
U: IL-18 peptide


Theoretical massNumber of molelcules
Total (without water)47,0343
Polymers47,0343
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-28 kcal/mol
Surface area18750 Å2
MethodPISA
6
K: Fab CJ11 Heavy chain
L: Fab CJ11 Light chain
V: IL-18 peptide


Theoretical massNumber of molelcules
Total (without water)47,0343
Polymers47,0343
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-26 kcal/mol
Surface area18750 Å2
MethodPISA
7
M: Fab CJ11 Heavy chain
N: Fab CJ11 Light chain
W: IL-18 peptide


Theoretical massNumber of molelcules
Total (without water)47,0343
Polymers47,0343
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-25 kcal/mol
Surface area18540 Å2
MethodPISA
8
O: Fab CJ11 Heavy chain
P: Fab CJ11 Light chain
X: IL-18 peptide


Theoretical massNumber of molelcules
Total (without water)47,0343
Polymers47,0343
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-28 kcal/mol
Surface area18760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.348, 83.524, 145.794
Angle α, β, γ (deg.)107.240, 106.530, 89.980
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain B and resid 2 through 215)
21(chain D and resid 2 through 215)
31(chain F and resid 2 through 215)
41(chain H and resid 2 through 215)
51(chain J and resid 2 through 215)
61chain L
71chain N
81(chain P and resid 2 through 215)
12chain A
22chain C
32(chain E and (resid 1 through 135 or resid 137 through 215))
42(chain G and (resid 1 through 135 or resid 137 through 215))
52chain I
62(chain K and (resid 1 through 135 or resid 137 through 215))
72chain M
82(chain O and (resid 1 through 135 or resid 137 through 215))
13chain Q
23chain R
33chain S
43chain T
53chain U
63chain V
73chain X

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ILEILEGLYGLY(chain B and resid 2 through 215)BB2 - 2152 - 215
211ILEILEGLYGLY(chain D and resid 2 through 215)DD2 - 2152 - 215
311ILEILEGLYGLY(chain F and resid 2 through 215)FF2 - 2152 - 215
411ILEILEGLYGLY(chain H and resid 2 through 215)HH2 - 2152 - 215
511ILEILEGLYGLY(chain J and resid 2 through 215)JJ2 - 2152 - 215
611ILEILEGLYGLYchain LLL2 - 2152 - 215
711ILEILEGLYGLYchain NNN2 - 2152 - 215
811ILEILEGLYGLY(chain P and resid 2 through 215)PP2 - 2152 - 215
112GLNGLNPROPROchain AAA1 - 2151 - 215
212GLNGLNPROPROchain CCC1 - 2151 - 215
312GLNGLNGLYGLY(chain E and (resid 1 through 135 or resid 137 through 215))EE1 - 1351 - 135
322THRTHRPROPRO(chain E and (resid 1 through 135 or resid 137 through 215))EE137 - 215137 - 215
412GLNGLNGLYGLY(chain G and (resid 1 through 135 or resid 137 through 215))GG1 - 1351 - 135
422THRTHRPROPRO(chain G and (resid 1 through 135 or resid 137 through 215))GG137 - 215137 - 215
512GLNGLNPROPROchain III1 - 2151 - 215
612GLNGLNGLYGLY(chain K and (resid 1 through 135 or resid 137 through 215))KK1 - 1351 - 135
622THRTHRPROPRO(chain K and (resid 1 through 135 or resid 137 through 215))KK137 - 215137 - 215
712GLNGLNPROPROchain MMM1 - 2151 - 215
812GLNGLNGLYGLY(chain O and (resid 1 through 135 or resid 137 through 215))OO1 - 1351 - 135
822THRTHRPROPRO(chain O and (resid 1 through 135 or resid 137 through 215))OO137 - 215137 - 215
113GLYGLYASPASPchain QQQ30 - 351 - 6
213GLYGLYASPASPchain RRR30 - 351 - 6
313GLYGLYASPASPchain SSS30 - 351 - 6
413GLYGLYASPASPchain TTT30 - 351 - 6
513GLYGLYASPASPchain UUU30 - 351 - 6
613GLYGLYASPASPchain VVV30 - 351 - 6
713GLYGLYASPASPchain XXX30 - 351 - 6

NCS ensembles :
ID
1
2
3

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Components

#1: Antibody
Fab CJ11 Heavy chain


Mass: 23001.879 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody
Fab CJ11 Light chain


Mass: 23397.875 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Protein/peptide
IL-18 peptide


Mass: 634.592 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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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: 2.4 Å3/Da / Density % sol: 48.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6
Details: 0.1 Na citrate, pH 6, 20% PEG4000, 20% isopropanol; Fab was reductively methylated

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: h,-k,-h-l / Fraction: 0.12
ReflectionResolution: 3→25 Å / Num. obs: 60390 / % possible obs: 86.4 % / Redundancy: 1.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 6.5
Reflection shellResolution: 3→3.06 Å / Rmerge(I) obs: 0.1 / Num. unique obs: 500

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Processing

Software
NameVersionClassification
PHENIXdev_2747refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I8O

5i8o


Resolution: 3→23.972 Å / Cross valid method: THROUGHOUT / σ(F): 102.58 / Phase error: 41.42 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2604 3300 5.46 %
Rwork0.2348 57244 -
obs0.2507 60390 86.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 144.89 Å2 / Biso mean: 24.733 Å2 / Biso min: 0 Å2
Refinement stepCycle: final / Resolution: 3→23.972 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25753 0 0 0 25753
Num. residues----3437
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00426361
X-RAY DIFFRACTIONf_angle_d0.99835938
X-RAY DIFFRACTIONf_chiral_restr0.0574146
X-RAY DIFFRACTIONf_plane_restr0.0064575
X-RAY DIFFRACTIONf_dihedral_angle_d13.04315666
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B9973X-RAY DIFFRACTION8.698TORSIONAL
12D9973X-RAY DIFFRACTION8.698TORSIONAL
13F9973X-RAY DIFFRACTION8.698TORSIONAL
14H9973X-RAY DIFFRACTION8.698TORSIONAL
15J9973X-RAY DIFFRACTION8.698TORSIONAL
16L9973X-RAY DIFFRACTION8.698TORSIONAL
17N9973X-RAY DIFFRACTION8.698TORSIONAL
18P9973X-RAY DIFFRACTION8.698TORSIONAL
21A9577X-RAY DIFFRACTION8.698TORSIONAL
22C9577X-RAY DIFFRACTION8.698TORSIONAL
23E9577X-RAY DIFFRACTION8.698TORSIONAL
24G9577X-RAY DIFFRACTION8.698TORSIONAL
25I9577X-RAY DIFFRACTION8.698TORSIONAL
26K9577X-RAY DIFFRACTION8.698TORSIONAL
27M9577X-RAY DIFFRACTION8.698TORSIONAL
28O9577X-RAY DIFFRACTION8.698TORSIONAL
31Q196X-RAY DIFFRACTION8.698TORSIONAL
32R196X-RAY DIFFRACTION8.698TORSIONAL
33S196X-RAY DIFFRACTION8.698TORSIONAL
34T196X-RAY DIFFRACTION8.698TORSIONAL
35U196X-RAY DIFFRACTION8.698TORSIONAL
36V196X-RAY DIFFRACTION8.698TORSIONAL
37X196X-RAY DIFFRACTION8.698TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0004-3.05190.32531490.32282688283778
3.0519-3.10720.30941350.30462771290679
3.1072-3.16660.40081500.29582817296781
3.1666-3.23090.33911400.28962868300881
3.2309-3.30070.37911570.28662864302183
3.3007-3.3770.3111330.27652881301482
3.377-3.46090.28721410.26482896303783
3.4609-3.55380.31611290.25752847297682
3.5538-3.65750.26521810.26432814299581
3.6575-3.77450.36151340.25452881301583
3.7745-3.90810.25421130.23952915302883
3.9081-4.06290.27381410.23022809295081
4.0629-4.24550.21891950.22952887308283
4.2455-4.46610.22681160.20712954307085
4.4661-4.74110.23911460.20472927307384
4.7411-5.09940.21292080.20852903311183
5.0994-5.59860.24561870.23122909309683
5.5986-6.3770.25061100.24792883299383
6.377-7.9190.25991430.2522828297182
7.919-18.010.23281650.22732902306783

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