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- PDB-4j6g: CRYSTAL STRUCTURE OF LIGHT AND DcR3 COMPLEX -

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Basic information

Entry
Database: PDB / ID: 4j6g
TitleCRYSTAL STRUCTURE OF LIGHT AND DcR3 COMPLEX
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: 2.4 Å
AuthorsLiu, W. / Zhan, C. / Bonanno, J.B. / Bhosle, R.C. / Nathenson, S.G. / Almo, S.C. / Atoms-to-Animals: The Immune Function Network (IFN) / New York Structural Genomics Research Consortium (NYSGRC)
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
DepositionFeb 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2013Group: Structure summary
Revision 1.2Dec 31, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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_2 / _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
A: Tumor necrosis factor ligand superfamily member 14
B: Tumor necrosis factor ligand superfamily member 14
C: Tumor necrosis factor receptor superfamily member 6B
D: Tumor necrosis factor receptor superfamily member 6B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,55510
Polymers74,4664
Non-polymers1,0896
Water82946
1
A: Tumor necrosis factor ligand superfamily member 14
C: Tumor necrosis factor receptor superfamily member 6B
hetero molecules

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

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

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

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

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


Theoretical massNumber of molelcules
Total (without water)226,66530
Polymers223,39712
Non-polymers3,26818
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation4_545x+1/2,-y-1/2,-z1
crystal symmetry operation8_554-z,x+1/2,-y-1/21
crystal symmetry operation12_455-y-1/2,-z,x+1/21
Buried area39550 Å2
ΔGint-223 kcal/mol
Surface area75230 Å2
MethodPISA
2
A: Tumor necrosis factor ligand superfamily member 14
C: Tumor necrosis factor receptor superfamily member 6B
hetero molecules

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

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


  • defined by software
  • 114 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)114,12415
Polymers111,6986
Non-polymers2,4259
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area14570 Å2
ΔGint-88 kcal/mol
Surface area44670 Å2
MethodPISA
3
B: Tumor necrosis factor ligand superfamily member 14
D: Tumor necrosis factor receptor superfamily member 6B
hetero molecules

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

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


  • defined by software
  • 113 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)112,54115
Polymers111,6986
Non-polymers8439
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_445-z-1/2,-x-1,y+1/21
crystal symmetry operation10_444-y-1,z-1/2,-x-1/21
Buried area12500 Å2
ΔGint-112 kcal/mol
Surface area43050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.058, 149.058, 149.058
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 ABCD

#1: 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: 18188.549 Da / Num. of mol.: 2 / Fragment: UNP residues 83-240 / Mutation: K214E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFSF14, HVEML, LIGHT, UNQ391/PRO726 / Production host: Drosophila (fruit flies) / References: UniProt: O43557
#2: 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

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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
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 50 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 46 / 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: 3.71 Å3/Da / Density % sol: 66.81 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M SODIUM CHLORIDE, 0.1M SODIUM CITRATE:CITRIC ACID BUFFER 1.0M AMMONIUM PHOSPHATE DIBASIC, PH5.5,, 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
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 43288 / % possible obs: 100 % / Redundancy: 11.2 % / Rmerge(I) obs: 0.102 / Rsym value: 0.077 / Net I/σ(I): 27.2
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 3.5 / Rsym value: 0.774 / % possible all: 100

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4EN0

4en0


Resolution: 2.4→19.93 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.459 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23227 2176 5 %RANDOM
Rwork0.194 ---
obs0.19591 40985 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.906 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4604 0 68 46 4718
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0194826
X-RAY DIFFRACTIONr_bond_other_d0.0010.024373
X-RAY DIFFRACTIONr_angle_refined_deg1.9611.9656591
X-RAY DIFFRACTIONr_angle_other_deg0.9143.0089998
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5425597
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.04221.943211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.46115686
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4051547
X-RAY DIFFRACTIONr_chiral_restr0.1150.2713
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215478
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021163
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: 2.402→2.464 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 148 -
Rwork0.277 2996 -
obs--100 %

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