[English] 日本語
Yorodumi
- EMDB-70353: Clone 2.1 Fab in complex with chicken IgY CH2 domain (local refin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-70353
TitleClone 2.1 Fab in complex with chicken IgY CH2 domain (local refinement)
Map datasharpened map
Sample
  • Complex: Clone 2.1 Fab in complex with chicken IgY CH2 domain
    • Protein or peptide: chicken IgY heavy chain,Ig-like domain-containing protein
    • Protein or peptide: Clone 2.1 Fab heavy chain
    • Protein or peptide: Clone 2.1 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsgerminal center evolution / antibody / IMMUNE SYSTEM
Function / homology
Function and homology information


: / Immunoglobulin V-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 V-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
Ig-like domain-containing protein
Similarity search - Component
Biological speciesMus musculus (house mouse) / Gallus gallus (chicken)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsOzorowski G / Alkutkar T / Ward AB
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: bioRxiv / Year: 2025
Title: Replaying germinal center evolution on a quantified affinity landscape.
Authors: William S DeWitt / Ashni A Vora / Tatsuya Araki / Jared G Galloway / Tanwee Alkutkar / Juliana Bortolatto / Tiago B R Castro / Will Dumm / Chris Jennings-Shaffer / Tongqiu Jia / Luka Mesin / ...Authors: William S DeWitt / Ashni A Vora / Tatsuya Araki / Jared G Galloway / Tanwee Alkutkar / Juliana Bortolatto / Tiago B R Castro / Will Dumm / Chris Jennings-Shaffer / Tongqiu Jia / Luka Mesin / Gabriel Ozorowski / Juhee Pae / Duncan K Ralph / Jesse D Bloom / Armita Nourmohammad / Yun S Song / Andrew B Ward / Tyler N Starr / Frederick A Matsen / Gabriel D Victora /
Abstract: Darwinian evolution of immunoglobulin genes within germinal centers (GC) underlies the progressive increase in antibody affinity following antigen exposure. Whereas the mechanics of how competition ...Darwinian evolution of immunoglobulin genes within germinal centers (GC) underlies the progressive increase in antibody affinity following antigen exposure. Whereas the mechanics of how competition between GC B cells drives increased affinity are well established, the dynamical evolutionary features of this process remain poorly characterized. We devised an experimental evolution model in which we "replay" over one hundred instances of a clonally homogenous GC reaction and follow the selective process by assigning affinities to all cells using deep mutational scanning. Our data reveal how GCs achieve predictable evolutionary outcomes through the cumulative effects of many rounds of imperfect selection, acting on a landscape shaped heavily by somatic hypermutation (SHM) targeting biases. Using time-calibrated models, we show that apparent features of GC evolution such as permissiveness to low-affinity lineages and early plateauing of affinity are best explained by survivorship biases that distort our view of how affinity progresses over time.
History
DepositionApr 26, 2025-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_70353.png

Downloads & links

-
Map

FileDownload / File: emd_70353.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 256 pix.
= 294.4 Å		1.15 Å/pix.
x 256 pix.
= 294.4 Å		1.15 Å/pix.
x 256 pix.
= 294.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.15 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.54027253 - 1.0693078
Average (Standard dev.)0.00026441703 (±0.022180472)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 294.4 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_70353_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map A

Fileemd_70353_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map B

Fileemd_70353_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Clone 2.1 Fab in complex with chicken IgY CH2 domain

EntireName: Clone 2.1 Fab in complex with chicken IgY CH2 domain
Components
  • Complex: Clone 2.1 Fab in complex with chicken IgY CH2 domain
    • Protein or peptide: chicken IgY heavy chain,Ig-like domain-containing protein
    • Protein or peptide: Clone 2.1 Fab heavy chain
    • Protein or peptide: Clone 2.1 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: Clone 2.1 Fab in complex with chicken IgY CH2 domain

SupramoleculeName: Clone 2.1 Fab in complex with chicken IgY CH2 domain / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Mus musculus (house mouse)

-
Macromolecule #1: chicken IgY heavy chain,Ig-like domain-containing protein

MacromoleculeName: chicken IgY heavy chain,Ig-like domain-containing protein
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Gallus gallus (chicken)
Molecular weightTheoretical: 59.474793 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AVTLDESGGG LQTPGGTLSL VCEGSGFTFS SFHMQWVRQA LGKGLEWVAG ISGSGKYTSY GAAVKGRATI SRDNGQSTVR LQLNNLKAE DTGTYYCTRS SCGGCCDWSP YTTGCGAYST GTIDAWGHGT EVIVSSASPT SPPRLYPLSA CCSDSAVPPA V GCLLSPSS ...String:
AVTLDESGGG LQTPGGTLSL VCEGSGFTFS SFHMQWVRQA LGKGLEWVAG ISGSGKYTSY GAAVKGRATI SRDNGQSTVR LQLNNLKAE DTGTYYCTRS SCGGCCDWSP YTTGCGAYST GTIDAWGHGT EVIVSSASPT SPPRLYPLSA CCSDSAVPPA V GCLLSPSS AGGISWEGSG GTAVAGRVSG TPVKLSFVRL SPGEKRKSFV CSAAPGGALL KKEVQVCRVD PVPPVAPEVQ VL HPSSCTP SQSESVELLC LVTGFSPASA EVEWLVDGVG GLLVASQSPA VRSGSTYSLS SRVNVSGTDW REGKSYSCRV RHP ATNTVV EDHVKGCPDG AQSCSPIQLY AIPPSPGELY ISLDAKLRCL VVNLPSDSSL SVTWTREKSG NLRPDPMVLQ EHFN GTYSA SSAVPVSTQD WLSGERFTCT VQHEELPLPL SKSVYRNTGP TTPPLIYPFA PHPEELSLSR VTLSCLVRGF RPRDI EIRW LRDHRAVPAT EFVTTAVLPE ERTANGAGGD GDTFFVYSKM SVETAKWNGG TVFACMAVHE ALPMRFSQRT LQKQAG K

UniProtKB: Ig-like domain-containing protein

-
Macromolecule #2: Clone 2.1 Fab heavy chain

MacromoleculeName: Clone 2.1 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 25.972678 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLQESGPS LVKPSQTLSL TCSVTGASIT SGYWNWIRKF PGNRLEYMGY ISYSGGTYYN PSLKSRISIT RDTSKNQYYL QLNSVTTED TATYYCARDF DVWGAGTTVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV TVSWNSGALT S GVHTFPAV ...String:
EVQLQESGPS LVKPSQTLSL TCSVTGASIT SGYWNWIRKF PGNRLEYMGY ISYSGGTYYN PSLKSRISIT RDTSKNQYYL QLNSVTTED TATYYCARDF DVWGAGTTVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV TVSWNSGALT S GVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK RVEPKSCDKT HTSRHHHHHH SGSDYKDDDD K

-
Macromolecule #3: Clone 2.1 Fab light chain

MacromoleculeName: Clone 2.1 Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.56107 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIVMTQSQKF MSTSVGDRVS VTCKASQNVG TNVGWFQQKP GQSPKSLIYS ASYRYSGVPD RFTGSGSGTD FTLTISNVQS EDLAEYFCH QYYSYPLTFG SGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIVMTQSQKF MSTSVGDRVS VTCKASQNVG TNVGWFQQKP GQSPKSLIYS ASYRYSGVPD RFTGSGSGTD FTLTISNVQS EDLAEYFCH QYYSYPLTFG SGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

-
Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 36000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: Gctf / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: ab initio
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 346259
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more