+Open data
-Basic information
Entry | Database: PDB / ID: 7xq8 | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of human B-cell antigen receptor of the IgM isotype | |||||||||||||||
Components |
| |||||||||||||||
Keywords | SIGNALING PROTEIN / immunology / B cell signalling / adaptive immunity / antibody | |||||||||||||||
Function / homology | Function and homology information IgM B cell receptor complex / IgD immunoglobulin complex / B cell receptor complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation ...IgM B cell receptor complex / IgD immunoglobulin complex / B cell receptor complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / B cell activation / B cell proliferation / FCGR activation / immunoglobulin mediated immune response / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / multivesicular body / FCERI mediated Ca+2 mobilization / B cell differentiation / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / antigen binding / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / transmembrane signaling receptor activity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / adaptive immune response / Potential therapeutics for SARS / blood microparticle / immune response / membrane raft / external side of plasma membrane / signal transduction / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||||||||
Authors | Chen, M.Y. / Su, Q. / Shi, Y.G. | |||||||||||||||
Funding support | China, 4items
| |||||||||||||||
Citation | Journal: Science / Year: 2022 Title: Cryo-EM structure of the human IgM B cell receptor. Authors: Qiang Su / Mengying Chen / Yan Shi / Xiaofeng Zhang / Gaoxingyu Huang / Bangdong Huang / Dongwei Liu / Zhangsuo Liu / Yigong Shi / Abstract: The B cell receptor (BCR) initiates immune responses through antigen recognition. We report a 3.3-angstrom cryo-electron microscopy structure of human immunoglobulin M (IgM)-BCR in the resting state. ...The B cell receptor (BCR) initiates immune responses through antigen recognition. We report a 3.3-angstrom cryo-electron microscopy structure of human immunoglobulin M (IgM)-BCR in the resting state. IgM-BCR comprises two heavy chains, two light chains, and the Igα/Igβ heterodimer. The ectodomains of the heavy chains closely stack against those of Igα/Igβ, with one heavy chain locked between Igα and Igβ in the juxtamembrane region. Extracellular interactions may determine isotype specificity of the BCR. The transmembrane helices of IgM-BCR form a four-helix bundle that appears to be conserved among all BCR isotypes. This structure contains 14 glycosylation sites on the IgM-BCR ectodomains and reveals three potential surface binding sites. Our work reveals the organizational principles of the BCR and may facilitate the design of antibody-based therapeutics. | |||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7xq8.cif.gz | 329.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7xq8.ent.gz | 250.2 KB | Display | PDB format |
PDBx/mmJSON format | 7xq8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xq8_validation.pdf.gz | 956.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7xq8_full_validation.pdf.gz | 968.7 KB | Display | |
Data in XML | 7xq8_validation.xml.gz | 59.1 KB | Display | |
Data in CIF | 7xq8_validation.cif.gz | 88.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xq/7xq8 ftp://data.pdbj.org/pub/pdb/validation_reports/xq/7xq8 | HTTPS FTP |
-Related structure data
Related structure data | 33390MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Antibody | Mass: 67895.641 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Specific N-terminal secretion signal peptide (1-19) Source: (gene. exp.) Homo sapiens (human) / Gene: IGHM / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P01871-2 #2: Antibody | Mass: 27350.191 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: N terminal specific signal peptide (1-19), Flag tag (20-40) Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P01834 #3: Protein | | Mass: 28144.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: C terminal twin-strep tag / Source: (gene. exp.) Homo sapiens (human) / Gene: CD79A / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P11912 #4: Protein | | Mass: 29163.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: C terminal twin-strep tag / Source: (gene. exp.) Homo sapiens (human) / Gene: CD79B / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P40259 #5: Sugar | ChemComp-NAG / Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
| ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Source (natural) |
| ||||||||||||||||||||||||||||||
Source (recombinant) |
| ||||||||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||
Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1400 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 697919 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
|