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- PDB-1jpy: Crystal structure of IL-17F -

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Basic information

Entry
Database: PDB / ID: 1jpy
TitleCrystal structure of IL-17F
Componentsinterleukin 17F
KeywordsIMMUNE SYSTEM / cystine-knot / cytokine / t-cell derived / dimer
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 / adaptive immune response / defense response to Gram-negative bacterium / 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 / MAD / Resolution: 2.85 Å
AuthorsHymowitz, S.G. / Filvaroff, E.H. / Yin, J. / Lee, J. / Cai, L. / Risser, P. / Maruoka, M. / Mao, W. / Foster, J. / Kelley, R. ...Hymowitz, S.G. / Filvaroff, E.H. / Yin, J. / Lee, J. / Cai, L. / Risser, P. / Maruoka, M. / Mao, W. / Foster, J. / Kelley, R. / Pan, G. / Gurney, A.L. / de Vos, A.M. / Starovasnik, M.A.
CitationJournal: EMBO J. / Year: 2001
Title: IL-17s adopt a cystine knot fold: structure and activity of a novel cytokine, IL-17F, and implications for receptor binding.
Authors: Hymowitz, S.G. / Filvaroff, E.H. / Yin, J.P. / Lee, J. / Cai, L. / Risser, P. / Maruoka, M. / Mao, W. / Foster, J. / Kelley, R.F. / Pan, G. / Gurney, A.L. / de Vos, A.M. / Starovasnik, M.A.
History
DepositionAug 3, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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_chiral / struct_asym / struct_conn / struct_ref_seq_dif / 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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
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 17F
B: interleukin 17F
X: interleukin 17F
Y: interleukin 17F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7309
Polymers61,3424
Non-polymers1,3875
Water48627
1
A: interleukin 17F
B: interleukin 17F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3174
Polymers30,6712
Non-polymers6462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7270 Å2
ΔGint-39 kcal/mol
Surface area14090 Å2
MethodPISA
2
X: interleukin 17F
Y: interleukin 17F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4135
Polymers30,6712
Non-polymers7423
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7580 Å2
ΔGint-55 kcal/mol
Surface area13790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.438, 126.438, 89.914
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Cell settinghexagonal
Space group name H-MP65
DetailsThe biologically active unit is a dimer. The assymetric unit is formed of two dimers.

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Components

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Protein , 1 types, 4 molecules ABXY

#1: Protein
interleukin 17F / IL-17F


Mass: 15335.575 Da / Num. of mol.: 4 / Fragment: Secreted IL-17F
Source method: isolated from a genetically manipulated source
Details: the first four residues, GSHM, are from the vector / Source: (gene. exp.) Homo sapiens (human) / Gene: IL-17F
Plasmid details: A modified plasmid was used which incorporated an N-terminal his tag and thrombin site under the control of the viral coat protein promotor
Production host: unidentified baculovirus / Strain (production host): Hi5 cells / References: GenBank: 15077800, UniProt: Q96PD4*PLUS

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Sugars , 3 types, 4 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-alpha-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
DGlcpNAca1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1a_1-5_2*NCC/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: 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
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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

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Non-polymers , 2 types, 28 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.3 Å3/Da / Density % sol: 64 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: well solution consisted of 1.0M Lithium Sulfate, 0.5M Ammonium Sulfate, 100mM Sodium Citrate, 1% Ethanol at 5.6, VAPOR DIFFUSION, HANGING DROP at 292K
Crystal grow
*PLUS
Temperature: 19 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.0 Mlithium sulfate1reservoir
20.5 Mammonium sulfate1reservoir
31 %ethanol1reservoir
4100 mMsodium citrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 13, 2001
RadiationMonochromator: SSRL beam line 9-2 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. all: 19294 / Num. obs: 19294 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 63.8 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 7.7
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.541 / Num. unique all: 1912 / Rsym value: 0.541 / % possible all: 100
Reflection
*PLUS
% possible obs: 100 % / Num. measured all: 141778
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SCALEPACKdata scaling
MLPHAREphasing
X-PLOR98.1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.85→30 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0.2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: The structure was solved using data collected at three different wavelenghts from crystals that had been soaked in the Hg containing compound thimerosal but was refined against a native data ...Details: The structure was solved using data collected at three different wavelenghts from crystals that had been soaked in the Hg containing compound thimerosal but was refined against a native data set collected on a crystal that was not derivatized. The crystollgraphic statistics presented here are for the native data set. Used maximum likelihood residual. The program REFMAC was used at the initial stages of refinement. A bulk solvent corrections was applied in Xplor98.1 as part of the refinement process. This correction has not been applied to the depositted structure factors
RfactorNum. reflection% reflectionSelection details
Rfree0.284 1127 5.9 %SHELLS
Rwork0.238 ---
all0.24 19258 --
obs0.238 19202 100 %-
Solvent computationSolvent model: BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å2-0.25 Å20 Å2
2--0.22 Å20 Å2
3----0.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3725 0 89 27 3841
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_dihedral_angle_d28.7
X-RAY DIFFRACTIONx_improper_angle_d0.87
X-RAY DIFFRACTIONx_mcbond_it3.691.5
X-RAY DIFFRACTIONx_mcangle_it6.242
X-RAY DIFFRACTIONx_scbond_it4.152
X-RAY DIFFRACTIONx_scangle_it6.092.5
LS refinement shellResolution: 2.85→3.03 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.377 178 5.6 %
Rwork0.318 2992 -
obs-1912 100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOP19.ION
X-RAY DIFFRACTION3PARAM19.IONPARAM19.SOL
X-RAY DIFFRACTION4PARAM3.CHOPARAM3.CHO
X-RAY DIFFRACTION5PARAM.SO4PARAM.SO4
Software
*PLUS
Name: X-PLOR / Version: 98.1 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 5.9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 47.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.87
X-RAY DIFFRACTIONx_mcbond_it3.691.5
X-RAY DIFFRACTIONx_scbond_it4.152
X-RAY DIFFRACTIONx_mcangle_it6.242
X-RAY DIFFRACTIONx_scangle_it6.092.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.377 / % reflection Rfree: 5.6 % / Rfactor Rwork: 0.318

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