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- PDB-6hgo: Crystal Structure of human IL-17F -

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Basic information

Entry
Database: PDB / ID: 6hgo
TitleCrystal Structure of human IL-17F
ComponentsInterleukin-17F
KeywordsIMMUNE SYSTEM / cystine-knot / cytokine
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 / regulation of interleukin-8 production / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / positive regulation of chemokine (C-X-C motif) ligand 1 production / interleukin-17-mediated signaling pathway / regulation of transforming growth factor beta receptor signaling pathway / cytokine receptor binding ...regulation of granulocyte macrophage colony-stimulating factor production / regulation of interleukin-2 production / positive regulation of lymphotoxin A production / regulation of interleukin-8 production / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / positive regulation of chemokine (C-X-C motif) ligand 1 production / interleukin-17-mediated signaling pathway / regulation of transforming growth factor beta receptor signaling pathway / cytokine receptor binding / positive regulation of cytokine production involved in inflammatory response / cartilage development / regulation of interleukin-6 production / cytokine binding / negative regulation of angiogenesis / positive regulation of cytokine production / cytokine activity / positive regulation of interleukin-6 production / Interleukin-4 and Interleukin-13 signaling / defense response to Gram-negative bacterium / adaptive immune response / defense response to Gram-positive bacterium / inflammatory response / protein heterodimerization activity / innate immune response / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsRondeau, J.M. / Goepfert, A.
CitationJournal: Immunity / Year: 2020
Title: Structural Analysis Reveals that the Cytokine IL-17F Forms a Homodimeric Complex with Receptor IL-17RC to Drive IL-17RA-Independent Signaling.
Authors: Goepfert, A. / Lehmann, S. / Blank, J. / Kolbinger, F. / Rondeau, J.M.
History
DepositionAug 23, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2020Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.country ..._chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)63,9689
Polymers62,7844
Non-polymers1,1845
Water4,035224
1
A: Interleukin-17F
B: Interleukin-17F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0374
Polymers31,3922
Non-polymers6462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7440 Å2
ΔGint-37 kcal/mol
Surface area14740 Å2
MethodPISA
2
C: Interleukin-17F
D: Interleukin-17F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9305
Polymers31,3922
Non-polymers5383
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7660 Å2
ΔGint-59 kcal/mol
Surface area14470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.195, 126.195, 88.539
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein
Interleukin-17F / IL-17F / Cytokine ML-1


Mass: 15695.895 Da / Num. of mol.: 4 / Fragment: IL-17F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL17F / Plasmid: pCI-derived / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: Q96PD4
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 3.24 Å3/Da / Density % sol: 62.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 200mM ammonium sulfate, 20.0% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99985 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 8, 2013 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99985 Å / Relative weight: 1
ReflectionResolution: 2.1→63.1 Å / Num. obs: 46829 / % possible obs: 100 % / Redundancy: 10.193 % / Biso Wilson estimate: 48.76 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rrim(I) all: 0.082 / Χ2: 1.027 / Net I/σ(I): 18.6 / Num. measured all: 477335 / Scaling rejects: 7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.1510.1171.4131.6634210.6031.488100
2.15-2.2110.5981.122.1533820.7511.177100
2.21-2.2810.4380.9372.6532550.7820.986100
2.28-2.3510.4120.6663.6331960.8880.701100
2.35-2.4210.2310.5354.5130700.9210.563100
2.42-2.519.7440.4185.6129920.9520.442100
2.51-2.69.9750.3267.2128740.9680.344100
2.6-2.7110.610.2469.7827530.980.259100
2.71-2.8310.6110.18512.5126610.990.194100
2.83-2.9710.5140.13816.8125440.9940.145100
2.97-3.1310.2740.10421.5324190.9960.11100
3.13-3.329.7260.07927.3622960.9980.083100
3.32-3.5510.0410.06235.6321470.9980.065100
3.55-3.8310.310.05241.2620140.9990.054100
3.83-4.210.0240.04247.5118510.9990.04599.9
4.2-4.79.3270.03850.7816820.9990.04100
4.7-5.429.7120.03553.4914680.9990.037100
5.42-6.6410.40.03552.4712720.9990.037100
6.64-9.399.5980.02855.9797310.03100
9.39-63.110.0750.02364.335590.9990.02499.6

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Processing

Software
NameVersionClassification
XDSSept. 26, 2012data reduction
XSCALEJuly 4, 2012data scaling
BUSTER2.11.7refinement
PDB_EXTRACT3.24data extraction
BUSTERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1JPY

1jpy


Resolution: 2.1→63.1 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.904 / SU R Cruickshank DPI: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.155 / SU Rfree Blow DPI: 0.137 / SU Rfree Cruickshank DPI: 0.137
RfactorNum. reflection% reflectionSelection details
Rfree0.22 2342 5 %RANDOM
Rwork0.199 ---
obs0.2 46829 100 %-
Displacement parametersBiso max: 180.18 Å2 / Biso mean: 60.96 Å2 / Biso min: 25.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.2041 Å20 Å20 Å2
2---0.2041 Å20 Å2
3---0.4082 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: final / Resolution: 2.1→63.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3862 0 75 224 4161
Biso mean--100.86 53.25 -
Num. residues----496
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1425SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes111HARMONIC2
X-RAY DIFFRACTIONt_gen_planes574HARMONIC5
X-RAY DIFFRACTIONt_it4041HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion554SEMIHARMONIC5
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_contact4559SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4041HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5508HARMONIC21.12
X-RAY DIFFRACTIONt_omega_torsion3.18
X-RAY DIFFRACTIONt_other_torsion16.59
LS refinement shellResolution: 2.1→2.15 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2415 171 5.01 %
Rwork0.2273 3242 -
all0.228 3413 -
obs--99.97 %
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)
13.13151.4795-1.95341.8027-0.9174.04930.2132-0.2171-0.04280.2251-0.0997-0.1556-0.75650.1802-0.1135-0.0654-0.0569-0.0397-0.1863-0.0011-0.096131.9053-37.79192.9862
21.7290.7915-1.27181.6104-0.63773.7507-0.05540.068-0.0256-0.12180.0175-0.0054-0.3347-0.17610.0379-0.131-0.0372-0.0294-0.11110.0208-0.091828.0549-42.4912-3.2951
33.26320.6821.23780.83680.24414.92480.1015-0.3439-0.2308-0.0806-0.0341-0.19140.85910.1712-0.0675-0.1354-0.04490.0185-0.1661-0.0024-0.126236.5956-67.3922.3203
42.15470.28380.24160.6595-0.34354.9532-0.0902-0.13510.0835-0.16280.0068-0.1340.37190.77120.0835-0.1878-0.01820.0177-0.0946-0.0379-0.130240.8928-62.9173-2.8244
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A38 - 163
2X-RAY DIFFRACTION2{ B|* }B37 - 158
3X-RAY DIFFRACTION3{ C|* }C34 - 160
4X-RAY DIFFRACTION4{ D|* }D38 - 158

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