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- PDB-5n92: Crystal Structure of Human IL-17AF -

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Basic information

Entry
Database: PDB / ID: 5n92
TitleCrystal Structure of Human IL-17AF
Components
  • Interleukin-17A
  • Interleukin-17F
KeywordsIMMUNE SYSTEM / Cystine-knot / heterodimer
Function / homology
Function and homology information


regulation of granulocyte macrophage colony-stimulating factor production / regulation of interleukin-2 production / positive regulation of lymphotoxin A production / positive regulation of interleukin-16 production / granulocyte migration / regulation of interleukin-8 production / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / intestinal epithelial structure maintenance / negative regulation of inflammatory response to wounding ...regulation of granulocyte macrophage colony-stimulating factor production / regulation of interleukin-2 production / positive regulation of lymphotoxin A production / positive regulation of interleukin-16 production / granulocyte migration / regulation of interleukin-8 production / 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 / regulation of transforming growth factor beta receptor signaling pathway / interleukin-17-mediated signaling pathway / positive regulation of bicellular tight junction assembly / cytokine receptor binding / fibroblast activation / positive regulation of cytokine production involved in inflammatory response / positive regulation of osteoclast differentiation / cartilage development / regulation of interleukin-6 production / cytokine binding / keratinocyte proliferation / cellular response to interleukin-1 / defense response to fungus / keratinocyte differentiation / Notch signaling pathway / positive regulation of interleukin-12 production / negative regulation of angiogenesis / positive regulation of interleukin-1 beta production / positive regulation of cytokine 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
Interleukin-17A / Interleukin-17F
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsRondeau, J.-M. / Goepfert, A.
CitationJournal: Sci Rep / Year: 2017
Title: The human IL-17A/F heterodimer: a two-faced cytokine with unique receptor recognition properties.
Authors: Goepfert, A. / Lehmann, S. / Wirth, E. / Rondeau, J.M.
History
DepositionFeb 24, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Sep 20, 2017Group: Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Feb 28, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-17A
F: Interleukin-17F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4133
Polymers30,8422
Non-polymers5711
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6090 Å2
ΔGint-27 kcal/mol
Surface area13950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.380, 87.380, 126.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122

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Components

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


Mass: 15146.124 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL17A, CTLA8, IL17 / Plasmid: pCI / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: Q16552
#2: Protein Interleukin-17F / IL-17F / Cytokine ML-1


Mass: 15695.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL17F / Plasmid: pCI / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: Q96PD4
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 3.91 Å3/Da / Density % sol: 68.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7 / Details: 0.1M Bis-Tris-Propane, 0.5M Succinic acid, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99997 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99997 Å / Relative weight: 1
ReflectionResolution: 2.3→15 Å / Num. obs: 22302 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 12.476 % / Biso Wilson estimate: 55.75 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.13 / Rrim(I) all: 0.136 / Χ2: 1.128 / Net I/σ(I): 14.67 / Num. measured all: 278250 / Scaling rejects: 930
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.3-2.3613.1711.4931.7516110.7211.554100
2.36-2.4212.5071.1352.2915860.8031.184100
2.42-2.4912.7650.9592.7515410.8730.998100
2.49-2.5713.3890.7723.4415030.910.802100
2.57-2.6613.530.6034.5814410.9420.627100
2.66-2.7513.3140.4645.9814080.960.483100
2.75-2.8513.0230.3687.2313570.9740.383100
2.85-2.9712.4020.2649.8513130.9860.275100
2.97-3.112.620.21612.1612750.9890.226100
3.1-3.2513.3230.16816.1212120.9940.175100
3.25-3.4312.9780.14219.3611560.9960.148100
3.43-3.6411.780.12921.6410820.9960.13597.7
3.64-3.898.5380.10722.139540.9930.11494
3.89-4.211.3160.08229.169500.9970.08697
4.2-4.612.5440.06635.489030.9980.069100
4.6-5.1412.0880.06136.628320.9990.064100
5.14-5.9411.490.06433.97260.9980.067100
5.94-7.2712.080.05536.676350.9980.057100
7.27-10.2911.3460.04340.395060.9990.045100
10.29-1510.2320.02941.8631110.03100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
BUSTER2.11.4refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→15 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.9167 / SU R Cruickshank DPI: 0.174 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.18 / SU Rfree Blow DPI: 0.167 / SU Rfree Cruickshank DPI: 0.164
RfactorNum. reflection% reflectionSelection details
Rfree0.2413 1110 5 %RANDOM
Rwork0.2053 ---
obs0.2071 22188 99.48 %-
Displacement parametersBiso max: 161.25 Å2 / Biso mean: 52.25 Å2 / Biso min: 11.01 Å2
Baniso -1Baniso -2Baniso -3
1--1.2941 Å20 Å20 Å2
2---1.2941 Å20 Å2
3---2.5882 Å2
Refine analyzeLuzzati coordinate error obs: 0.337 Å
Refinement stepCycle: final / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1821 0 38 96 1955
Biso mean--90.79 49.62 -
Num. residues----229
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d667SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes52HARMONIC2
X-RAY DIFFRACTIONt_gen_planes269HARMONIC5
X-RAY DIFFRACTIONt_it1909HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion261SEMIHARMONIC5
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_contact2037SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1909HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2607HARMONIC21.21
X-RAY DIFFRACTIONt_omega_torsion3.9
X-RAY DIFFRACTIONt_other_torsion17.58
LS refinement shellResolution: 2.3→2.41 Å / Rfactor Rfree error: 0 / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2537 145 5.01 %
Rwork0.223 2747 -
all0.2245 2892 -
obs--99.48 %
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)
12.91.32080.31121.296-0.01520.6158-0.06690.11960.1717-0.18630.06730.1115-0.1205-0.0777-0.0004-0.0640.0253-0.0045-0.0258-0.0283-0.128323.3654-15.608-0.7215
21.35870.19560.1880.97590.25830.76360.02890.1209-0.22320.05540.0723-0.09050.06370.1419-0.1012-0.07730.0010.0091-0.0362-0.024-0.133525.7288-24.41464.6123
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A39 - 153
2X-RAY DIFFRACTION2{ F|* }F44 - 163

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