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- PDB-4nzd: Interleukin 21 receptor -

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Basic information

Entry
Database: PDB / ID: 4nzd
TitleInterleukin 21 receptor
ComponentsInterleukin-21 receptor
KeywordsSIGNALING PROTEIN / Fibronectine III domain / Interleukin 21 / Glycosylated
Function / homology
Function and homology information


interleukin-21 receptor activity / Interleukin-21 signaling / natural killer cell activation / cytokine receptor activity / immunoglobulin mediated immune response / cytokine-mediated signaling pathway / transmembrane signaling receptor activity / external side of plasma membrane / membrane / plasma membrane
Similarity search - Function
Short hematopoietin receptor family 1 signature. / Short hematopoietin receptor, family 1, conserved site / 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
alpha-D-mannopyranose / L(+)-TARTARIC ACID / Interleukin-21 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsHamming, O.T. / Kang, L. / Siupka, P. / Gad, H.H. / Hartmann, R.
CitationJournal: To be Published
Title: Interleukin 21 receptor structure and function
Authors: Hamming, O.T. / Kang, L. / Siupka, P. / Gad, H.H. / Hartmann, R.
History
DepositionDec 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_unobs_or_zero_occ_atoms.label_asym_id
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_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / 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 / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_atom_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-21 receptor
B: Interleukin-21 receptor
C: Interleukin-21 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,59629
Polymers76,3543
Non-polymers4,24226
Water2,846158
1
A: Interleukin-21 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,03712
Polymers25,4511
Non-polymers1,58611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Interleukin-21 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8549
Polymers25,4511
Non-polymers1,4028
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Interleukin-21 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7058
Polymers25,4511
Non-polymers1,2547
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: Interleukin-21 receptor
hetero molecules

A: Interleukin-21 receptor
hetero molecules

B: Interleukin-21 receptor
C: Interleukin-21 receptor
hetero molecules

B: Interleukin-21 receptor
C: Interleukin-21 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,19258
Polymers152,7086
Non-polymers8,48452
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation6_564-x+1/2,-y+3/2,z-1/21
crystal symmetry operation7_545-x+1/2,y-1/2,-z+1/21
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area39290 Å2
ΔGint-293 kcal/mol
Surface area65100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.330, 125.260, 178.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Interleukin-21 receptor / / IL-21 receptor / IL-21R / Novel interleukin receptor


Mass: 25451.297 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL21R, NILR, UNQ3121/PRO10273 / Cell line (production host): HEK293 cells / Production host: homo sapiens (human) / References: UniProt: Q9HBE5

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Sugars , 2 types, 6 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-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: 894.823 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-MAN / alpha-D-mannopyranose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 178 molecules

#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O6
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 4.18 Å3/Da / Density % sol: 70.57 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 5 mg/ml Protein in 10 mM Hepes, 150 mM NaCl, pH7.5 Crystalized in 1M Potassium sodium tartrate tetrahydrate, 3% W/V Peg5000 and 0.1 M tris Ph 8.5. Drops were 1:1, VAPOR DIFFUSION, SITTING DROP, temperature 278K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 2.75→29.78 Å / Num. all: 33646 / Num. obs: 33261 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.75→2.848 Å / % possible all: 99

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Processing

Software
NameVersionClassification
DNAdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→29.778 Å / SU ML: 0.38 / σ(F): 1.36 / Phase error: 27.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2749 1999 6.01 %5 percent of data
Rwork0.2386 ---
obs0.2407 33241 98.9 %-
all-33261 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.75→29.778 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5069 0 263 158 5490
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055503
X-RAY DIFFRACTIONf_angle_d1.1427510
X-RAY DIFFRACTIONf_dihedral_angle_d22.8562044
X-RAY DIFFRACTIONf_chiral_restr0.076846
X-RAY DIFFRACTIONf_plane_restr0.004933
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.81870.38721410.2872194X-RAY DIFFRACTION99
2.8187-2.89480.37211410.27752214X-RAY DIFFRACTION100
2.8948-2.97990.33131430.25822235X-RAY DIFFRACTION100
2.9799-3.0760.3371440.25732245X-RAY DIFFRACTION100
3.076-3.18590.29471400.25442199X-RAY DIFFRACTION99
3.1859-3.31320.32321430.24232237X-RAY DIFFRACTION100
3.3132-3.46380.33711420.31182207X-RAY DIFFRACTION99
3.4638-3.64610.30261370.27832130X-RAY DIFFRACTION95
3.6461-3.87410.40611380.3432163X-RAY DIFFRACTION97
3.8741-4.17250.33331410.28712221X-RAY DIFFRACTION99
4.1725-4.5910.22451460.18822277X-RAY DIFFRACTION100
4.591-5.25220.17791450.14892261X-RAY DIFFRACTION100
5.2522-6.60530.17231470.1662300X-RAY DIFFRACTION100
6.6053-29.780.17751510.1892359X-RAY DIFFRACTION99

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