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- PDB-8hxq: Nanobody1 in complex with human BCMA ECD -

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Basic information

Entry
Database: PDB / ID: 8hxq
TitleNanobody1 in complex with human BCMA ECD
Components
  • Nanobody1
  • Tumor necrosis factor receptor superfamily member 17
KeywordsIMMUNE SYSTEM / complex / Nanobody
Function / homology
Function and homology information


lymphocyte homeostasis / TNFs bind their physiological receptors / endomembrane system / tumor necrosis factor-mediated signaling pathway / signaling receptor activity / adaptive immune response / signal transduction / membrane / plasma membrane
Similarity search - Function
BCMA, TALL-1 binding / Tumour necrosis factor receptor 17 / BCMA, TALL-1 binding / Tumor necrosis factor receptor 13C/17
Similarity search - Domain/homology
Tumor necrosis factor receptor superfamily member 17
Similarity search - Component
Biological speciesVicugna pacos (alpaca)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSun, Y. / Zhang, B.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)82230006 China
CitationJournal: Signal Transduct Target Ther / Year: 2023
Title: Antigen-induced chimeric antigen receptor multimerization amplifies on-tumor cytotoxicity.
Authors: Sun, Y. / Yang, X.N. / Yang, S.S. / Lyu, Y.Z. / Zhang, B. / Liu, K.W. / Li, N. / Cui, J.C. / Huang, G.X. / Liu, C.L. / Xu, J. / Mi, J.Q. / Chen, Z. / Fan, X.H. / Chen, S.J. / Chen, S.
History
DepositionJan 5, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 3, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nanobody1
C: Tumor necrosis factor receptor superfamily member 17
B: Nanobody1
D: Tumor necrosis factor receptor superfamily member 17


Theoretical massNumber of molelcules
Total (without water)39,6624
Polymers39,6624
Non-polymers00
Water39622
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.773, 66.773, 174.237
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw

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Components

#1: Antibody Nanobody1


Mass: 13927.472 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#2: Protein Tumor necrosis factor receptor superfamily member 17 / B-cell maturation protein


Mass: 5903.708 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q02223
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.45 Å3/Da / Density % sol: 49.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: 0.2 M Ammonium sulfate, 20% w/v Polyethylene glycol 3350, pH6.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.39→50 Å / Num. obs: 16468 / % possible obs: 99.6 % / Redundancy: 12.6 % / CC1/2: 0.994 / Rmerge(I) obs: 0.136 / Rrim(I) all: 0.142 / Net I/σ(I): 11.33
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Diffraction-IDRrim(I) all
2.39-2.451.37111420.8471
2.45-2.521.04411400.9211
2.52-2.590.7111230.98210.738
2.59-2.670.57811180.97610.602
2.67-2.760.45810510.98410.478
2.76-2.850.34210400.98910.358
2.85-2.960.28810080.98910.3
2.96-3.080.2379390.99210.247
3.08-3.220.199400.98510.198
3.22-3.370.1619020.99410.168
3.37-3.560.1348470.99510.14
3.56-3.770.1238040.98210.129
3.77-4.030.1137660.99310.119
4.03-4.360.17180.99410.105
4.36-4.770.0996770.99410.103
4.77-5.340.0966080.99210.1
5.34-6.160.0995440.99310.103
6.16-7.550.0974740.99410.102
7.55-10.670.0883830.99110.093
2.39-2.450.0932440.99510.098

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Processing

Software
NameVersionClassification
XSCALEdata scaling
XDSdata reduction
PHENIX1.16_3549refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→47.22 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2735 1612 -
Rwork0.227 --
obs-16141 99.6 %
Displacement parametersBiso mean: 66.14 Å2
Refinement stepCycle: LAST / Resolution: 2.4→47.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2518 0 0 22 2540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00762564
X-RAY DIFFRACTIONf_angle_d1.08423462
X-RAY DIFFRACTIONf_chiral_restr0.084377
X-RAY DIFFRACTIONf_plane_restr0.0053451
X-RAY DIFFRACTIONf_dihedral_angle_d18.43431568
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.47070.38481310.34971174X-RAY DIFFRACTION99
2.4707-2.55050.43631290.30231171X-RAY DIFFRACTION99
2.5505-2.64160.32571310.28261175X-RAY DIFFRACTION100
2.6416-2.74740.35471300.27091185X-RAY DIFFRACTION100
2.7474-2.87240.33551310.26711195X-RAY DIFFRACTION100
2.8724-3.02380.33871330.27611186X-RAY DIFFRACTION99
3.0238-3.21320.31091320.28611195X-RAY DIFFRACTION100
3.2132-3.46130.31091340.2451202X-RAY DIFFRACTION100
3.4613-3.80940.26231360.21431220X-RAY DIFFRACTION100
3.8094-4.36030.26421360.19661225X-RAY DIFFRACTION100
4.3603-5.49220.20031400.18021257X-RAY DIFFRACTION100
5.4922-47.22480.24691490.21381344X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 28.5216 Å / Origin y: -7.9636 Å / Origin z: 16.7264 Å
111213212223313233
T0.3395 Å2-0.0795 Å2-0.0058 Å2-0.4692 Å20.0662 Å2--0.3698 Å2
L0.8217 °2-0.9222 °20.4943 °2-1.6262 °2-0.5749 °2--2.0241 °2
S-0.0507 Å °-0.0104 Å °-0.0332 Å °-0.1051 Å °-0.006 Å °-0.0893 Å °0.0165 Å °0.2591 Å °0.0327 Å °
Refinement TLS groupSelection details: all

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