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- PDB-6bwv: Crystal Structure of the 4-1BB/4-1BBL Complex -

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Basic information

Entry
Database: PDB / ID: 6bwv
TitleCrystal Structure of the 4-1BB/4-1BBL Complex
Components
  • Tumor necrosis factor ligand superfamily member 9
  • Tumor necrosis factor receptor superfamily member 9
KeywordsIMMUNE SYSTEM / TNF superfamily / TNFR superfamily / CD137
Function / homology
Function and homology information


tumor necrosis factor receptor superfamily binding / positive regulation of cytotoxic T cell differentiation / TNFs bind their physiological receptors / regulation of immature T cell proliferation in thymus / tumor necrosis factor receptor binding / regulation of T cell proliferation / positive regulation of activated T cell proliferation / cytokine activity / cell-cell signaling / signaling receptor activity ...tumor necrosis factor receptor superfamily binding / positive regulation of cytotoxic T cell differentiation / TNFs bind their physiological receptors / regulation of immature T cell proliferation in thymus / tumor necrosis factor receptor binding / regulation of T cell proliferation / positive regulation of activated T cell proliferation / cytokine activity / cell-cell signaling / signaling receptor activity / regulation of cell population proliferation / regulation of apoptotic process / immune response / negative regulation of cell population proliferation / external side of plasma membrane / signaling receptor binding / apoptotic process / extracellular space / plasma membrane
Similarity search - Function
Tumor necrosis factor ligand superfamily member 9 / Tumour necrosis factor receptor 9 / Tumour necrosis factor receptor 9, N-terminal / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. / TNF(Tumour Necrosis Factor) family / TNFR/NGFR family cysteine-rich region domain profile. ...Tumor necrosis factor ligand superfamily member 9 / Tumour necrosis factor receptor 9 / Tumour necrosis factor receptor 9, N-terminal / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. / 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 (TNF) homology domain (THD) profile. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Growth factor receptor cysteine-rich domain superfamily / Ribbon / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Tumor necrosis factor ligand superfamily member 9 / Tumor necrosis factor receptor superfamily member 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsOganesyan, V. / Gilbreth, R.N. / Baca, M.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Crystal structure of the human 4-1BB/4-1BBL complex.
Authors: Gilbreth, R.N. / Oganesyan, V.Y. / Amdouni, H. / Novarra, S. / Grinberg, L. / Barnes, A. / Baca, M.
History
DepositionDec 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jul 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tumor necrosis factor ligand superfamily member 9
B: Tumor necrosis factor ligand superfamily member 9
D: Tumor necrosis factor receptor superfamily member 9
E: Tumor necrosis factor receptor superfamily member 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2205
Polymers63,1144
Non-polymers1061
Water81145
1
A: Tumor necrosis factor ligand superfamily member 9
E: Tumor necrosis factor receptor superfamily member 9
hetero molecules

A: Tumor necrosis factor ligand superfamily member 9
E: Tumor necrosis factor receptor superfamily member 9
hetero molecules

A: Tumor necrosis factor ligand superfamily member 9
E: Tumor necrosis factor receptor superfamily member 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,9899
Polymers94,6706
Non-polymers3183
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
2
B: Tumor necrosis factor ligand superfamily member 9
D: Tumor necrosis factor receptor superfamily member 9

B: Tumor necrosis factor ligand superfamily member 9
D: Tumor necrosis factor receptor superfamily member 9

B: Tumor necrosis factor ligand superfamily member 9
D: Tumor necrosis factor receptor superfamily member 9


Theoretical massNumber of molelcules
Total (without water)94,6706
Polymers94,6706
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Unit cell
Length a, b, c (Å)161.571, 161.571, 161.571
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11B-317-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12D
22E

NCS domain segments:

Component-ID: _ / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNAA89 - 2423 - 156
21GLNGLNBB89 - 2423 - 156
12ASPASPDC26 - 1603 - 137
22ASPASPED26 - 1603 - 137

NCS ensembles :
ID
1
2

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Components

#1: Protein Tumor necrosis factor ligand superfamily member 9 / 4-1BB ligand / 4-1BBL


Mass: 16438.717 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFSF9 / Production host: Escherichia coli (E. coli) / References: UniProt: P41273
#2: Protein Tumor necrosis factor receptor superfamily member 9 / 4-1BB ligand receptor / CDw137 / T-cell antigen 4-1BB homolog / T-cell antigen ILA


Mass: 15118.044 Da / Num. of mol.: 2 / Mutation: C121S, N138D, N149Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFRSF9, CD137, ILA / Production host: Homo sapiens (human) / References: UniProt: Q07011
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
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: 2.6 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Potassium citrate tribasic monohydrate 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: May 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.4→38 Å / Num. obs: 27518 / % possible obs: 100 % / Redundancy: 20.6 % / Biso Wilson estimate: 46 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.053 / Rrim(I) all: 0.173 / Net I/σ(I): 12.4
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 10.3 % / Rmerge(I) obs: 1.449 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2863 / CC1/2: 0.799 / Rpim(I) all: 0.467 / Rrim(I) all: 1.523 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2X29

2x29


Resolution: 2.4→38 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.925 / SU B: 10.02 / SU ML: 0.218 / Cross valid method: THROUGHOUT / ESU R: 0.364 / ESU R Free: 0.257 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26479 1086 3.9 %RANDOM
Rwork0.22651 ---
obs0.22799 26418 99.95 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.182 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.4→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4150 0 7 45 4202
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0194250
X-RAY DIFFRACTIONr_bond_other_d0.0010.023848
X-RAY DIFFRACTIONr_angle_refined_deg1.1221.9575748
X-RAY DIFFRACTIONr_angle_other_deg0.82738947
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5115548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.54223.702181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.00715686
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2411532
X-RAY DIFFRACTIONr_chiral_restr0.070.2630
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214782
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02862
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_it2.7516.1432216
X-RAY DIFFRACTIONr_mcbond_other2.7516.142215
X-RAY DIFFRACTIONr_mcangle_it4.3969.1932756
X-RAY DIFFRACTIONr_mcangle_other4.3969.1962757
X-RAY DIFFRACTIONr_scbond_it2.9276.4912034
X-RAY DIFFRACTIONr_scbond_other2.9276.4912034
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7439.592993
X-RAY DIFFRACTIONr_long_range_B_refined7.00671.1194239
X-RAY DIFFRACTIONr_long_range_B_other6.99871.1044236
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A79400.07
12B79400.07
21D75540.08
22E75540.08
LS refinement shellResolution: 2.401→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 92 -
Rwork0.375 1913 -
obs--100 %

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