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- EMDB-32763: Structure of a membrane protein M -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-32763
TitleStructure of a membrane protein M
Map data
Sample
  • Complex: complex
    • Protein or peptide: B-cell antigen receptor complex-associated protein alpha chain
    • Protein or peptide: B-cell antigen receptor complex-associated protein beta chain
    • Protein or peptide: Isoform 2 of Immunoglobulin heavy constant mu
    • Protein or peptide: Isoform 2 of Immunoglobulin heavy constant mu
Keywordsmembrane / IMMUNE SYSTEM
Function / homology
Function and homology information


hexameric IgM immunoglobulin complex / IgM B cell receptor complex / pentameric IgM immunoglobulin complex / B cell receptor complex / pre-B cell allelic exclusion / IgM immunoglobulin complex / CD22 mediated BCR regulation / B cell activation / B cell proliferation / antigen binding ...hexameric IgM immunoglobulin complex / IgM B cell receptor complex / pentameric IgM immunoglobulin complex / B cell receptor complex / pre-B cell allelic exclusion / IgM immunoglobulin complex / CD22 mediated BCR regulation / B cell activation / B cell proliferation / antigen binding / multivesicular body / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / B cell differentiation / Cell surface interactions at the vascular wall / B cell receptor signaling pathway / response to bacterium / antibacterial humoral response / transmembrane signaling receptor activity / defense response to Gram-negative bacterium / blood microparticle / Potential therapeutics for SARS / adaptive immune response / immune response / membrane raft / innate immune response / external side of plasma membrane / cell surface / signal transduction / extracellular space / 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 ...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/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
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: 4.09 Å
AuthorsMa X / Zhu Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of a membrane protein M
Authors: Ma X / Zhu Y / Chen Y / Huang Z
History
DepositionJan 30, 2022-
Header (metadata) releaseFeb 1, 2023-
Map releaseFeb 1, 2023-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32763.png

Downloads & links

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Map

FileDownload / File: emd_32763.map.gz / Format: CCP4 / Size: 64 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 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 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: 0.347
Minimum - Maximum-1.6982644 - 2.6934707
Average (Standard dev.)0.0025124988 (±0.055152643)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : complex

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

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Supramolecule #1: complex

SupramoleculeName: complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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: B-cell antigen receptor complex-associated protein beta chain

MacromoleculeName: B-cell antigen receptor complex-associated protein beta chain
type: protein_or_peptide / ID: 2 / 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 #3: Isoform 2 of Immunoglobulin heavy constant mu

MacromoleculeName: Isoform 2 of Immunoglobulin heavy constant mu / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.470355 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: IAELPPKVSV FVPPRDGFFG NPRKSKLICQ ATGFSPRQIQ VSWLREGKQV GSGVTTDQVQ AEAKESGPTT YKVTSTLTIK ESDWLGQSM FTCRVDHRGL TFQQNASSMC VPDQDTAIRV FAIPPSFASI FLTKSTKLTC LVTDLTTYDS VTISWTRQNG E AVKTHTNI ...String:
IAELPPKVSV FVPPRDGFFG NPRKSKLICQ ATGFSPRQIQ VSWLREGKQV GSGVTTDQVQ AEAKESGPTT YKVTSTLTIK ESDWLGQSM FTCRVDHRGL TFQQNASSMC VPDQDTAIRV FAIPPSFASI FLTKSTKLTC LVTDLTTYDS VTISWTRQNG E AVKTHTNI SESHPNATFS AVGEASICED DWNSGERFTC TVTHTDLPSP LKQTISRPKG VALHRPDVYL LPPAREQLNL RE SATITCL VTGFSPADVF VQWMQRGQPL SPEKYVTSAP MPEPQAPGRY FAHSILTVSE EEWNTGETYT CVVAHEALPN RVT ERTVDK STEGEVSADE EGFENLWATA STFIVLFLLS LFYSTTVTLF

UniProtKB: Immunoglobulin heavy constant mu

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Macromolecule #4: Isoform 2 of Immunoglobulin heavy constant mu

MacromoleculeName: Isoform 2 of Immunoglobulin heavy constant mu / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.599535 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: IAELPPKVSV FVPPRDGFFG NPRKSKLICQ ATGFSPRQIQ VSWLREGKQV GSGVTTDQVQ AEAKESGPTT YKVTSTLTIK ESDWLGQSM FTCRVDHRGL TFQQNASSMC VPDQDTAIRV FAIPPSFASI FLTKSTKLTC LVTDLTTYDS VTISWTRQNG E AVKTHTNI ...String:
IAELPPKVSV FVPPRDGFFG NPRKSKLICQ ATGFSPRQIQ VSWLREGKQV GSGVTTDQVQ AEAKESGPTT YKVTSTLTIK ESDWLGQSM FTCRVDHRGL TFQQNASSMC VPDQDTAIRV FAIPPSFASI FLTKSTKLTC LVTDLTTYDS VTISWTRQNG E AVKTHTNI SESHPNATFS AVGEASICED DWNSGERFTC TVTHTDLPSP LKQTISRPKG VALHRPDVYL LPPAREQLNL RE SATITCL VTGFSPADVF VQWMQRGQPL SPEKYVTSAP MPEPQAPGRY FAHSILTVSE EEWNTGETYT CVVAHEALPN RVT ERTVDK STEGEVSADE EGFENLWATA STFIVLFLLS LFYSTTVTLF K

UniProtKB: Immunoglobulin heavy constant mu

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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
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: 1.5 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: PDB ENTRY
PDB model - PDB ID:

7k0c

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.09 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 47428
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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