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- PDB-9mqo: Crystal structure of BCMA in complex with CA10v2 Fab -

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Basic information

Entry
Database: PDB / ID: 9mqo
TitleCrystal structure of BCMA in complex with CA10v2 Fab
Components
  • CA10v2 Fab heavy chain
  • CA10v2 Fab light chain
  • Tumor necrosis factor receptor superfamily member 17
KeywordsIMMUNE SYSTEM / antibody / B-cell receptor / BCMA
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.181 Å
AuthorsQiu, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of BCMA in complex with CA10v2 Fab
Authors: Qiu, Y.
History
DepositionJan 4, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tumor necrosis factor receptor superfamily member 17
B: CA10v2 Fab heavy chain
C: CA10v2 Fab light chain
D: Tumor necrosis factor receptor superfamily member 17
E: CA10v2 Fab heavy chain
F: CA10v2 Fab light chain
G: Tumor necrosis factor receptor superfamily member 17
H: CA10v2 Fab heavy chain
I: CA10v2 Fab light chain
J: Tumor necrosis factor receptor superfamily member 17
K: CA10v2 Fab heavy chain
L: CA10v2 Fab light chain
M: Tumor necrosis factor receptor superfamily member 17
N: CA10v2 Fab heavy chain
O: CA10v2 Fab light chain
P: Tumor necrosis factor receptor superfamily member 17
Q: CA10v2 Fab heavy chain
R: CA10v2 Fab light chain


Theoretical massNumber of molelcules
Total (without water)330,61418
Polymers330,61418
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.164, 94.784, 108.130
Angle α, β, γ (deg.)81.39, 81.40, 62.67
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Tumor necrosis factor receptor superfamily member 17 / B-cell maturation protein


Mass: 6057.875 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: BCMA was produced as GST-PreScission-BCMA (1-54) in E. Coli BCMA was prepared by PreScission cleavage, followed by GST and SEC purification
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFRSF17, BCM, BCMA / Production host: Escherichia coli (E. coli) / References: UniProt: Q02223
#2: Antibody
CA10v2 Fab heavy chain


Mass: 25949.916 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody
CA10v2 Fab light chain


Mass: 23094.582 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
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: 2.45 Å3/Da / Density % sol: 49.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.18 M Sodium Chloride, 0.09 M Phosphate/citrate pH 4.2, 20 % w/v PEG 8000, 0.1M Sodium Malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 3.18→84.15 Å / Num. obs: 53814 / % possible obs: 98.4 % / Redundancy: 1.9 % / Rrim(I) all: 0.235 / Net I/σ(I): 1.9
Reflection shellResolution: 3.18→3.27 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 3972 / Rrim(I) all: 0.595 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.181→83.847 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2716 --
Rwork0.2321 --
obs-28731 67.4 %
Refinement stepCycle: LAST / Resolution: 3.181→83.847 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20814 0 0 0 20814

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