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- PDB-5vb9: IL-17A in complex with peptide -

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Basic information

Entry
Database: PDB / ID: 5vb9
TitleIL-17A in complex with peptide
Components
  • Interleukin-17A
  • Peptide inhibitor
KeywordsIMMUNE SYSTEM / INHIBITOR / IL17 / inhibitor / IMMUNE SYSTEM - INHIBITOR complex
Function / homology
Function and homology information


positive regulation of interleukin-16 production / granulocyte migration / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / intestinal epithelial structure maintenance / negative regulation of inflammatory response to wounding / interleukin-17A-mediated signaling pathway / positive regulation of interleukin-23 production / cell death / positive regulation of chemokine (C-X-C motif) ligand 1 production ...positive regulation of interleukin-16 production / granulocyte migration / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / intestinal epithelial structure maintenance / negative regulation of inflammatory response to wounding / interleukin-17A-mediated signaling pathway / positive regulation of interleukin-23 production / cell death / positive regulation of chemokine (C-X-C motif) ligand 1 production / interleukin-17-mediated signaling pathway / positive regulation of bicellular tight junction assembly / fibroblast activation / 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 / response to wounding / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / cell-cell signaling / gene expression / Interleukin-4 and Interleukin-13 signaling / defense response to Gram-negative bacterium / adaptive immune response / defense response to Gram-positive bacterium / inflammatory response / immune 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 Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Ribbon / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsAntonysamy, S. / Russell, M. / Zhang, A. / Groshong, C. / Manglicmot, D. / Lu, F. / Benach, J. / Wasserman, S.R. / Zhang, F. / Afshar, S. ...Antonysamy, S. / Russell, M. / Zhang, A. / Groshong, C. / Manglicmot, D. / Lu, F. / Benach, J. / Wasserman, S.R. / Zhang, F. / Afshar, S. / Bina, H. / Broughton, H. / Chalmers, M. / Dodge, J. / Espada, A. / Jones, S. / Ting, J.P. / Woodman, M.
CitationJournal: PLoS ONE / Year: 2018
Title: Utilization of peptide phage display to investigate hotspots on IL-17A and what it means for drug discovery.
Authors: Ting, J.P. / Tung, F. / Antonysamy, S. / Wasserman, S. / Jones, S.B. / Zhang, F.F. / Espada, A. / Broughton, H. / Chalmers, M.J. / Woodman, M.E. / Bina, H.A. / Dodge, J.A. / Benach, J. / ...Authors: Ting, J.P. / Tung, F. / Antonysamy, S. / Wasserman, S. / Jones, S.B. / Zhang, F.F. / Espada, A. / Broughton, H. / Chalmers, M.J. / Woodman, M.E. / Bina, H.A. / Dodge, J.A. / Benach, J. / Zhang, A. / Groshong, C. / Manglicmot, D. / Russell, M. / Afshar, S.
History
DepositionMar 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-17A
B: Interleukin-17A
C: Peptide inhibitor
D: Peptide inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4138
Polymers31,1914
Non-polymers2224
Water5,044280
1
A: Interleukin-17A
C: Peptide inhibitor
hetero molecules

A: Interleukin-17A
C: Peptide inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4408
Polymers31,1914
Non-polymers2484
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
Buried area8400 Å2
ΔGint-41 kcal/mol
Surface area13630 Å2
MethodPISA
2
B: Interleukin-17A
D: Peptide inhibitor
hetero molecules

B: Interleukin-17A
D: Peptide inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3868
Polymers31,1914
Non-polymers1954
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
Buried area9210 Å2
ΔGint-66 kcal/mol
Surface area11250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.771, 55.122, 143.953
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-314-

HOH

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Components

#1: Protein Interleukin-17A / IL-17A / Cytotoxic T-lymphocyte-associated antigen 8 / CTLA-8


Mass: 13750.489 Da / Num. of mol.: 2 / Fragment: UNP residues 38-155
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL17A, CTLA8, IL17 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: Q16552
#2: Protein/peptide Peptide inhibitor


Mass: 1845.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O

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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: 2.34 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein at 7.1 mg/ml in 10mM Bis-Tris pH 6.5, 10% glycerol, 150mM NaCl with 2 mM of peptide, equilibrated against a reservoir containing 20% PEG 3350 and 200mM Lithium Chloride.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.7→22.47 Å / Num. all: 32769 / Num. obs: 32769 / % possible obs: 99.1 % / Redundancy: 6.7 % / Biso Wilson estimate: 23.54 Å2 / Rpim(I) all: 0.036 / Rrim(I) all: 0.094 / Rsym value: 0.08 / Net I/av σ(I): 5.2 / Net I/σ(I): 12.6 / Num. measured all: 220360
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.7-1.796.30.5121.52955646610.2380.6080.512398.3
1.79-1.96.50.3042.52871444330.1410.3650.3044.798.6
1.9-2.036.60.1983.62761142030.0910.2350.1987.299.2
2.03-2.196.70.1345.12626139120.0610.1590.13410.599.1
2.19-2.46.80.1116.12478936270.0510.1330.11112.999.2
2.4-2.697.10.0867.72357533200.0380.1010.08616.499.7
2.69-3.17.20.078.52114829530.030.0810.0720.699.8
3.1-3.87.10.0628.91779825190.0270.0730.06224.899.8
3.8-5.386.90.069.21381520060.0260.070.0627.199.6
5.38-71.9776.20.05710709311350.0260.0670.05724.796.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA3.3.22data scaling
PHASERphasing
BUSTER2.11.6refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→22.47 Å / Cor.coef. Fo:Fc: 0.9562 / Cor.coef. Fo:Fc free: 0.944 / SU R Cruickshank DPI: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.106 / SU Rfree Blow DPI: 0.101 / SU Rfree Cruickshank DPI: 0.095
RfactorNum. reflection% reflectionSelection details
Rfree0.2113 1639 5.02 %RANDOM
Rwork0.1819 ---
obs0.1834 32662 98.51 %-
Displacement parametersBiso max: 143.24 Å2 / Biso mean: 38.6 Å2 / Biso min: 10.22 Å2
Baniso -1Baniso -2Baniso -3
1--2.5327 Å20 Å20 Å2
2--1.1839 Å20 Å2
3---1.3488 Å2
Refine analyzeLuzzati coordinate error obs: 0.221 Å
Refinement stepCycle: final / Resolution: 1.7→22.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1942 0 13 282 2237
Biso mean--31.8 46.87 -
Num. residues----239
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d685SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes51HARMONIC2
X-RAY DIFFRACTIONt_gen_planes294HARMONIC5
X-RAY DIFFRACTIONt_it2044HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion259SEMIHARMONIC5
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_contact2396SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2044HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2789HARMONIC20.99
X-RAY DIFFRACTIONt_omega_torsion3.91
X-RAY DIFFRACTIONt_other_torsion14.68
LS refinement shellResolution: 1.7→1.76 Å / Rfactor Rfree error: 0 / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2374 149 5.04 %
Rwork0.1987 2809 -
all0.2006 2958 -
obs--98.21 %
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)
10.3879-0.08270.06560.58570.05712.84470.0552-0.0014-0.00470.0517-0.07420.0515-0.1668-0.16150.019-0.02950.00630.0029-0.0875-0.0089-0.04814.655259.5365147.842
20.71310.55030.07330.35550.04719.35130.1706-0.32580.05930.1946-0.1524-0.0186-0.8323-0.0051-0.01820.2005-0.04640.0026-0.0353-0.03-0.245618.322261.2469204.171
32.6895-0.54040.08465.6263.12974.4417-0.0247-0.10360.1079-0.0984-0.0573-0.2915-0.50430.46750.0820.0408-0.07330.0119-0.05660.0228-0.018524.911665.9944155.22
46.8579-1.8101-1.8128.7209-0.29130.0063-0.0076-0.13620.14860.26440.19080.6668-0.1344-0.6032-0.18320.08340.11210.08710.0260.0219-0.18347.404361.3894197.088
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A14 - 131
2X-RAY DIFFRACTION2{ B|* }B17 - 127
3X-RAY DIFFRACTION3{ C|* }C1 - 15
4X-RAY DIFFRACTION4{ D|* }D1 - 15

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