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- EMDB-47564: Locally Refined Cryo-EM map of 2G12 IgG BCR receptor lacking Fab ... -

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Basic information

Entry
Database: EMDB / ID: EMD-47564
TitleLocally Refined Cryo-EM map of 2G12 IgG BCR receptor lacking Fab region view
Map dataLocally Refined Cryo-EM map of 2G12 IgG BCR receptor lacking Fab region view
Sample
  • Complex: A complex of detergent solubilized 2G12 IgG BCR from Ramos B cell lines
    • Complex: Immunoglobulin heavy constant gamma 1
      • Protein or peptide: Immunoglobulin heavy constant gamma 1
    • Complex: B-cell antigen receptor complex-associated protein alpha chain
      • Protein or peptide: B-cell antigen receptor complex-associated protein alpha chain
    • Complex: B-cell antigen receptor complex-associated protein beta chain
      • Protein or peptide: B-cell antigen receptor complex-associated protein beta chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsRecombinantly purified B cell receptor / IgG / immunoglobulin / Human / IMMUNE SYSTEM
Function / homology
Function and homology information


IgM B cell receptor complex / B cell receptor complex / CD22 mediated BCR regulation / complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / immunoglobulin receptor binding / Initial triggering of complement ...IgM B cell receptor complex / B cell receptor complex / CD22 mediated BCR regulation / complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / immunoglobulin receptor binding / Initial triggering of complement / IgG immunoglobulin complex / B cell proliferation / FCGR activation / B cell activation / complement activation, classical pathway / Role of phospholipids in phagocytosis / antigen binding / multivesicular body / FCGR3A-mediated IL10 synthesis / Regulation of Complement cascade / B cell differentiation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / B cell receptor signaling pathway / response to bacterium / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / transmembrane signaling receptor activity / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / blood microparticle / Potential therapeutics for SARS / adaptive immune response / immune response / membrane raft / external side of plasma membrane / signal transduction / : / extracellular exosome / extracellular region / 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 gamma 1 / 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: 4.4 Å
AuthorsThakur B / Acharya P
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54-AI170752 United States
CitationJournal: To Be Published
Title: Anti-HIV-1 B cell antigen receptor signaling and structure
Authors: Thakur B / Acharya P
History
DepositionOct 30, 2024-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47564.png

Downloads & links

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Map

FileDownload / File: emd_47564.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocally Refined Cryo-EM map of 2G12 IgG BCR receptor lacking Fab region view
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 432 pix.
= 466.56 Å		1.08 Å/pix.
x 432 pix.
= 466.56 Å		1.08 Å/pix.
x 432 pix.
= 466.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.151
Minimum - Maximum-0.33341604 - 0.74912393
Average (Standard dev.)0.00004310562 (±0.009946973)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 466.56003 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_47564_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_47564_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : A complex of detergent solubilized 2G12 IgG BCR from Ramos B cell...

EntireName: A complex of detergent solubilized 2G12 IgG BCR from Ramos B cell lines
Components
  • Complex: A complex of detergent solubilized 2G12 IgG BCR from Ramos B cell lines
    • Complex: Immunoglobulin heavy constant gamma 1
      • Protein or peptide: Immunoglobulin heavy constant gamma 1
    • Complex: B-cell antigen receptor complex-associated protein alpha chain
      • Protein or peptide: B-cell antigen receptor complex-associated protein alpha chain
    • Complex: B-cell antigen receptor complex-associated protein beta chain
      • 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: A complex of detergent solubilized 2G12 IgG BCR from Ramos B cell...

SupramoleculeName: A complex of detergent solubilized 2G12 IgG BCR from Ramos B cell lines
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / Details: Extracted by detergent solubilization
Molecular weightTheoretical: 120 KDa

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Supramolecule #2: Immunoglobulin heavy constant gamma 1

SupramoleculeName: Immunoglobulin heavy constant gamma 1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: B-cell antigen receptor complex-associated protein alpha chain

SupramoleculeName: B-cell antigen receptor complex-associated protein alpha chain
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: B-cell antigen receptor complex-associated protein beta chain

SupramoleculeName: B-cell antigen receptor complex-associated protein beta chain
type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Immunoglobulin heavy constant gamma 1

MacromoleculeName: Immunoglobulin heavy constant gamma 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.129305 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GGPSVFLFPP KPKDTLMISR TPEVTCVVVD VSHEDPEVKF NWYVDGVEVH NAKTKPREEQ YNATYRVVSV LTVLHQDWLN GKEYKCKVS NKALPAPIAA TISKAKGQPR EPQVYTLPPS REEMTKNQVS LTCLVKGFYP SDIAVEWESN GQPENNYKTT P PVLDSDGS ...String:
GGPSVFLFPP KPKDTLMISR TPEVTCVVVD VSHEDPEVKF NWYVDGVEVH NAKTKPREEQ YNATYRVVSV LTVLHQDWLN GKEYKCKVS NKALPAPIAA TISKAKGQPR EPQVYTLPPS REEMTKNQVS LTCLVKGFYP SDIAVEWESN GQPENNYKTT P PVLDSDGS FFLYSKLTVD KSRWQQGNVF SCSVMHEALH AHYTQKSLSL SPELQL

UniProtKB: Immunoglobulin heavy constant gamma 1

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Macromolecule #2: B-cell antigen receptor complex-associated protein alpha chain

MacromoleculeName: B-cell antigen receptor complex-associated protein alpha chain
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.493682 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
LWMHKVPASL MVSLGEDAHF QCPHNSSNNA NVTWWRVLHG NYTWPPEFLG PGEDPNGTLI IQNVNKSHGG IYVCRVQEGN ESYQQSCGT YLRV

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

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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: 11.675191 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
ACSRIWQSPR FIARKRGFTV KMHCYMNSAS GNVSWLWKQE MDENPQQLKL EKGRMEESQN ESLATLTIQG IRFEDNGIYF CQQKCNNTS EVYQGCGTEL R

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: 5 / 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

Concentration2.1 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 298 K / Instrument: LEICA EM CPC

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 59.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 2.3000000000000003 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 733878
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 42635
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-9e6g:
Locally Refined Cryo-EM map of 2G12 IgG BCR receptor lacking Fab region view

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