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- PDB-6wio: Fab antigen complex -

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Basic information

Entry
Database: PDB / ID: 6wio
TitleFab antigen complex
Components
  • Fab Heavy chain
  • Fab Light chain
  • Interleukin-17A
KeywordsCYTOKINE/IMMUNE SYSTEM / Fab / Il-17 / CYTOKINE / CYTOKINE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


positive regulation of interleukin-16 production / granulocyte migration / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / cell death / interleukin-17A-mediated signaling pathway / positive regulation of interleukin-23 production / negative regulation of inflammatory response to wounding / positive regulation of chemokine (C-X-C motif) ligand 1 production / interleukin-17-mediated signaling pathway ...positive regulation of interleukin-16 production / granulocyte migration / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / cell death / interleukin-17A-mediated signaling pathway / positive regulation of interleukin-23 production / negative regulation of inflammatory response to wounding / positive regulation of chemokine (C-X-C motif) ligand 1 production / interleukin-17-mediated signaling pathway / intestinal epithelial structure maintenance / fibroblast activation / positive regulation of bicellular tight junction assembly / positive regulation of osteoclast differentiation / positive regulation of cytokine production involved in inflammatory response / keratinocyte proliferation / cellular response to interleukin-1 / defense response to fungus / keratinocyte differentiation / Notch signaling pathway / positive regulation of interleukin-12 production / positive regulation of interleukin-1 beta production / cytokine activity / positive regulation of interleukin-6 production / response to wounding / positive regulation of tumor necrosis factor production / cell-cell signaling / defense response to Gram-negative bacterium / Interleukin-4 and Interleukin-13 signaling / gene expression / adaptive immune response / defense response to Gram-positive bacterium / immune response / inflammatory response / protein heterodimerization activity / external side of plasma membrane / innate immune response / apoptotic process / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region
Similarity search - Function
Interleukin-17, chordata / Interleukin-17 family / Interleukin-17 / Cystine-knot cytokine / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsAntonysamy, S.
CitationJournal: Plos One / Year: 2020
Title: Rapid and robust antibody Fab fragment crystallization utilizing edge-to-edge beta-sheet packing.
Authors: Lieu, R. / Antonysamy, S. / Druzina, Z. / Ho, C. / Kang, N.R. / Pustilnik, A. / Wang, J. / Atwell, S.
History
DepositionApr 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _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

Downloads & links

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Assembly

Deposited unit
A: Fab Heavy chain
B: Fab Light chain
C: Interleukin-17A


Theoretical massNumber of molelcules
Total (without water)66,5663
Polymers66,5663
Non-polymers00
Water2,936163
1
A: Fab Heavy chain
B: Fab Light chain
C: Interleukin-17A

A: Fab Heavy chain
B: Fab Light chain
C: Interleukin-17A


Theoretical massNumber of molelcules
Total (without water)133,1316
Polymers133,1316
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_645y+1,x-1,-z1
Buried area14710 Å2
ΔGint-97 kcal/mol
Surface area48930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.256, 73.256, 316.384
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Antibody Fab Heavy chain


Mass: 25036.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: unidentified baculovirus
#2: Antibody Fab Light chain


Mass: 23172.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: unidentified baculovirus
#3: Protein Interleukin-17A / IL-17A / Cytotoxic T-lymphocyte-associated antigen 8 / CTLA-8


Mass: 18356.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL17A, CTLA8, IL17 / Production host: unidentified baculovirus / References: UniProt: Q16552
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 3.19 Å3/Da / Density % sol: 61.42 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 20% PEG 3350 + 200mM Ammonium Chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.17→79.1 Å / Num. obs: 46955 / % possible obs: 100 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 23.9
Reflection shellResolution: 2.17→2.28 Å / Num. unique obs: 88363 / Rpim(I) all: 0.3 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VB9

5vb9


Resolution: 2.17→79.1 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.94 / SU R Cruickshank DPI: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.177 / SU Rfree Blow DPI: 0.151 / SU Rfree Cruickshank DPI: 0.15
RfactorNum. reflection% reflectionSelection details
Rfree0.227 2362 5.03 %RANDOM
Rwork0.208 ---
obs0.209 46955 100 %-
Displacement parametersBiso max: 233.06 Å2 / Biso mean: 69.14 Å2 / Biso min: 38.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.3586 Å20 Å20 Å2
2--0.3586 Å20 Å2
3----0.7173 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: final / Resolution: 2.17→79.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4185 0 0 163 4348
Biso mean---61.71 -
Num. residues----545
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1408SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes723HARMONIC5
X-RAY DIFFRACTIONt_it4298HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion560SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4636SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4298HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg5860HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion3.48
X-RAY DIFFRACTIONt_other_torsion17.59
LS refinement shellResolution: 2.17→2.19 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2457 42 4.47 %
Rwork0.2136 898 -
all0.2149 940 -
obs--100 %
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)
15.0101-0.6122-1.08452.0732-0.45932.57250.3029-0.10170.29250.16920.0009-0.1246-0.61640.3705-0.30380.205-0.10830.0937-0.2046-0.0583-0.164650.999-8.905622.0292
22.11390.5913-1.44534.258-0.52252.87870.1166-0.11010.0350.2886-0.12370.00720.07370.03210.0070.23330.00690.1113-0.17560.04290.064522.2612-19.527141.7225
32.49880.1029-1.04483.2475-1.54793.0455-0.1363-0.2394-0.41510.1980.09760.0740.08680.46230.03870.07840.03470.0232-0.07770.0008-0.037652.7272-30.887824.2803
43.8004-0.1691-0.71272.5061-0.11211.5958-0.08760.1166-0.1817-0.2302-0.0390.24310.0815-0.21170.12660.19080.01990.1011-0.23050.01590.030417.5902-32.032333.1459
53.3779-0.24990.19691.58810.16884.37560.04480.37910.864-0.17460.1058-0.4778-1.03130.7145-0.15060.3328-0.3040.15460.09-0.01880.124268.7621.98170.2148
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|126 }A1 - 126
2X-RAY DIFFRACTION2{ A|127 - A|230 }A127 - 230
3X-RAY DIFFRACTION3{ B|1 - B|108 }B1 - 108
4X-RAY DIFFRACTION4{ B|109 - B|213 }B109 - 213
5X-RAY DIFFRACTION5{ C|60 - C|161 }C60 - 161

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