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- PDB-4kgq: Crystal structure of a human light loop mutant in complex with dcr3 -

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Basic information

Entry
Database: PDB / ID: 4kgq
TitleCrystal structure of a human light loop mutant in complex with dcr3
Components(Tumor necrosis factor ...) x 2
KeywordsIMMUNE SYSTEM / LIGHT / DCR3 / TNF / TNFR / TNF14 / STRUCTURAL GENOMICS / PSI-BIOLOGY / NEW HVEM / N-GLYCOSYLATION / MEMBRANE / SECRETED PROTEIN / CYTOKINE / IFN / JELLY-ROLL FOLD / BIND TNF RECEPTOR HVEM AND LTBR / LTBR / PROTEIN STRUCTURE INITIATIVE / ATOMS-TO-ANIMALS: THE IMMUNE FUNCTION NETWORK / NEW YORK STRUCTURAL GENOMICS RESEARCH CONSORTIUM / NYSGRC
Function / homology
Function and homology information


TNFs bind their physiological receptors / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / positive regulation of T cell chemotaxis / T cell chemotaxis / tumor necrosis factor receptor binding / positive regulation of myoblast fusion / T cell homeostasis / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / positive regulation of myoblast differentiation / T cell proliferation ...TNFs bind their physiological receptors / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / positive regulation of T cell chemotaxis / T cell chemotaxis / tumor necrosis factor receptor binding / positive regulation of myoblast fusion / T cell homeostasis / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / positive regulation of myoblast differentiation / T cell proliferation / T cell costimulation / T cell activation / cytokine activity / TNFR2 non-canonical NF-kB pathway / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to mechanical stimulus / signaling receptor activity / immune response / signaling receptor binding / apoptotic process / negative regulation of apoptotic process / signal transduction / extracellular space / extracellular region / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Tumor necrosis factor receptor 6B, N-terminal / Tumour necrosis factor / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / Tumour necrosis factor family. / TNF family profile. / TNF(Tumour Necrosis Factor) family / TNFR/NGFR family cysteine-rich region domain profile. / Tumour necrosis factor domain / TNFR/NGFR cysteine-rich region ...Tumor necrosis factor receptor 6B, N-terminal / Tumour necrosis factor / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / Tumour necrosis factor family. / TNF family profile. / TNF(Tumour Necrosis Factor) family / TNFR/NGFR family cysteine-rich region domain profile. / Tumour necrosis factor domain / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Ribbon / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tumor necrosis factor ligand superfamily member 14 / Tumor necrosis factor receptor superfamily member 6B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsLiu, W. / Zhan, C. / Bonanno, J.B. / Sampathkumar, P. / Toro, R. / Nathenson, S.G. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) / Atoms-to-Animals: The Immune Function Network (IFN)
CitationJournal: Structure / Year: 2014
Title: Mechanistic basis for functional promiscuity in the TNF and TNF receptor superfamilies: structure of the LIGHT:DcR3 assembly.
Authors: Liu, W. / Zhan, C. / Cheng, H. / Kumar, P.R. / Bonanno, J.B. / Nathenson, S.G. / Almo, S.C.
History
DepositionApr 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
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 / 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_struct_conn_angle / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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
Revision 2.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Tumor necrosis factor receptor superfamily member 6B
D: Tumor necrosis factor receptor superfamily member 6B
A: Tumor necrosis factor ligand superfamily member 14
B: Tumor necrosis factor ligand superfamily member 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,0198
Polymers72,7984
Non-polymers1,2224
Water2,288127
1
C: Tumor necrosis factor receptor superfamily member 6B
D: Tumor necrosis factor receptor superfamily member 6B
A: Tumor necrosis factor ligand superfamily member 14
B: Tumor necrosis factor ligand superfamily member 14
hetero molecules

C: Tumor necrosis factor receptor superfamily member 6B
D: Tumor necrosis factor receptor superfamily member 6B
A: Tumor necrosis factor ligand superfamily member 14
B: Tumor necrosis factor ligand superfamily member 14
hetero molecules

C: Tumor necrosis factor receptor superfamily member 6B
D: Tumor necrosis factor receptor superfamily member 6B
A: Tumor necrosis factor ligand superfamily member 14
B: Tumor necrosis factor ligand superfamily member 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,05824
Polymers218,39312
Non-polymers3,66512
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_454-z-1/2,-x,y-1/21
crystal symmetry operation10_554-y,z+1/2,-x-1/21
Buried area39100 Å2
ΔGint-157 kcal/mol
Surface area76050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.269, 149.269, 149.269
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

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Tumor necrosis factor ... , 2 types, 4 molecules CDAB

#1: Protein Tumor necrosis factor receptor superfamily member 6B / Decoy receptor 3 / DcR3 / Decoy receptor for Fas ligand / M68


Mass: 19044.217 Da / Num. of mol.: 2 / Fragment: UNP residues 30-195
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFRSF6B, DCR3, TR6, UNQ186/PRO212 / Production host: DROSOPHILA (fruit flies) / References: UniProt: O95407
#2: Protein Tumor necrosis factor ligand superfamily member 14 / Herpes virus entry mediator ligand / HVEM-L / Herpesvirus entry mediator ligand / Tumor necrosis ...Herpes virus entry mediator ligand / HVEM-L / Herpesvirus entry mediator ligand / Tumor necrosis factor ligand superfamily member 14 / membrane form / Tumor necrosis factor ligand superfamily member 14 / soluble form


Mass: 17354.574 Da / Num. of mol.: 2 / Fragment: UNP residues 83-240 / Mutation: R226D, L227Y, R228T, D229K, G230E, T231D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFSF14, HVEML, LIGHT, UNQ391/PRO726 / Plasmid: PET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-phys / References: UniProt: O43557

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Sugars , 2 types, 2 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: 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

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Non-polymers , 2 types, 129 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 3.81 Å3/Da / Density % sol: 67.69 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Imidazole:HCl, pH 8.0, 2.5 M Sodium Chloride, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.27→50 Å / Num. obs: 51516 / % possible obs: 100 % / Redundancy: 11.6 % / Rmerge(I) obs: 0.104 / Rsym value: 0.083 / Net I/σ(I): 23.091
Reflection shellResolution: 2.27→2.31 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 4.429 / Rsym value: 0.553 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4J6G

4j6g


Resolution: 2.27→37.35 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.487 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23803 2609 5.1 %RANDOM
Rwork0.19491 ---
obs0.19705 48820 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.551 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.27→37.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4658 0 80 127 4865
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0194890
X-RAY DIFFRACTIONr_bond_other_d0.0020.024387
X-RAY DIFFRACTIONr_angle_refined_deg2.0991.9666681
X-RAY DIFFRACTIONr_angle_other_deg0.9623.00810045
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5855601
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.18522.372215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.3615689
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6841542
X-RAY DIFFRACTIONr_chiral_restr0.1320.2723
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0215541
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021165
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.268→2.327 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 183 -
Rwork0.237 3607 -
obs--99.92 %

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