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- PDB-3e0g: Structure of the Leukemia Inhibitory Factor Receptor (LIF-R) doma... -

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Basic information

Entry
Database: PDB / ID: 3e0g
TitleStructure of the Leukemia Inhibitory Factor Receptor (LIF-R) domains D1-D5
ComponentsLeukemia inhibitory factor receptor
KeywordsSIGNALING PROTEIN/CYTOKINE / Ig domain / Cytokine Binding Homology Region (CHR) / Cell membrane / Disease mutation / Glycoprotein / Membrane / Receptor / Secreted / Transmembrane / SIGNALING PROTEIN-CYTOKINE COMPLEX
Function / homology
Function and homology information


leukemia inhibitory factor receptor activity / oncostatin-M-mediated signaling pathway / leukemia inhibitory factor signaling pathway / RUNX1 regulates transcription of genes involved in interleukin signaling / ciliary neurotrophic factor receptor binding / ciliary neurotrophic factor-mediated signaling pathway / IL-6-type cytokine receptor ligand interactions / cytokine receptor activity / growth factor binding / cytokine binding ...leukemia inhibitory factor receptor activity / oncostatin-M-mediated signaling pathway / leukemia inhibitory factor signaling pathway / RUNX1 regulates transcription of genes involved in interleukin signaling / ciliary neurotrophic factor receptor binding / ciliary neurotrophic factor-mediated signaling pathway / IL-6-type cytokine receptor ligand interactions / cytokine receptor activity / growth factor binding / cytokine binding / response to cytokine / cytokine-mediated signaling pathway / receptor complex / cell surface receptor signaling pathway / external side of plasma membrane / positive regulation of cell population proliferation / extracellular exosome / plasma membrane
Similarity search - Function
Leukemia inhibitory factor receptor, N-terminal / Leukemia inhibitory factor receptor N-terminal domain / Leukemia inhibitory factor receptor, D2 domain / : / Leukemia inhibitory factor receptor D2 domain / Leukemia inhibitory factor receptor, Ig-like domain / Long hematopoietin receptor, Gp130 family 2, conserved site / Long hematopoietin receptor, gp130 family signature. / : / Fibronectin type III domain ...Leukemia inhibitory factor receptor, N-terminal / Leukemia inhibitory factor receptor N-terminal domain / Leukemia inhibitory factor receptor, D2 domain / : / Leukemia inhibitory factor receptor D2 domain / Leukemia inhibitory factor receptor, Ig-like domain / Long hematopoietin receptor, Gp130 family 2, conserved site / Long hematopoietin receptor, gp130 family signature. / : / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Leukemia inhibitory factor receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsLupardus, P.J. / Garcia, K.C.
CitationJournal: Mol.Cell / Year: 2008
Title: Structural organization of a full-length gp130/LIF-R cytokine receptor transmembrane complex.
Authors: Skiniotis, G. / Lupardus, P.J. / Martick, M. / Walz, T. / Garcia, K.C.
History
DepositionJul 31, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / 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_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 / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _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_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Oct 30, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / refine
Item: _refine.pdbx_starting_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leukemia inhibitory factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0675
Polymers54,9151
Non-polymers2,1524
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.008, 143.169, 80.362
Angle α, β, γ (deg.)90.00, 110.38, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Leukemia inhibitory factor receptor / LIF receptor / LIF-R


Mass: 54914.973 Da / Num. of mol.: 1 / Fragment: UNP residues 52 to 534 / Mutation: N19Q/N40Q/N95Q/N143Q/N195Q
Source method: isolated from a genetically manipulated source
Details: Gp67 signal sequence at N-terminus and 6xHis tag at C-terminus
Source: (gene. exp.) Homo sapiens (human) / Gene: LIFR / Plasmid: pACGP67 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): HiFive / References: UniProt: P42702
#2: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][b-L-Fucp]{}}}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.: 2
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: 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
Has protein modificationY

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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: 4.42 Å3/Da / Density % sol: 72.17 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 M Sodium Citrate pH 5.0, 0.1 M Lithium Sulfate, 8% PEG-3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 140 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. obs: 16991 / % possible obs: 98.2 % / Redundancy: 3.1 % / Biso Wilson estimate: 74.762 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 10.8
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.611 / Mean I/σ(I) obs: 2 / Num. unique all: 2480 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→30 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.868 / SU B: 60.725 / SU ML: 0.476 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.456 / ESU R Free: 0.489 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30862 872 5.1 %RANDOM
Rwork0.25184 ---
obs0.25476 16071 97.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 94.338 Å2
Baniso -1Baniso -2Baniso -3
1-5.72 Å20 Å26.84 Å2
2---0.88 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 3.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3844 0 143 0 3987
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224099
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3631.9785599
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9755477
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.90424.719178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.91115675
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6751516
X-RAY DIFFRACTIONr_chiral_restr0.080.2660
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022987
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.290.21962
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3230.22839
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2119
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3350.228
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2610.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2081.52440
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.89923925
X-RAY DIFFRACTIONr_scbond_it1.20231866
X-RAY DIFFRACTIONr_scangle_it1.9184.51674
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 65 -
Rwork0.342 1173 -
obs--98.88 %
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)
14.74731.38440.52548.9133-0.43312.89340.3255-0.1567-0.67480.0688-0.3003-0.01420.33050.2303-0.0252-0.1079-0.0789-0.0602-0.01330.1565-0.089710.8589-64.009454.1635
21.50421.207-2.36241.9093-2.91586.16360.05770.2347-0.01160.01530.03980.1204-0.146-0.4382-0.0975-0.1023-0.0104-0.13620.10530.0198-0.089220.8145-38.34434.0438
32.0132-0.2095-1.37185.10161.71163.03060.06090.19080.2278-0.1170.1041-0.29440.1298-0.2695-0.165-0.070.0436-0.08940.04130.0237-0.177139.083-27.62128.9297
42.0165-3.0761-0.21614.94650.3010.02640.0919-0.12020.2523-0.4982-0.1235-0.6191-0.0018-0.06240.03170.0170.1153-0.0092-0.0241-0.06960.01629.04077.409620.337
52.63841.0547-1.46872.2916-1.70511.48590.0781-0.18460.2871-0.7281-0.4168-0.4-0.07180.35240.33880.25350.04340.0973-0.1902-0.12950.30735.749241.394713.9559
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 827 - 82
2X-RAY DIFFRACTION2AA83 - 20283 - 202
3X-RAY DIFFRACTION3AA203 - 282203 - 282
4X-RAY DIFFRACTION4AA283 - 379283 - 379
5X-RAY DIFFRACTION5AA - B380 - 486380

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