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- PDB-4mhl: The crystal structure of human interleukin-11 -

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Basic information

Entry
Database: PDB / ID: 4mhl
TitleThe crystal structure of human interleukin-11
ComponentsInterleukin-11
KeywordsPROTEIN BINDING / Four-helix bundle / Long-chain helical cytokine / Cytokine / Growth factor / Interleukin-11 receptor subunit alpha / Membrane glycoprotein 130 / Secreted
Function / homology
Function and homology information


interleukin-11 receptor binding / megakaryocyte differentiation / negative regulation of hormone secretion / interleukin-11-mediated signaling pathway / IL-6-type cytokine receptor ligand interactions / positive regulation of peptidyl-tyrosine phosphorylation / fat cell differentiation / positive regulation of peptidyl-serine phosphorylation / B cell differentiation / cytokine activity ...interleukin-11 receptor binding / megakaryocyte differentiation / negative regulation of hormone secretion / interleukin-11-mediated signaling pathway / IL-6-type cytokine receptor ligand interactions / positive regulation of peptidyl-tyrosine phosphorylation / fat cell differentiation / positive regulation of peptidyl-serine phosphorylation / B cell differentiation / cytokine activity / growth factor activity / cell population proliferation / positive regulation of MAPK cascade / positive regulation of cell population proliferation / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / cytoplasm
Similarity search - Function
Interleukin-11, mammalian / Interleukin-11 / Interleukin 11 / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
FORMAMIDE / Interleukin-11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsGriffin, M.D.W.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: The structure of human interleukin-11 reveals receptor-binding site features and structural differences from interleukin-6.
Authors: Putoczki, T.L. / Dobson, R.C. / Griffin, M.D.
History
DepositionAug 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3947
Polymers19,0721
Non-polymers3216
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.862, 28.169, 41.806
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Interleukin-11 / IL-11 / Adipogenesis inhibitory factor / AGIF


Mass: 19072.248 Da / Num. of mol.: 1 / Fragment: unp residues 23-199
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL11 / Production host: Escherichia coli (E. coli) / References: UniProt: P20809
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-ARF / FORMAMIDE


Type: L-peptide NH3 amino terminus / Mass: 45.041 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH3NO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 1.83 Å3/Da / Density % sol: 32.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 1.25 M ammonium sulfate, 0.2 M lithium sulfate, 0.1 M bis-tris propane, 10% formamide, 0.02% sodium azide, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.09→41.81 Å / Num. obs: 8862 / % possible obs: 99.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 29.4 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.12 / Net I/σ(I): 11.5
Reflection shellResolution: 2.09→2.15 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 2.9 / Num. unique all: 648 / Rsym value: 0.611 / % possible all: 97.5

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.7.0032refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1ALU

1alu


Resolution: 2.09→41.81 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.925 / SU B: 10.593 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.263 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24155 624 7.1 %RANDOM
Rwork0.18435 ---
obs0.18855 8203 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.419 Å2
Baniso -1Baniso -2Baniso -3
1-2.53 Å20 Å20 Å2
2---1.01 Å20 Å2
3----1.52 Å2
Refinement stepCycle: LAST / Resolution: 2.09→41.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1214 0 20 75 1309
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191249
X-RAY DIFFRACTIONr_bond_other_d0.0010.021270
X-RAY DIFFRACTIONr_angle_refined_deg1.3892.0251692
X-RAY DIFFRACTIONr_angle_other_deg0.79732887
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1435158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.20220.68244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.64515205
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9351516
X-RAY DIFFRACTIONr_chiral_restr0.0660.2204
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211386
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02297
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6782.503651
X-RAY DIFFRACTIONr_mcbond_other1.6782.503651
X-RAY DIFFRACTIONr_mcangle_it2.9433.698801
X-RAY DIFFRACTIONr_mcangle_other2.9423.7802
X-RAY DIFFRACTIONr_scbond_it1.5382.559598
X-RAY DIFFRACTIONr_scbond_other1.5372.561599
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6453.855892
X-RAY DIFFRACTIONr_long_range_B_refined6.10319.2711465
X-RAY DIFFRACTIONr_long_range_B_other619.1591450
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.09→2.144 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 45 -
Rwork0.199 584 -
obs-629 98.13 %
Refinement TLS params.Method: refined / Origin x: 17.5909 Å / Origin y: 5.3165 Å / Origin z: 46.4114 Å
111213212223313233
T0.0485 Å2-0.0042 Å20.0098 Å2-0.0284 Å2-0.0115 Å2--0.0167 Å2
L0.6198 °2-0.2335 °20.3045 °2-0.7973 °2-0.2173 °2--0.589 °2
S-0.0149 Å °0.0137 Å °0.0321 Å °0.0397 Å °-0.0351 Å °0.0616 Å °0.0236 Å °-0.0344 Å °0.0499 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A34 - 199
2X-RAY DIFFRACTION1A201 - 206
3X-RAY DIFFRACTION1A301 - 375

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