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- PDB-7d4b: Crystal structure of 4-1BB in complex with a VHH -

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Basic information

Entry
Database: PDB / ID: 7d4b
TitleCrystal structure of 4-1BB in complex with a VHH
Components
  • Tumor necrosis factor receptor superfamily member 9
  • anti-4-1BB VHH
KeywordsIMMUNE SYSTEM / antibody / Complex / VHH
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 / plasma membrane
Similarity search - Function
Tumour necrosis factor receptor 9 / Tumour necrosis factor receptor 9, N-terminal / TNFR/NGFR family cysteine-rich region domain profile. / 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 / Growth factor receptor cysteine-rich domain superfamily / Immunoglobulins / Immunoglobulin-like ...Tumour necrosis factor receptor 9 / Tumour necrosis factor receptor 9, N-terminal / TNFR/NGFR family cysteine-rich region domain profile. / 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 / Growth factor receptor cysteine-rich domain superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tumor necrosis factor receptor superfamily member 9
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.14 Å
AuthorsWang, C.
CitationJournal: J Immunother Cancer / Year: 2021
Title: Generation of a safe and efficacious llama single-domain antibody fragment (vHH) targeting the membrane-proximal region of 4-1BB for engineering therapeutic bispecific antibodies for cancer.
Authors: Zhai, T. / Wang, C. / Xu, Y. / Huang, W. / Yuan, Z. / Wang, T. / Dai, S. / Peng, S. / Pang, T. / Jiang, W. / Huang, Y. / Zou, Y. / Xu, Y. / Sun, J. / Gong, X. / Zhang, J. / Tsun, A. / Li, B. / Miao, X.
History
DepositionSep 23, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tumor necrosis factor receptor superfamily member 9
B: anti-4-1BB VHH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,20712
Polymers28,8982
Non-polymers2,30810
Water1267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-3 kcal/mol
Surface area16640 Å2
Unit cell
Length a, b, c (Å)106.851, 106.851, 146.410
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein / Antibody , 2 types, 2 molecules AB

#1: Protein Tumor necrosis factor receptor superfamily member 9 / 4-1BB ligand receptor / CDw137 / T-cell antigen 4-1BB homolog / T-cell antigen ILA


Mass: 15046.007 Da / Num. of mol.: 1
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
#2: Antibody anti-4-1BB VHH


Mass: 13852.370 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Homo sapiens (human)

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Sugars , 2 types, 2 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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: 1219.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-3-4/a4-b1_a6-g1_b4-c1_c3-d1_c6-e1_e3-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 15 molecules

#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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

Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 8.5
Details: 1.5 M lithium sulfate, 100 mM Tris (pH 8.5), 10 mM nickel sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.14→47.79 Å / Num. obs: 15429 / % possible obs: 99.9 % / Redundancy: 12.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.047 / Net I/σ(I): 16.1
Reflection shellResolution: 3.14→3.36 Å / Redundancy: 12.8 % / Rmerge(I) obs: 1.241 / Num. unique obs: 2723 / CC1/2: 0.894 / Rpim(I) all: 0.359 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.25data extraction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MGP, 4XTA

6mgp

4xta


Resolution: 3.14→47.79 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.918 / SU B: 15.886 / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.409 / ESU R Free: 0.318 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2581 726 4.7 %RANDOM
Rwork0.2113 ---
obs0.2136 14654 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 258.79 Å2 / Biso mean: 90.054 Å2 / Biso min: 46.83 Å2
Baniso -1Baniso -2Baniso -3
1-4.12 Å2-0 Å2-0 Å2
2--4.12 Å2-0 Å2
3----8.24 Å2
Refinement stepCycle: final / Resolution: 3.14→47.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1994 0 146 7 2147
Biso mean--155.05 61.15 -
Num. residues----265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132229
X-RAY DIFFRACTIONr_bond_other_d0.0020.0181948
X-RAY DIFFRACTIONr_angle_refined_deg2.1421.7393028
X-RAY DIFFRACTIONr_angle_other_deg1.5551.6624535
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2615268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.38122.162111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.98115342
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8431516
X-RAY DIFFRACTIONr_chiral_restr0.0850.2313
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022470
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02508
LS refinement shellResolution: 3.14→3.222 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.563 55 -
Rwork0.39 1056 -
all-1111 -
obs--99.91 %

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