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- PDB-6brb: Novel non-antibody protein scaffold targeting CD40L -

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Basic information

Entry
Database: PDB / ID: 6brb
TitleNovel non-antibody protein scaffold targeting CD40L
Components
  • CD40 ligand
  • Tn3-like
KeywordsSTRUCTURAL PROTEIN/IMMUNE SYSTEM / Tn3 related / TNF ligand related / STRUCTURAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


CD40 receptor binding / perisynaptic extracellular matrix / tenascin complex / interstitial matrix / extracellular matrix of synaptic cleft / mesenchymal-epithelial cell signaling involved in prostate gland development / peripheral nervous system axon regeneration / bud outgrowth involved in lung branching / syndecan binding / CD40 signaling pathway ...CD40 receptor binding / perisynaptic extracellular matrix / tenascin complex / interstitial matrix / extracellular matrix of synaptic cleft / mesenchymal-epithelial cell signaling involved in prostate gland development / peripheral nervous system axon regeneration / bud outgrowth involved in lung branching / syndecan binding / CD40 signaling pathway / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / cellular response to prostaglandin D stimulus / response to fibroblast growth factor / cellular response to vitamin D / prostate gland epithelium morphogenesis / negative regulation of cell adhesion / isotype switching / tumor necrosis factor receptor binding / regulation of immunoglobulin production / positive regulation of extrinsic apoptotic signaling pathway / extracellular matrix structural constituent / leukocyte cell-cell adhesion / Syndecan interactions / neuromuscular junction development / positive regulation of interleukin-4 production / odontogenesis of dentin-containing tooth / B cell proliferation / positive regulation of interleukin-10 production / basement membrane / positive regulation of endothelial cell apoptotic process / ECM proteoglycans / Integrin cell surface interactions / regulation of cell adhesion / response to mechanical stimulus / positive regulation of T cell proliferation / cellular response to retinoic acid / T cell costimulation / positive regulation of interleukin-12 production / B cell differentiation / regulation of cell migration / protein serine/threonine kinase activator activity / cytokine activity / morphogenesis of an epithelium / integrin-mediated signaling pathway / TNFR2 non-canonical NF-kB pathway / Post-translational protein phosphorylation / regulation of cell growth / platelet activation / response to wounding / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of NF-kappaB transcription factor activity / osteoblast differentiation / integrin binding / regulation of inflammatory response / : / response to ethanol / positive regulation of canonical NF-kappaB signal transduction / cell surface receptor signaling pathway / cell adhesion / inflammatory response / endoplasmic reticulum lumen / external side of plasma membrane / focal adhesion / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of apoptotic process / glutamatergic synapse / cell surface / Golgi apparatus / extracellular space / extracellular region / membrane / plasma membrane
Similarity search - Function
CD40 ligand / Tenascin, EGF-like domain / Tenascin EGF domain / Tumour necrosis factor, conserved site / Teneurin-like EGF domain / Tumor necrosis factor (TNF) homology domain (THD) signature. / : / Tumour necrosis factor family. / TNF(Tumour Necrosis Factor) family / Tumour necrosis factor domain ...CD40 ligand / Tenascin, EGF-like domain / Tenascin EGF domain / Tumour necrosis factor, conserved site / Teneurin-like EGF domain / 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. / Fibrinogen-related domains (FReDs) / Fibrinogen beta and gamma chains, C-terminal globular domain / Jelly Rolls - #40 / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile. / Tumour necrosis factor-like domain superfamily / EGF-like domain, extracellular / EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Fibronectin type III domain / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Jelly Rolls / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tenascin / CD40 ligand
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 Å
AuthorsOganesyan, V. / Baca, M. / Thisted, T. / Grinberg, L. / Wu, H. / Dall'Acqua, W.F.
CitationJournal: Sci Transl Med / Year: 2019
Title: A CD40L-targeting protein reduces autoantibodies and improves disease activity in patients with autoimmunity.
Authors: Karnell, J.L. / Albulescu, M. / Drabic, S. / Wang, L. / Moate, R. / Baca, M. / Oganesyan, V. / Gunsior, M. / Thisted, T. / Yan, L. / Li, J. / Xiong, X. / Eck, S.C. / de Los Reyes, M. / ...Authors: Karnell, J.L. / Albulescu, M. / Drabic, S. / Wang, L. / Moate, R. / Baca, M. / Oganesyan, V. / Gunsior, M. / Thisted, T. / Yan, L. / Li, J. / Xiong, X. / Eck, S.C. / de Los Reyes, M. / Yusuf, I. / Streicher, K. / Muller-Ladner, U. / Howe, D. / Ettinger, R. / Herbst, R. / Drappa, J.
History
DepositionNov 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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.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 / _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 4, 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
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CD40 ligand
D: Tn3-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8693
Polymers25,2822
Non-polymers5871
Water30617
1
A: CD40 ligand
D: Tn3-like
hetero molecules

A: CD40 ligand
D: Tn3-like
hetero molecules

A: CD40 ligand
D: Tn3-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,6079
Polymers75,8476
Non-polymers1,7603
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area13000 Å2
ΔGint-25 kcal/mol
Surface area29790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.528, 93.528, 66.685
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein CD40 ligand / CD40-L / T-cell antigen Gp39 / TNF-related activation protein / TRAP / Tumor necrosis factor ligand ...CD40-L / T-cell antigen Gp39 / TNF-related activation protein / TRAP / Tumor necrosis factor ligand superfamily member 5


Mass: 15398.442 Da / Num. of mol.: 1 / Fragment: UNP residues 120-261
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD40LG, CD40L, TNFSF5, TRAP / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P29965
#2: Protein Tn3-like


Mass: 9883.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P24821*PLUS
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 3.33 Å3/Da / Density % sol: 63.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 40% v/v PEG600, 0.1 M sodium acetate, 0.2 M magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Dec 15, 2010
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.82→51.48 Å / Num. obs: 8406 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 7.9 % / Rmerge(I) obs: 0.195 / Rpim(I) all: 0.073 / Rrim(I) all: 0.208 / Rsym value: 0.195 / Net I/σ(I): 8.1
Reflection shellResolution: 2.82→2.83 Å / Rmerge(I) obs: 0.796 / Num. unique obs: 549 / Rpim(I) all: 0.349

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1ALY & 1TEN

1aly

1ten


Resolution: 2.82→51.48 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.879 / SU B: 25.709 / SU ML: 0.25 / Cross valid method: THROUGHOUT / ESU R: 0.425 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27321 829 9.9 %RANDOM
Rwork0.22515 ---
obs0.22988 7531 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 74.941 Å2
Baniso -1Baniso -2Baniso -3
1-26.53 Å20 Å20 Å2
2--26.53 Å20 Å2
3----53.05 Å2
Refinement stepCycle: 1 / Resolution: 2.82→51.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1779 0 39 17 1835
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191864
X-RAY DIFFRACTIONr_bond_other_d0.0010.021669
X-RAY DIFFRACTIONr_angle_refined_deg1.2711.9672540
X-RAY DIFFRACTIONr_angle_other_deg0.82433886
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3465227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.58524.10378
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.40715294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.995158
X-RAY DIFFRACTIONr_chiral_restr0.0690.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022041
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02376
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_it0.7273.904914
X-RAY DIFFRACTIONr_mcbond_other0.7283.904913
X-RAY DIFFRACTIONr_mcangle_it1.2715.8561139
X-RAY DIFFRACTIONr_mcangle_other1.275.8551140
X-RAY DIFFRACTIONr_scbond_it0.6744.078950
X-RAY DIFFRACTIONr_scbond_other0.6744.077951
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.1936.0861402
X-RAY DIFFRACTIONr_long_range_B_refined2.37244.351881
X-RAY DIFFRACTIONr_long_range_B_other2.35944.3481881
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.82→2.892 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 57 -
Rwork0.306 546 -
obs--99.83 %
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)
11.79670.4251-0.09735.6594-0.53445.3876-0.1840.0103-0.2639-0.42040.1847-0.4610.43990.0859-0.00080.13930.02510.02680.0372-0.0360.0822-37.990713.8183-36.0439
23.93880.8782-2.78151.946-1.31098.8636-0.1662-0.04770.00820.0777-0.0844-0.2167-0.0830.63630.25050.13770.0184-0.05010.0717-0.00780.1008-33.115521.4437-21.9645
31.62480.620.25863.26-0.15363.1512-0.0526-0.09910.03770.05620.0065-0.1803-0.10540.16950.04610.02170.0093-0.01530.0254-0.00940.0182-39.027120.6151-25.6591
43.9223-4.8075-3.599111.8904-1.67369.49710.34770.3277-0.2916-0.7209-0.34980.61760.0801-0.29590.00210.28560.0396-0.01380.0885-0.09080.1145-39.5221-2.0968-17.339
53.17653.93221.873512.3468.97647.28150.18630.3849-0.33090.2606-0.66470.61690.1765-0.96020.47840.20370.0109-0.03920.3425-0.02980.4032-55.68966.8236-14.8498
63.9639-3.47971.62496.5636-0.73813.3982-0.1036-0.3325-0.47130.27590.27410.29880.3216-0.0391-0.17050.2279-0.05220.03770.06920.02130.0782-42.2119-2.1025-8.1035
79.1881-3.53030.69176.15841.72863.7096-0.55340.5604-0.61480.5396-0.00140.99340.2225-0.51020.55480.2976-0.10330.07450.2686-0.00090.2476-47.8209-3.7899-10.8091
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A120 - 173
2X-RAY DIFFRACTION2A174 - 203
3X-RAY DIFFRACTION3A204 - 261
4X-RAY DIFFRACTION4D1 - 17
5X-RAY DIFFRACTION5D18 - 25
6X-RAY DIFFRACTION6D26 - 68
7X-RAY DIFFRACTION7D69 - 87

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