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- PDB-6wir: Fab antigen complex -

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Basic information

Entry
Database: PDB / ID: 6wir
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 / molecular replacement / Resolution: 2.96 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)67,5793
Polymers67,5793
Non-polymers00
Water1,29772
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)135,1576
Polymers135,1576
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_645y+1,x-1,-z1
Buried area12850 Å2
ΔGint-100 kcal/mol
Surface area46790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.400, 73.400, 326.409
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: 26049.090 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.: 72 / 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: 3.25 Å3/Da / Density % sol: 62.19 %
Crystal growTemperature: 274 K / Method: vapor diffusion, sitting drop
Details: 100mM Hepes pH 7, 15% PEG4K, 200mM Magnesium 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 6M / Detector: PIXEL / Date: Jun 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.96→71.61 Å / Num. obs: 19713 / % possible obs: 100 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 20.2
Reflection shellResolution: 2.96→3.12 Å / Mean I/σ(I) obs: 2.9 / Num. unique obs: 2781 / Rpim(I) all: 0.242

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Phasing

PhasingMethod: molecular replacement

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Processing

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

5vb9


Resolution: 2.96→71.61 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.907 / SU R Cruickshank DPI: 0.726 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.88 / SU Rfree Blow DPI: 0.355 / SU Rfree Cruickshank DPI: 0.351
RfactorNum. reflection% reflectionSelection details
Rfree0.26 977 4.96 %RANDOM
Rwork0.217 ---
obs0.219 19713 100 %-
Displacement parametersBiso max: 263.39 Å2 / Biso mean: 111.61 Å2 / Biso min: 61.74 Å2
Baniso -1Baniso -2Baniso -3
1--1.8445 Å20 Å20 Å2
2---1.8445 Å20 Å2
3---3.6889 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: final / Resolution: 2.96→71.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4053 0 0 72 4125
Biso mean---92.23 -
Num. residues----528
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1367SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes700HARMONIC5
X-RAY DIFFRACTIONt_it4158HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion542SEMIHARMONIC5
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_contact4627SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4158HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5668HARMONIC21.24
X-RAY DIFFRACTIONt_omega_torsion3.1
X-RAY DIFFRACTIONt_other_torsion21.58
LS refinement shellResolution: 2.96→2.98 Å / Rfactor Rfree error: 0 / Total num. of bins used: 48
RfactorNum. reflection% reflection
Rfree0.2937 24 5.84 %
Rwork0.2275 387 -
all0.231 411 -
obs--100 %
Refinement TLS params.

T11: 0.304 Å2 / 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 °)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.5155-2.6942-2.43274.51260.35010-0.0989-0.04110.37960.51790.348-0.3895-0.43720.5442-0.2492-0.1520.0409-0.304-0.0825-0.30449.9663-10.341322.2078
21.1246-0.9857-2.29598.31552.91048.31550.1515-0.18510.14290.4353-0.2308-0.0992-0.26760.0360.07920.02640.152-0.3040.06930.253622.0729-21.190442.4345
32.77990.26510.72677.8652-2.42912.993-0.229-0.1445-0.54420.5280.067-0.03470.12090.54420.162-0.00520.1438-0.304-0.0721-0.202952.2273-32.283524.3199
401.1116-1.85985.12440.5771.2025-0.05950.2968-0.0465-0.328-0.19560.32510.0552-0.41020.25510.05740.152-0.3040.02410.092817.4007-33.792334.4554
53.11122.91040.25456.26280.14156.8017-0.00630.48620.54420.0281-0.1133-0.5442-0.46750.46270.1196-0.1520.13690.22370.07970.296766.85713.48111.1259
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|227 }A127 - 227
3X-RAY DIFFRACTION3{ B|1 - B|108 }B1 - 108
4X-RAY DIFFRACTION4{ B|109 - B|212 }B109 - 212
5X-RAY DIFFRACTION5{ C|41 - C|129 }C41 - 129

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