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- PDB-7jwq: Fab CJ11 in complex IL-1beta peptide liberated by Caspase cleavage -

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Basic information

Entry
Database: PDB / ID: 7jwq
TitleFab CJ11 in complex IL-1beta peptide liberated by Caspase cleavage
Components
  • Fab CJ11 Heavy chain
  • Fab CJ11 Light chain
  • IL-1beta peptide
KeywordsIMMUNE SYSTEM / IL-1beta / caspase
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
V: IL-1beta peptide
P: IL-1beta peptide


Theoretical massNumber of molelcules
Total (without water)94,3376
Polymers94,3376
Non-polymers00
Water8,521473
1
A: Fab CJ11 Heavy chain
B: Fab CJ11 Light chain
V: IL-1beta peptide


Theoretical massNumber of molelcules
Total (without water)47,1693
Polymers47,1693
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-29 kcal/mol
Surface area18920 Å2
MethodPISA
2
C: Fab CJ11 Heavy chain
D: Fab CJ11 Light chain
P: IL-1beta peptide


Theoretical massNumber of molelcules
Total (without water)47,1693
Polymers47,1693
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-27 kcal/mol
Surface area18940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.037, 109.550, 65.900
Angle α, β, γ (deg.)90.000, 90.030, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Fab CJ11 Heavy chain


Mass: 23001.879 Da / Num. of mol.: 2
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.: 2
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-1beta peptide


Mass: 768.853 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 473 / Source method: isolated from a natural source / Formula: H2O
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: 2.53 Å3/Da / Density % sol: 51.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5
Details: 0.2 M calcium acetate, 0.1 M sodium cacodylate pH 6.5, 18% PEG8000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 54078 / % possible obs: 85.7 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 11.97
Reflection shellResolution: 2→2.04 Å / Rmerge(I) obs: 0.681 / 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: 2.001→29.527 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 32.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2321 2753 5.09 %
Rwork0.2042 51325 -
obs0.2057 54078 85.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.52 Å2 / Biso mean: 46.1521 Å2 / Biso min: 21.7 Å2
Refinement stepCycle: final / Resolution: 2.001→29.527 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6494 0 0 473 6967
Biso mean---43.32 -
Num. residues----865
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036650
X-RAY DIFFRACTIONf_angle_d0.6319066
X-RAY DIFFRACTIONf_chiral_restr0.0471046
X-RAY DIFFRACTIONf_plane_restr0.0041152
X-RAY DIFFRACTIONf_dihedral_angle_d10.4673946
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.001-2.03510.3945690.3617130945
2.0351-2.07210.4028860.365154952
2.0721-2.11190.3931640.3563176758
2.1119-2.1550.33771050.3197186164
2.155-2.20190.35121470.3137207569
2.2019-2.25310.3372870.305224576
2.2531-2.30940.36671520.2852242081
2.3094-2.37180.36231140.2719257286
2.3718-2.44160.25591530.2716279293
2.4416-2.52040.34011800.2646285996
2.5204-2.61040.28491100.2492298299
2.6104-2.71480.25651330.2354300199
2.7148-2.83830.24821950.2273296799
2.8383-2.98780.22151660.2182292799
2.9878-3.17480.25461650.1952299899
3.1748-3.41960.21971650.18452985100
3.4196-3.76310.18351480.17082995100
3.7631-4.30620.18141770.15112974100
4.3062-5.41980.16011860.13683003100
5.4198-29.5270.22061510.195304499

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