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- PDB-6mkz: Crystal structure of murine 4-1BB/4-1BBL complex -

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Basic information

Entry
Database: PDB / ID: 6mkz
TitleCrystal structure of murine 4-1BB/4-1BBL complex
Components
  • Tumor necrosis factor ligand superfamily member 9
  • Tumor necrosis factor receptor superfamily member 9
KeywordsSIGNALING PROTEIN / TNF / TNFR
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 / signaling receptor activity / regulation of cell population proliferation / 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 / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. / Tumor necrosis factor (TNF) homology domain (THD) profile. / TNF(Tumour Necrosis Factor) family / Tumour necrosis factor domain / TNFR/NGFR cysteine-rich region ...Tumor necrosis factor ligand superfamily member 9 / Tumour necrosis factor receptor 9 / Tumour necrosis factor receptor 9, N-terminal / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. / Tumor necrosis factor (TNF) homology domain (THD) profile. / TNF(Tumour Necrosis Factor) family / 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 / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tumor necrosis factor receptor superfamily member 9 / Tumor necrosis factor ligand superfamily member 9
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 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 26, 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: Atomic model / Data collection ...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 / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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 receptor superfamily member 9
C: Tumor necrosis factor ligand superfamily member 9
D: Tumor necrosis factor receptor superfamily member 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9856
Polymers68,8124
Non-polymers1,1732
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7510 Å2
ΔGint-19 kcal/mol
Surface area26110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.499, 88.478, 155.158
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 19258.646 Da / Num. of mol.: 2 / 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
#2: Protein Tumor necrosis factor receptor superfamily member 9 / 4-1BB ligand receptor / T-cell antigen 4-1BB


Mass: 15147.186 Da / Num. of mol.: 2 / Fragment: residues 24-160
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tnfrsf9, Cd137, Ila, Ly63 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P20334
#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.: 2
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 3.07 Å3/Da / Density % sol: 59.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 4000, 0.2M ammonium chloride

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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 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.624→76.859 Å / Num. obs: 25447 / % possible obs: 97.6 % / Redundancy: 13.7 % / Biso Wilson estimate: 76.59 Å2 / CC1/2: 0.96 / Net I/σ(I): 5.6 / Num. measured all: 349768
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
2.624-2.6887.5941412630.7551.771
7.354-76.859121572813060.9497.899.8

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
Aimlessdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WI8, 6MKB

5wi8

6mkb


Resolution: 2.65→30.76 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.897 / SU R Cruickshank DPI: 0.384 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.417 / SU Rfree Blow DPI: 0.261 / SU Rfree Cruickshank DPI: 0.258
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1239 4.93 %RANDOM
Rwork0.204 ---
obs0.206 25124 99.2 %-
Displacement parametersBiso max: 218.79 Å2 / Biso mean: 85.39 Å2 / Biso min: 24.15 Å2
Baniso -1Baniso -2Baniso -3
1-1.2289 Å20 Å20 Å2
2--5.7475 Å20 Å2
3----6.9764 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: final / Resolution: 2.65→30.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3926 0 78 175 4179
Biso mean--130.12 66.09 -
Num. residues----528
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1822SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes696HARMONIC5
X-RAY DIFFRACTIONt_it4124HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion557SEMIHARMONIC5
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_contact4421SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4124HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5638HARMONIC21.24
X-RAY DIFFRACTIONt_omega_torsion3.59
X-RAY DIFFRACTIONt_other_torsion2.85
LS refinement shellResolution: 2.65→2.67 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3208 24 4.77 %
Rwork0.2462 479 -
all0.2501 503 -
obs--91.57 %
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)
15.4541-0.65621.2722.0636-1.29294.1569-0.197-0.9927-0.88080.22770.2680.08990.3339-0.5031-0.071-0.26450.05980.07670.01980.2654-0.23118.51649.154223.2319
28.5164-3.0157-1.75474.56860.77874.97330.3318-0.45991.08720.2259-0.1568-0.7298-0.70610.1037-0.175-0.10420.1192-0.0291-0.13120.0775-0.261814.790123.757338.9345
36.1382-0.33840.08030.18880.28550-0.2181-0.70410.6629-0.07450.02360.0143-0.0694-0.07250.1945-0.18440.0572-0.04230.1886-0.1096-0.0630.495328.1847.7093
45.5144-1.8235-3.42054.95180.40452.93980.0598-0.7653-0.50330.6508-0.39820.01630.1872-0.08270.33840.09870.2190.04270.35420.243-0.58025.612.023555.8389
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ C|145 - C|306 C|500 - C|502 }C145 - 306
2X-RAY DIFFRACTION1{ C|145 - C|306 C|500 - C|502 }C500 - 502
3X-RAY DIFFRACTION2{ A|144 - A|308 A|500 - A|502 }A144 - 308
4X-RAY DIFFRACTION2{ A|144 - A|308 A|500 - A|502 }A500 - 502
5X-RAY DIFFRACTION3{ B|22 - B|155 }B22 - 155
6X-RAY DIFFRACTION4{ D|28 - D|112 }D28 - 112

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