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- EMDB-33440: Structure of a membrane protein M3 -

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Basic information

Entry
Database: EMDB / ID: EMD-33440
TitleStructure of a membrane protein M3
Map data
Sample
  • Complex: protein M
    • Protein or peptide: B-cell antigen receptor complex-associated protein alpha chain
    • Protein or peptide: Isoform 2 of Immunoglobulin heavy constant mu
    • Protein or peptide: B-cell antigen receptor complex-associated protein beta chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsmembrane protein / immune / IMMUNE SYSTEM
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 / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / B cell differentiation / B cell receptor signaling pathway / response to bacterium ...IgM B cell receptor complex / B cell receptor complex / CD22 mediated BCR regulation / B cell activation / B cell proliferation / multivesicular body / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / B cell differentiation / B cell receptor signaling pathway / response to bacterium / transmembrane signaling receptor activity / Potential therapeutics for SARS / adaptive immune response / immune response / membrane raft / external side of plasma membrane / signal transduction / extracellular exosome / identical protein binding / plasma membrane
Similarity search - Function
Immunoreceptor tyrosine-based activation motif / Phosphorylated immunoreceptor signalling ITAM / ITAM motif mammalian type profile. / Immunoreceptor tyrosine-based activation motif / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype ...Immunoreceptor tyrosine-based activation motif / Phosphorylated immunoreceptor signalling ITAM / ITAM motif mammalian type profile. / Immunoreceptor tyrosine-based activation motif / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Isoform 2 of Immunoglobulin heavy constant mu / B-cell antigen receptor complex-associated protein alpha chain / B-cell antigen receptor complex-associated protein beta chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.63 Å
AuthorsMa X / Zhu Y / Chen Y / Huang Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: 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
DepositionMay 16, 2022-
Header (metadata) releaseAug 31, 2022-
Map releaseAug 31, 2022-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33440.png

Downloads & links

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Map

FileDownload / File: emd_33440.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 360 pix.
= 396. Å		1.1 Å/pix.
x 360 pix.
= 396. Å		1.1 Å/pix.
x 360 pix.
= 396. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.45
Minimum - Maximum-5.1815853 - 6.7201295
Average (Standard dev.)0.00008112416 (±0.06825963)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 396.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_33440_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_33440_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : protein M

EntireName: protein M
Components
  • Complex: protein M
    • Protein or peptide: B-cell antigen receptor complex-associated protein alpha chain
    • Protein or peptide: Isoform 2 of Immunoglobulin heavy constant mu
    • Protein or peptide: B-cell antigen receptor complex-associated protein beta chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: protein M

SupramoleculeName: protein M / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: B-cell antigen receptor complex-associated protein alpha chain

MacromoleculeName: B-cell antigen receptor complex-associated protein alpha chain
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.504718 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
LWMHKVPASL MVSLGEDAHF QCPHNSSNNA NVTWWRVLHG NYTWPPEFLG PGEDPNGTLI IQNVNKSHGG IYVCRVQEGN ESYQQSCGT YLRVRQPPPR PFLDMGEGTK NRIITAEGII LLFCAVVPGT LLLFRKRW

UniProtKB: B-cell antigen receptor complex-associated protein alpha chain

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Macromolecule #2: Isoform 2 of Immunoglobulin heavy constant mu

MacromoleculeName: Isoform 2 of Immunoglobulin heavy constant mu / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.286188 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

UniProtKB: Isoform 2 of Immunoglobulin heavy constant mu

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Macromolecule #3: B-cell antigen receptor complex-associated protein beta chain

MacromoleculeName: B-cell antigen receptor complex-associated protein beta chain
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.143744 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
SRIWQSPRFI ARKRGFTVKM HCYMNSASGN VSWLWKQEMD ENPQQLKLEK GRMEESQNES LATLTIQGIR FEDNGIYFCQ QKCNNTSEV YQGCGTELRV MGFSTLAQLK QRNTLKDGII MIQTLLIILF IIVPIFLLLD

UniProtKB: B-cell antigen receptor complex-associated protein beta chain

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 12 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.63 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 272710
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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