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- PDB-5wi8: Crystal structure of murine 4-1BB from HEK293T cells in P21 space... -

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Basic information

Entry
Database: PDB / ID: 5wi8
TitleCrystal structure of murine 4-1BB from HEK293T cells in P21 space group
ComponentsTumor necrosis factor receptor superfamily member 9
KeywordsIMMUNE SYSTEM / Tumor necrosis factor / apoptosis
Function / homology
Function and homology information


TNFs bind their physiological receptors / regulation of immature T cell proliferation in thymus / signaling receptor activity / regulation of cell population proliferation / negative regulation of cell population proliferation / external side of plasma membrane / apoptotic process
Similarity search - Function
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 / 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 / Ribbon / Mainly Beta
Similarity search - Domain/homology
Tumor necrosis factor receptor superfamily member 9
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsZajonc, D.M. / Bitra, A.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Crystal structure of murine 4-1BB and its interaction with 4-1BBL support a role for galectin-9 in 4-1BB signaling.
Authors: Bitra, A. / Doukov, T. / Wang, J. / Picarda, G. / Benedict, C.A. / Croft, M. / Zajonc, D.M.
History
DepositionJul 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / 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 / struct_asym / struct_conn / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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.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
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: Tumor necrosis factor receptor superfamily member 9
B: Tumor necrosis factor receptor superfamily member 9
C: Tumor necrosis factor receptor superfamily member 9
D: Tumor necrosis factor receptor superfamily member 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,39326
Polymers62,5754
Non-polymers4,81822
Water1,63991
1
A: Tumor necrosis factor receptor superfamily member 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8998
Polymers15,6441
Non-polymers1,2557
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tumor necrosis factor receptor superfamily member 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1308
Polymers15,6441
Non-polymers1,4867
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Tumor necrosis factor receptor superfamily member 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5474
Polymers15,6441
Non-polymers9033
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Tumor necrosis factor receptor superfamily member 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8176
Polymers15,6441
Non-polymers1,1735
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.011, 61.763, 110.750
Angle α, β, γ (deg.)90.000, 91.530, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A27 - 159
2010B27 - 159
1020A27 - 159
2020C27 - 159
1030A27 - 159
2030D27 - 159
1040B27 - 159
2040C27 - 159
1050B27 - 159
2050D27 - 159
1060C27 - 160
2060D27 - 160

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Tumor necrosis factor receptor superfamily member 9 / 4-1BB ligand receptor / T-cell antigen 4-1BB


Mass: 15643.854 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tnfrsf9, Cd137, Ila, Ly63
Production host: Mammalian expression vector pcDNA3-N-HA-LIC (others)
References: UniProt: P20334

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Sugars , 4 types, 5 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...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: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: 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.: 2
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)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: 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
#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / 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, 108 molecules

#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 3.55 Å3/Da / Density % sol: 65.37 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M sodium acetate pH 4.5, 30% w/V polyethylene glycol (PEG) 8000, and 0.2 M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 10, 2016
RadiationMonochromator: Liquid nitrogen-cooled double crystal monochromator, non fixed exit slit
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.95→40 Å / Num. obs: 17070 / % possible obs: 91.8 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.084 / Rrim(I) all: 0.154 / Χ2: 3.725 / Net I/σ(I): 6.9 / Num. measured all: 53045
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.95-3.062.40.28312370.9160.1990.3480.58167.5
3.06-3.182.40.24514370.950.1740.3030.57178.7
3.18-3.322.70.23416640.9490.1630.2860.6989.6
3.32-3.53.10.26617800.7480.1750.321.93197.1
3.5-3.723.20.22618280.2740.1650.2821.58398.3
3.72-43.20.18217600.6090.1210.221.8895.7
4-4.413.50.118330.9890.0620.1181.80998.3
4.41-5.043.40.11518450.990.0710.1354.42498.5
5.04-6.353.40.09218290.9850.0570.1093.84297.4
6.35-403.30.08218570.9840.0510.09714.90296.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→40 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.864 / SU B: 14.687 / SU ML: 0.284 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.448
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2791 881 5.2 %RANDOM
Rwork0.2353 ---
obs0.2376 16177 91.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 143.75 Å2 / Biso mean: 71.576 Å2 / Biso min: 24.57 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å2-0.01 Å2
2--0 Å20 Å2
3---0.07 Å2
Refinement stepCycle: final / Resolution: 2.95→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3923 0 319 91 4333
Biso mean--93.93 54.83 -
Num. residues----539
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194368
X-RAY DIFFRACTIONr_bond_other_d0.0050.023715
X-RAY DIFFRACTIONr_angle_refined_deg1.4852.0225934
X-RAY DIFFRACTIONr_angle_other_deg1.2738683
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1725535
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.69923.818165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.36115602
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6921527
X-RAY DIFFRACTIONr_chiral_restr0.070.2679
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214780
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02935
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A109340.1
12B109340.1
21A109600.1
22C109600.1
31A108900.1
32D108900.1
41B109420.12
42C109420.12
51B109280.11
52D109280.11
61C113820.08
62D113820.08
LS refinement shellResolution: 2.951→3.028 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 50 -
Rwork0.283 747 -
all-797 -
obs--60.15 %

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