+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33440 | |||||||||
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Title | Structure of a membrane protein M3 | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information IgM B cell receptor complex / B cell receptor complex / CD22 mediated BCR regulation / B cell activation / B cell proliferation / multivesicular body / B cell differentiation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / B cell receptor signaling pathway / transmembrane signaling receptor activity ...IgM B cell receptor complex / B cell receptor complex / CD22 mediated BCR regulation / B cell activation / B cell proliferation / multivesicular body / B cell differentiation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / B cell receptor signaling pathway / transmembrane signaling receptor activity / adaptive immune response / Potential therapeutics for SARS / immune response / membrane raft / external side of plasma membrane / signal transduction / extracellular exosome / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.63 Å | |||||||||
Authors | Ma X / Zhu Y / Chen Y / Huang Z | |||||||||
Funding support | China, 1 items
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Citation | Journal: Science / Year: 2022 Title: Cryo-EM structures of two human B cell receptor isotypes. Authors: Xinyu Ma / Yuwei Zhu / De Dong / Yan Chen / Shubo Wang / Dehui Yang / Zhuo Ma / Anqi Zhang / Fan Zhang / Changyou Guo / Zhiwei Huang / Abstract: The B cell receptor (BCR) complex plays a critical role in B cell development and immune responses. The assembly mechanisms underlying the BCR complex remain unknown. We determined the cryo-electron ...The B cell receptor (BCR) complex plays a critical role in B cell development and immune responses. The assembly mechanisms underlying the BCR complex remain unknown. We determined the cryo-electron microscopy (cryo-EM) structures of human IgG-BCR and IgM-BCR, which consist of membrane-bound immunoglobulin molecules (mIg) and Igα/β subunits at a 1:1 stoichiometry. Assembly of both BCR complexes involves their extracellular domains, membrane-proximal connection peptides, and transmembrane (TM) helices. The TM helices of mIgG and mIgM share a conserved set of hydrophobic and polar interactions with Igα/β TM helices. By contrast, the IgG-Cγ3 and IgM-Cμ4 domains interact with extracellular Ig-like domains of Igα/β through head-to-tail and side-by-side modes, respectively. This work reveals the structural basis for BCR assembly and provides insights into BCR triggering. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33440.map.gz | 168 MB | EMDB map data format | |
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Header (meta data) | emd-33440-v30.xml emd-33440.xml | 16.2 KB 16.2 KB | Display Display | EMDB header |
Images | emd_33440.png | 69.7 KB | ||
Others | emd_33440_half_map_1.map.gz emd_33440_half_map_2.map.gz | 165.2 MB 165.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33440 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33440 | HTTPS FTP |
-Related structure data
Related structure data | 7xt6MC 7wsoC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_33440.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_33440_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_33440_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : protein M
Entire | Name: protein M |
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Components |
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-Supramolecule #1: protein M
Supramolecule | Name: protein M / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
-Macromolecule #1: B-cell antigen receptor complex-associated protein alpha chain
Macromolecule | Name: B-cell antigen receptor complex-associated protein alpha chain type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 15.504718 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: LWMHKVPASL MVSLGEDAHF QCPHNSSNNA NVTWWRVLHG NYTWPPEFLG PGEDPNGTLI IQNVNKSHGG IYVCRVQEGN ESYQQSCGT YLRVRQPPPR PFLDMGEGTK NRIITAEGII LLFCAVVPGT LLLFRKRW |
-Macromolecule #2: Isoform 2 of Immunoglobulin heavy constant mu
Macromolecule | Name: Isoform 2 of Immunoglobulin heavy constant mu / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 40.286188 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: LPPKVSVFVP PRDGFFGNPR KSKLICQATG FSPRQIQVSW LREGKQVGSG VTTDQVQAEA KESGPTTYKV TSTLTIKESD WLGQSMFTC RVDHRGLTFQ QNASSMCVPD QDTAIRVFAI PPSFASIFLT KSTKLTCLVT DLTTYDSVTI SWTRQNGEAV K THTNISES ...String: LPPKVSVFVP PRDGFFGNPR KSKLICQATG FSPRQIQVSW LREGKQVGSG VTTDQVQAEA KESGPTTYKV TSTLTIKESD WLGQSMFTC RVDHRGLTFQ QNASSMCVPD QDTAIRVFAI PPSFASIFLT KSTKLTCLVT DLTTYDSVTI SWTRQNGEAV K THTNISES HPNATFSAVG EASICEDDWN SGERFTCTVT HTDLPSPLKQ TISRPKGVAL HRPDVYLLPP AREQLNLRES AT ITCLVTG FSPADVFVQW MQRGQPLSPE KYVTSAPMPE PQAPGRYFAH SILTVSEEEW NTGETYTCVV AHEALPNRVT ERT VDKSTE GEVSADEEGF ENLWATASTF IVLFLLSLFY STTVTLFK |
-Macromolecule #3: B-cell antigen receptor complex-associated protein beta chain
Macromolecule | Name: B-cell antigen receptor complex-associated protein beta chain type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 16.143744 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: SRIWQSPRFI ARKRGFTVKM HCYMNSASGN VSWLWKQEMD ENPQQLKLEK GRMEESQNES LATLTIQGIR FEDNGIYFCQ QKCNNTSEV YQGCGTELRV MGFSTLAQLK QRNTLKDGII MIQTLLIILF IIVPIFLLLD |
-Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 12 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: NITROGEN |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
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Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.63 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 272710 |