1JPY

Crystal structure of IL-17F

> Summary

Summary for 1JPY

Descriptorinterleukin 17F
Functional Keywordscystine-knot, cytokine, t-cell derived, dimer, immune system
Biological sourceHomo sapiens (human)
Total number of polymer chains6
Total molecular weight62729.99
Authors
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. (deposition date: 2001-08-03, release date: 2001-09-28, modification date: 2011-07-13)
Primary citation
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.
IL-17s adopt a cystine knot fold: structure and activity of a novel cytokine, IL-17F, and implications for receptor binding.
EMBO J., 20:5332-5341, 2001
PubMed: 11574464
DOI: 10.1093/emboj/20.19.5332
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2.85 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.280201.3%9.5%4.0%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 1jpy
no rotation
Molmil generated image of 1jpy
rotated about x axis by 90°
Molmil generated image of 1jpy
rotated about y axis by 90°

More Biological unit images

Molmil generated image of 1jpy
no rotation
Molmil generated image of 1jpy
rotated about x axis by 90°
Molmil generated image of 1jpy
rotated about y axis by 90°
(*)In the case of coarse surface representation, the asymmetric unit is shown as red ribbon representation.
Coordinate files for Biological unit (1jpy.pdb1.gz [41.71 KB])
Coordinate files for Biological unit (1jpy.pdb2.gz [40.85 KB])

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, B, X, Yinterleukin 17Fpolymer13715335.74
GenBank (AAK83350)
Pfam (PF06083)
UniProt (by SIFTS) (Q96PD4)
Homo sapiens (human)@PDBjIL-17F
SUGAR (N-ACETYL-D-GLUCOSAMINE)non-polymer221.21
SUGAR (NAG-NAG)polymer424.41
SUGAR (2-MER)polymer424.41
SUGAR (N-ACETYL-D-GLUCOSAMINE)non-polymer221.21
SULFATE IONnon-polymer96.11
waterwater18.027

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains6
Total molecular weight62191.5
Non-Polymers*Number of molecules3
Total molecular weight538.5
All*Total molecular weight62730.0
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.85 Å)

Cell axes126.438126.43889.914
Cell angles90.0090.00120.00
SpacegroupP 65
Resolution limits30.00 - 2.85
the highest resolution shell value3.030 - 2.850
R-factor0.238
R-work0.23800
the highest resolution shell value0.318
R-free0.28400
the highest resolution shell value0.377
RMSD bond length0.012
RMSD bond angle1.600

Data Collection Statistics

Resolution limits50.00 - 2.85
the highest resolution shell value -
Number of reflections19294
Number of measurements141778*
Rmerge_l_obs0.088
the highest resolution shell value0.541
Completeness100.0
the highest resolution shell value100.*
Redundancy7.3
the highest resolution shell value7.3
I/sigma(I)-3

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP5.6292 (19*)*

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
11reservoirlithium sulfate1.0 (M)
21reservoirammonium sulfate0.5 (M)
31reservoirethanol1 (%)
41reservoirsodium citrate100 (mM)
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
A0005576cellular_componentextracellular region
A0005615cellular_componentextracellular space
A0005125molecular_functioncytokine activity
A0019955molecular_functioncytokine binding
A0005126molecular_functioncytokine receptor binding
A0042803molecular_functionprotein homodimerization activity
A0051216biological_processcartilage development
A0042089biological_processcytokine biosynthetic process
A0006954biological_processinflammatory response
A0042109biological_processlymphotoxin A biosynthetic process
A0016525biological_processnegative regulation of angiogenesis
A1900017biological_processpositive regulation of cytokine production involved in inflammatory response
A2000778biological_processpositive regulation of interleukin-6 secretion
A0045944biological_processpositive regulation of transcription from RNA polymerase II promoter
A0045423biological_processregulation of granulocyte macrophage colony-stimulating factor biosynthetic process
A0045076biological_processregulation of interleukin-2 biosynthetic process
A0045408biological_processregulation of interleukin-6 biosynthetic process
A0045414biological_processregulation of interleukin-8 biosynthetic process
A0017015biological_processregulation of transforming growth factor beta receptor signaling pathway
B0005576cellular_componentextracellular region
B0005615cellular_componentextracellular space
B0005125molecular_functioncytokine activity
B0019955molecular_functioncytokine binding
B0005126molecular_functioncytokine receptor binding
B0042803molecular_functionprotein homodimerization activity
B0051216biological_processcartilage development
B0042089biological_processcytokine biosynthetic process
B0006954biological_processinflammatory response
B0042109biological_processlymphotoxin A biosynthetic process
B0016525biological_processnegative regulation of angiogenesis
B1900017biological_processpositive regulation of cytokine production involved in inflammatory response
B2000778biological_processpositive regulation of interleukin-6 secretion
B0045944biological_processpositive regulation of transcription from RNA polymerase II promoter
B0045423biological_processregulation of granulocyte macrophage colony-stimulating factor biosynthetic process
B0045076biological_processregulation of interleukin-2 biosynthetic process
B0045408biological_processregulation of interleukin-6 biosynthetic process
B0045414biological_processregulation of interleukin-8 biosynthetic process
B0017015biological_processregulation of transforming growth factor beta receptor signaling pathway
X0005576cellular_componentextracellular region
X0005615cellular_componentextracellular space
X0005125molecular_functioncytokine activity
X0019955molecular_functioncytokine binding
X0005126molecular_functioncytokine receptor binding
X0042803molecular_functionprotein homodimerization activity
X0051216biological_processcartilage development
X0042089biological_processcytokine biosynthetic process
X0006954biological_processinflammatory response
X0042109biological_processlymphotoxin A biosynthetic process
X0016525biological_processnegative regulation of angiogenesis
X1900017biological_processpositive regulation of cytokine production involved in inflammatory response
X2000778biological_processpositive regulation of interleukin-6 secretion
X0045944biological_processpositive regulation of transcription from RNA polymerase II promoter
X0045423biological_processregulation of granulocyte macrophage colony-stimulating factor biosynthetic process
X0045076biological_processregulation of interleukin-2 biosynthetic process
X0045408biological_processregulation of interleukin-6 biosynthetic process
X0045414biological_processregulation of interleukin-8 biosynthetic process
X0017015biological_processregulation of transforming growth factor beta receptor signaling pathway
Y0005576cellular_componentextracellular region
Y0005615cellular_componentextracellular space
Y0005125molecular_functioncytokine activity
Y0019955molecular_functioncytokine binding
Y0005126molecular_functioncytokine receptor binding
Y0042803molecular_functionprotein homodimerization activity
Y0051216biological_processcartilage development
Y0042089biological_processcytokine biosynthetic process
Y0006954biological_processinflammatory response
Y0042109biological_processlymphotoxin A biosynthetic process
Y0016525biological_processnegative regulation of angiogenesis
Y1900017biological_processpositive regulation of cytokine production involved in inflammatory response
Y2000778biological_processpositive regulation of interleukin-6 secretion
Y0045944biological_processpositive regulation of transcription from RNA polymerase II promoter
Y0045423biological_processregulation of granulocyte macrophage colony-stimulating factor biosynthetic process
Y0045076biological_processregulation of interleukin-2 biosynthetic process
Y0045408biological_processregulation of interleukin-6 biosynthetic process
Y0045414biological_processregulation of interleukin-8 biosynthetic process
Y0017015biological_processregulation of transforming growth factor beta receptor signaling pathway
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC12BINDING SITE FOR RESIDUE NDG A 241
ChainResidue
AASN53
AARG73

AC23BINDING SITE FOR RESIDUE NAG B 241
ChainResidue
BASN53
BARG73
BNDG242

AC31BINDING SITE FOR RESIDUE NDG B 242
ChainResidue
BNAG241

AC44BINDING SITE FOR RESIDUE NAG X 241
ChainResidue
XSER16
XASN53
XARG73
XNAG242

AC51BINDING SITE FOR RESIDUE NAG X 242
ChainResidue
XNAG241

AC62BINDING SITE FOR RESIDUE NAG Y 241
ChainResidue
YASN53
YGLN71

AC76BINDING SITE FOR RESIDUE SO4 X 243
ChainResidue
XSER41
XARG42
XGLN105
XGLY106
XCYS107
XHOH244

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
NDG_1jpy_A_24122-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE binding site
ChainResidueligand
AASN53NDG: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
AARG73NDG: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

NAG_1jpy_B_2414N-ACETYL-D-GLUCOSAMINE binding site
ChainResidueligand
BASN53NAG: N-ACETYL-D-GLUCOSAMINE
BGLN71-ARG73NAG: N-ACETYL-D-GLUCOSAMINE

NAG_1jpy_X_2415N-ACETYL-D-GLUCOSAMINE binding site
ChainResidueligand
XASN53NAG: N-ACETYL-D-GLUCOSAMINE
XGLN71-ASN74NAG: N-ACETYL-D-GLUCOSAMINE

NAG_1jpy_Y_2414N-ACETYL-D-GLUCOSAMINE binding site
ChainResidueligand
YASN53NAG: N-ACETYL-D-GLUCOSAMINE
YGLN71-ARG73NAG: N-ACETYL-D-GLUCOSAMINE

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
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Catalytic Information from CSA

site_idNumber of ResiduesDetails
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Catalytic Information from CATRES

site_idNumber of ResiduesDetails

> Sequence Neighbor

> Downloads

Resources

File formatFile name (file size)
PDBallpdb1jpy.ent.gz (85.38 KB)
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all (no-compress)pdb1jpy.ent (361.73 KB)
header onlypdb1jpy.ent.gz (7.28 KB)
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PDBx/mmCIF1jpy.cif.gz (103.76 KB)
PDBMLall1jpy.xml.gz (162.8 KB)
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no-atom1jpy-noatom.xml.gz (26.39 KB)
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ext-atom1jpy-extatom.xml.gz (91.95 KB)
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PDBMLplusall1jpy-plus.xml.gz (165.85 KB)
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no-atom1jpy-plus-noatom.xml.gz (29.44 KB)
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add only1jpy-add.xml.gz (3.05 KB)
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RDF1jpy.rdf.gz (49.25 KB)
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Structure factorsr1jpysf.ent.gz (143.77 KB)
Biological unit (PDB format)1jpy.pdb1.gz (41.71 KB) (A,B)
*author and software defined assembly, 2 molecule(s) (dimeric)
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1jpy.pdb2.gz (40.85 KB) (X,Y)
*author and software defined assembly, 2 molecule(s) (dimeric)
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Validation reportsPDF1jpy​_validation.pdf.gz (347.97 KB)
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PDF-full1jpy​_full​_validation.pdf.gz (363.38 KB)
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XML1jpy​_validation.xml.gz (23.21 KB)
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PNG1jpy​_multipercentile​_validation.png.gz (150.64 KB)
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SVG1jpy​_multipercentile​_validation.svg.gz (945 B)
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Sequence (fasta)1jpy​_seq.txt
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