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- PDB-6mkb: Crystal structure of murine 4-1BB ligand -

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Basic information

Entry
Database: PDB / ID: 6mkb
TitleCrystal structure of murine 4-1BB ligand
ComponentsTumor necrosis factor ligand superfamily member 9
KeywordsSIGNALING PROTEIN / TNF / dimer
Function / homology
Function and homology information


TNFs bind their physiological receptors / tumor necrosis factor receptor superfamily binding / positive regulation of cytotoxic T cell differentiation / regulation of immature T cell proliferation in thymus / myeloid dendritic cell differentiation / tumor necrosis factor receptor binding / positive regulation of activated T cell proliferation / positive regulation of interleukin-12 production / cytokine activity / positive regulation of interleukin-6 production ...TNFs bind their physiological receptors / tumor necrosis factor receptor superfamily binding / positive regulation of cytotoxic T cell differentiation / regulation of immature T cell proliferation in thymus / myeloid dendritic cell differentiation / tumor necrosis factor receptor binding / positive regulation of activated T cell proliferation / positive regulation of interleukin-12 production / cytokine activity / positive regulation of interleukin-6 production / positive regulation of type II interferon production / immune response / signaling receptor binding / extracellular space / plasma membrane
Similarity search - Function
Tumor necrosis factor ligand superfamily member 9 / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. / TNF(Tumour Necrosis Factor) family / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Jelly Rolls ...Tumor necrosis factor ligand superfamily member 9 / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. / TNF(Tumour Necrosis Factor) family / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tumor necrosis factor ligand superfamily member 9
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBitra, A. / Zajonc, D.M. / Doukov, T.
CitationJournal: J. Biol. Chem. / Year: 2019
Title: Crystal structure of the m4-1BB/4-1BBL complex reveals an unusual dimeric ligand that undergoes structural changes upon 4-1BB receptor binding.
Authors: Bitra, A. / Doukov, T. / Destito, G. / Croft, M. / Zajonc, D.M.
History
DepositionSep 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Feb 20, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_unobs_or_zero_occ_atoms / 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.pdbx_formal_charge / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 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 9
B: Tumor necrosis factor ligand superfamily member 9
C: Tumor necrosis factor ligand superfamily member 9
D: Tumor necrosis factor ligand superfamily member 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,93622
Polymers77,0354
Non-polymers3,90118
Water5,152286
1
A: Tumor necrosis factor ligand superfamily member 9
B: Tumor necrosis factor ligand superfamily member 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,30611
Polymers38,5172
Non-polymers1,7889
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-70 kcal/mol
Surface area17130 Å2
MethodPISA
2
C: Tumor necrosis factor ligand superfamily member 9
D: Tumor necrosis factor ligand superfamily member 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,63011
Polymers38,5172
Non-polymers2,1139
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-76 kcal/mol
Surface area17070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.362, 77.362, 118.236
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 19258.646 Da / Num. of mol.: 4 / Fragment: residues 139-309
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tnfsf9, Cd137l, Cd157l, Ly63l / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P41274

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Sugars , 4 types, 4 molecules

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


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: 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)-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
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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_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]{}}}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 300 molecules

#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: Na
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.63 Å3/Da / Density % sol: 53.27 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 2.4 M Ammonium sulfate, 0.1M MES pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 27191 / % possible obs: 99.7 % / Redundancy: 10.4 % / Biso Wilson estimate: 72.5 Å2 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.025 / Rrim(I) all: 0.081 / Χ2: 0.653 / Net I/σ(I): 4.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.5910.40.79127270.8270.2560.8320.4299.9
2.59-2.6910.30.59226880.8970.1920.6230.42499.4
2.69-2.829.20.41627000.9420.1430.4410.43399
2.82-2.9610.70.25527440.9820.0810.2670.43899.8
2.96-3.15110.1827220.990.0570.1890.501100
3.15-3.3910.80.11327140.9960.0360.1190.491100
3.39-3.7310.60.07927350.9980.0250.0830.52599.9
3.73-4.279.60.05727160.9990.0190.060.54399.2
4.27-5.3811.10.04927150.9990.0150.0520.63199.9
5.38-5010.50.0527300.9950.0160.0532.08899.8

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6D3N

6d3n


Resolution: 2.5→29.14 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.922 / SU R Cruickshank DPI: 0.552 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.517 / SU Rfree Blow DPI: 0.27 / SU Rfree Cruickshank DPI: 0.277
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1306 4.81 %RANDOM
Rwork0.188 ---
obs0.191 27146 99.7 %-
Displacement parametersBiso max: 155.97 Å2 / Biso mean: 66.18 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1--0.5219 Å20 Å20 Å2
2---0.5219 Å20 Å2
3---1.0439 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: final / Resolution: 2.5→29.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5158 0 245 286 5689
Biso mean--91.38 64.54 -
Num. residues----650
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2529SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes908HARMONIC5
X-RAY DIFFRACTIONt_it5603HARMONIC20
X-RAY DIFFRACTIONt_nbd6SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion730SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5936SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5603HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg7659HARMONIC21.18
X-RAY DIFFRACTIONt_omega_torsion3.82
X-RAY DIFFRACTIONt_other_torsion3.04
LS refinement shellResolution: 2.5→2.52 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.1646 8 1.47 %
Rwork0.2018 535 -
all0.2012 543 -
obs--99.26 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.06790.1699-0.26971.9936-1.24223.89850.2056-0.11060.17550.186-0.11890.3019-0.4876-0.2493-0.0866-0.2110.09560.04580.0183-0.1535-0.062674.0581-20.601328.685
21.58681.0238-0.93411.7722-0.93262.8882-0.06890.0128-0.1047-0.2340.0969-0.15330.1503-0.249-0.028-0.18440.0120.01270.0025-0.0058-0.059168.8443-35.939312.0938
32.50050.8579-0.76250.743-0.55052.4376-0.0318-0.2409-0.1621-0.01620.08340.0019-0.12820.269-0.0516-0.0335-0.0725-0.002-0.15690.0105-0.053335.461-10.9877-1.161
42.2811-0.0893-1.26641.86790.4993.8431-0.00260.28830.35540.0080.0897-0.0158-0.4879-0.2587-0.08710.0471-0.0476-0.1108-0.2420.1103-0.067719.484-7.6745-17.6005
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A145 - 908
2X-RAY DIFFRACTION2{ B|* }B145 - 309
3X-RAY DIFFRACTION3{ C|* }C145 - 309
4X-RAY DIFFRACTION4{ D|* }D145 - 908

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