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- PDB-8il3: Cryo-EM structure of CD38 in complex with FTL004 -

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Basic information

Entry
Database: PDB / ID: 8il3
TitleCryo-EM structure of CD38 in complex with FTL004
Components
  • ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
  • Heavy chain
  • Light chain
KeywordsHYDROLASE / monoclonal antibody
Function / homology
Function and homology information


2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / phosphorus-oxygen lyase activity / Nicotinate metabolism / artery smooth muscle contraction / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ metabolic process / NAD+ nucleosidase activity, cyclic ADP-ribose generating / long-term synaptic depression / negative regulation of bone resorption / response to hydroperoxide ...2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / phosphorus-oxygen lyase activity / Nicotinate metabolism / artery smooth muscle contraction / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ metabolic process / NAD+ nucleosidase activity, cyclic ADP-ribose generating / long-term synaptic depression / negative regulation of bone resorption / response to hydroperoxide / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / positive regulation of vasoconstriction / B cell proliferation / response to retinoic acid / positive regulation of B cell proliferation / response to interleukin-1 / response to progesterone / B cell receptor signaling pathway / apoptotic signaling pathway / female pregnancy / positive regulation of insulin secretion / response to estradiol / negative regulation of neuron projection development / transferase activity / positive regulation of cytosolic calcium ion concentration / positive regulation of cell growth / nuclear membrane / basolateral plasma membrane / response to hypoxia / response to xenobiotic stimulus / negative regulation of DNA-templated transcription / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / cell surface / signal transduction / extracellular exosome / identical protein binding / membrane / plasma membrane
Similarity search - Function
ADP-ribosyl cyclase (CD38/157) / ADP-ribosyl cyclase / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.86 Å
AuthorsYang, J. / Wang, Y. / Zhang, G.
Funding support China, United Kingdom, 11items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32070049 China
National Natural Science Foundation of China (NSFC)32222040 China
National Natural Science Foundation of China (NSFC)81872907 China
Other government2020YFSY0025
Other government2021YJ0454
Other government2019YFS0003
Ministry of Science and Technology (MoST, China)2021YFA1301900 China
Other government20822041D4057
CAMS Innovation Fund for Medical Sciences (CIFMS)2021-I2M-5-075 United Kingdom
Other government2018ZX09201018-021
Other government2017ZX09302010
CitationJournal: J Hematol Oncol / Year: 2022
Title: FTL004, an anti-CD38 mAb with negligible RBC binding and enhanced pro-apoptotic activity, is a novel candidate for treatments of multiple myeloma and non-Hodgkin lymphoma.
Authors: Guangbing Zhang / Cuiyu Guo / Yan Wang / Xianda Zhang / Shuang Liu / Wen Qu / Chunxia Chen / Lingli Yan / Zhouning Yang / Zhixiong Zhang / Xiaohua Jiang / Xiaofeng Chen / Hong Liu / Qinhuai ...Authors: Guangbing Zhang / Cuiyu Guo / Yan Wang / Xianda Zhang / Shuang Liu / Wen Qu / Chunxia Chen / Lingli Yan / Zhouning Yang / Zhixiong Zhang / Xiaohua Jiang / Xiaofeng Chen / Hong Liu / Qinhuai Lai / Xian Wei / Ying Lu / Shengyan Zhao / Han Deng / Yuxi Wang / Lin Yu / Hongbin Yu / Yu Wu / Zhaoming Su / Pengyu Chen / Ziqing Ren / Meng Yu / Feng Qu / Yong Luo / Lantu Gou / Qing Li / Ying Huang / Fanxin Ma / Jinliang Yang /
Abstract: Anti-CD38 monoclonal antibodies (mAbs), daratumumab, and isatuximab have represented a breakthrough in the treatment of multiple myeloma (MM). Recently, CD38-based mAbs were expected to achieve ...Anti-CD38 monoclonal antibodies (mAbs), daratumumab, and isatuximab have represented a breakthrough in the treatment of multiple myeloma (MM). Recently, CD38-based mAbs were expected to achieve increasing potential beyond MM, which encouraged us to develop new anti-CD38 mAbs to meet clinical needs. In this study, we developed a novel humanized anti-CD38 antibody, FTL004, which exhibited enhanced pro-apoptotic ability and negligible binding to red blood cells (RBCs). FTL004 presented a better ability to induce direct apoptosis independent of Fc-mediated cross-linking against lymphoma and MM cell lines as well as primary myeloma cells derived from MM patients. For instance, FTL004 induced RPMI 8226 cells with 55% early apoptosis cells compared with 20% in the isatuximab-treated group. Of interest, FTL004 showed ignorable binding to CD38 on human RBCs in contrast to tumor cells, even at concentrations up to 30 μg/mL. Furthermore, with an engineered Fc domain, FTL004 displayed stronger antibody-dependent cellular cytotoxicity (ADCC) against CD38+ malignant cells. In vivo MM and non-Hodgkin lymphoma tumor xenograft models showed that FTL004 possessed an effective anti-tumor effect. Cryo-electron microscopy structure resolved two epitope centers of FTL004 on CD38: one of which was unique while the other partly overlapped with that of isatuximab. Taken together, FTL004 distinguishes it from other CD38 targeting mAbs and represents a potential candidate for the treatment of MM and non-Hodgkin lymphoma.
History
DepositionMar 1, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.0Mar 29, 2023Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 29, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 29, 2023Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 29, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 29, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Mar 29, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 29, 2023Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 29, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 29, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update
Revision 1.2Jun 18, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jun 18, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Light chain
B: Heavy chain
C: ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1


Theoretical massNumber of molelcules
Total (without water)73,5823
Polymers73,5823
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Antibody Light chain


Mass: 23929.572 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody Heavy chain


Mass: 22817.510 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Protein ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 / 2'-phospho-ADP-ribosyl cyclase / 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose ...2'-phospho-ADP-ribosyl cyclase / 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / 2'-phospho-cyclic-ADP-ribose transferase / ADP-ribosyl cyclase 1 / ADPRC 1 / Cyclic ADP-ribose hydrolase 1 / cADPr hydrolase 1 / T10


Mass: 26834.471 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD38 / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
References: UniProt: P28907, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of CD38 in complex with FTL004 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2826 nm / Nominal defocus min: 752 nm
Image recordingElectron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k)
Image scansMovie frames/image: 5

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Processing

SoftwareName: PHENIX / Version: 1.15.2_3472: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 34435 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0085381
ELECTRON MICROSCOPYf_angle_d1.2077312
ELECTRON MICROSCOPYf_dihedral_angle_d5.2743220
ELECTRON MICROSCOPYf_chiral_restr0.073812
ELECTRON MICROSCOPYf_plane_restr0.012942

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