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- PDB-7wsp: Structure of a membrane protein M -

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Basic information

Entry
Database: PDB / ID: 7wsp
TitleStructure of a membrane protein M
Components
  • (Isoform 2 of Immunoglobulin heavy constant mu) x 2
  • B-cell antigen receptor complex-associated protein alpha chain
  • B-cell antigen receptor complex-associated protein beta chain
KeywordsIMMUNE SYSTEM / membrane
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 / adaptive immune response / Potential therapeutics for SARS / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.09 Å
AuthorsMa, X. / Zhu, Y. / Chen, Y. / Huang, Z.
Funding support China, 1items
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, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 16, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: B-cell antigen receptor complex-associated protein alpha chain
C: B-cell antigen receptor complex-associated protein beta chain
B: Isoform 2 of Immunoglobulin heavy constant mu
D: Isoform 2 of Immunoglobulin heavy constant mu


Theoretical massNumber of molelcules
Total (without water)112,7184
Polymers112,7184
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: Protein B-cell antigen receptor complex-associated protein alpha chain / Ig-alpha / MB-1 membrane glycoprotein / Membrane-bound immunoglobulin-associated protein / Surface ...Ig-alpha / MB-1 membrane glycoprotein / Membrane-bound immunoglobulin-associated protein / Surface IgM-associated protein


Mass: 15504.718 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD79A, IGA, MB1 / Production host: Homo sapiens (human) / References: UniProt: P11912
#2: Protein B-cell antigen receptor complex-associated protein beta chain / B-cell-specific glycoprotein B29 / Ig-beta / Immunoglobulin-associated B29 protein


Mass: 16143.744 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD79B, B29, IGB / Production host: Homo sapiens (human) / References: UniProt: P40259
#3: Protein Isoform 2 of Immunoglobulin heavy constant mu / Ig mu chain C region / Ig mu chain C region BOT / Ig mu chain C region GAL / Ig mu chain C region OU


Mass: 40470.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHM / Production host: Homo sapiens (human) / References: UniProt: P01871
#4: Protein Isoform 2 of Immunoglobulin heavy constant mu / Ig mu chain C region / Ig mu chain C region BOT / Ig mu chain C region GAL / Ig mu chain C region OU


Mass: 40599.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHM / Production host: Homo sapiens (human) / References: UniProt: P01871
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: complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: NITROGEN

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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: 2500 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 1.5 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.09 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 47428 / Symmetry type: POINT

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