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- EMDB-6099: Exploring IgG1 Antibody Conformational Flexibility in Three Dimensions -

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Open data

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Basic information

Entry

Database: EMDB / ID: EMD-6099

Title

Exploring IgG1 Antibody Conformational Flexibility in Three Dimensions

Map data

Tomographic reconstruction of IgG1 antibody

Sample

Sample: Human IgG1Immunoglobulin G
Protein or peptide: immunoglobulin G subclass 1

Keywords

antibody dynamics / structural equilibrium / fluctuation /

electron microscopy / individual-particle electron tomography / focused electron tomographic reconstruction

Biological species

Homo sapiens (human)

Method

electron tomography /

negative staining / Resolution: 20.0 Å

Authors

Zhang X / Zhang L / Tong H / Peng B / Rames MJ / Zhang S / Ren G

Citation

Journal: Sci Rep / Year: 2015
Title: 3D Structural Fluctuation of IgG1 Antibody Revealed by Individual Particle Electron Tomography.
Authors: Xing Zhang / Lei Zhang / Huimin Tong / Bo Peng / Matthew J Rames / Shengli Zhang / Gang Ren /

Abstract: Commonly used methods for determining protein structure, including X-ray crystallography and single-particle reconstruction, often provide a single and unique three-dimensional (3D) structure. ...

History

Deposition	Sep 14, 2014	-
Header (metadata) release	Sep 24, 2014	-
Map release	Jun 3, 2015	-
Update	Jun 3, 2015	-
Current status	Jun 3, 2015	Processing site: RCSB / Status: Released

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Structure visualization

Movie	Surface view with section colored by density value Surface level: 1 Imaged by UCSF Chimera Download Surface view colored by radius Surface level: 1 Imaged by UCSF Chimera Download Movie viewer
Structure viewer	EM map: SurfViewMolmilJmol/JSmol
Supplemental images	400_6099.gif

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Downloads & links

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EMDB archive

Map data	emd_6099.map.gz	22.1 MB		EMDB map data format
Header (meta data)	emd-6099-v30.xml emd-6099.xml	11.4 KB 11.4 KB	Display Display	EMDB header
Images	400_6099.gif 80_6099.gif	26.7 KB 2.8 KB
Others	submit-120-p002.map.gz submit-120-p003.map.gz submit-120-p004.map.gz submit-120-p005.map.gz submit-120-p006.map.gz submit-120-p007.map.gz submit-120-p008.map.gz submit-120-p009.map.gz submit-120-p010.map.gz submit-120-p011.map.gz submit-120-p012.map.gz submit-120-p013.map.gz submit-120-p014.map.gz submit-120-p015.map.gz submit-120-p016.map.gz submit-120-p017.map.gz submit-120-p018.map.gz submit-120-p019.map.gz submit-120-p020.map.gz submit-120-p021.map.gz submit-120-p022.map.gz submit-120-p023.map.gz submit-120-p024.map.gz submit-120-p025.map.gz submit-120-p026.map.gz submit-120-p027.map.gz submit-120-p028.map.gz submit-120-p029.map.gz submit-120-p030.map.gz submit-120-p031.map.gz submit-120-p032.map.gz submit-120-p033.map.gz submit-120-p034.map.gz submit-120-p035.map.gz submit-120-p036.map.gz submit-120-p037.map.gz submit-120-p038.map.gz submit-120-p039.map.gz submit-120-p040.map.gz submit-120-p041.map.gz submit-120-p042.map.gz submit-120-p043.map.gz submit-120-p044.map.gz submit-120-p045.map.gz submit-120-p046.map.gz submit-120-p047.map.gz submit-120-p048.map.gz submit-120-p049.map.gz submit-120-p050.map.gz submit-120-p051.map.gz submit-120-p052.map.gz submit-120-p053.map.gz submit-120-p054.map.gz submit-120-p055.map.gz submit-120-p056.map.gz submit-120-p057.map.gz submit-120-p058.map.gz submit-120-p059.map.gz submit-120-p060.map.gz submit-120-p061.map.gz submit-120-p062.map.gz submit-120-p063.map.gz submit-120-p064.map.gz submit-120-p065.map.gz submit-120-p066.map.gz submit-120-p067.map.gz submit-120-p068.map.gz submit-120-p069.map.gz submit-120-p070.map.gz submit-120-p071.map.gz submit-120-p072.map.gz submit-120-p073.map.gz submit-120-p074.map.gz submit-120-p075.map.gz submit-120-p076.map.gz submit-120-p077.map.gz submit-120-p078.map.gz submit-120-p079.map.gz submit-120-p080.map.gz submit-120-p081.map.gz submit-120-p082.map.gz submit-120-p083.map.gz submit-120-p084.map.gz submit-120-p085.map.gz submit-120-p086.map.gz submit-120-p087.map.gz submit-120-p088.map.gz submit-120-p089.map.gz submit-120-p090.map.gz submit-120-p091.map.gz submit-120-p092.map.gz submit-120-p093.map.gz submit-120-p094.map.gz submit-120-p095.map.gz submit-120-p096.map.gz submit-120-p097.map.gz submit-120-p098.map.gz submit-120-p099.map.gz submit-120-p100.map.gz submit-120-p101.map.gz submit-120-p102.map.gz submit-120-p103.map.gz submit-120-p104.map.gz submit-120-p105.map.gz submit-120-p106.map.gz submit-120-p107.map.gz submit-120-p108.map.gz submit-120-p109.map.gz submit-120-p110.map.gz submit-120-p111.map.gz submit-120-p112.map.gz submit-120-p113.map.gz submit-120-p114.map.gz submit-120-p115.map.gz submit-120-p116.map.gz submit-120-p117.map.gz submit-120-p118.map.gz submit-120-p119.map.gz submit-120-p120.map.gz	19.1 MB 19.5 MB 18.1 MB 21.1 MB 20.8 MB 19.6 MB 20.5 MB 20 MB 19.9 MB 19.5 MB 20.2 MB 21.4 MB 22.4 MB 28.4 MB 28.4 MB 21.4 MB 20.8 MB 22.1 MB 30.1 MB 30.5 MB 28.9 MB 31.7 MB 28 MB 30.3 MB 29.9 MB 28.6 MB 30 MB 29.7 MB 30.2 MB 28.9 MB 28.8 MB 28.2 MB 29.8 MB 31.1 MB 29 MB 29.5 MB 29.6 MB 31.2 MB 29.8 MB 30.3 MB 30 MB 29.3 MB 30.5 MB 29.8 MB 29.2 MB 31.1 MB 29.6 MB 30.1 MB 29.3 MB 29.2 MB 30.4 MB 29.9 MB 30.1 MB 30.3 MB 29.5 MB 30.3 MB 30 MB 29.3 MB 28.7 MB 32 MB 30.5 MB 31.2 MB 28.9 MB 30.8 MB 31.1 MB 31.8 MB 31.2 MB 30.3 MB 30.7 MB 30.3 MB 31.1 MB 32.4 MB 30.4 MB 31 MB 30.9 MB 30.1 MB 29.8 MB 31.6 MB 19.1 MB 19.2 MB 19.5 MB 18.9 MB 20.1 MB 19.3 MB 19.7 MB 19.5 MB 18.8 MB 19.4 MB 19.6 MB 20.5 MB 19.2 MB 19.3 MB 20 MB 18.9 MB 19.4 MB 20.1 MB 19.8 MB 19.6 MB 19.7 MB 19.8 MB 19.1 MB 19.9 MB 20.5 MB 19.9 MB 20.1 MB 19.4 MB 20 MB 20.3 MB 20.5 MB 19.9 MB 19.6 MB 19.2 MB 19.8 MB 18.8 MB 20.1 MB 19.8 MB 19.3 MB 19.8 MB 19.9 MB
Archive directory	http://ftp.pdbj.org/pub/emdb/structures/EMD-6099 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6099	HTTPS FTP

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Related structure data

Similar structure data	2qtj-1 3667 2qtj-2 Search similar-shape structures by Omokage search (details)

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Links

EMDB pages	EMDB (EBI/PDBe) / EMDataResource

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Map

File

Download / File: emd_6099.map.gz / Format: CCP4 / Size: 39.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)

Annotation

Tomographic reconstruction of IgG1 antibody

Voxel size

X=Y=Z: 1.48 Å

Density

Contour Level	By AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum	-0.02284613 - 4.23763609
Average (Standard dev.)	0.0 (±0.16507562)

Symmetry

Space group: 1

Details

EMDB XML:

Map geometry

Axis order	X	Y	Z
Origin	17	8	8
Dimensions	220	220	220
Spacing	220	220	220

Cell

A=B=C: 325.6 Å
α=β=γ: 90.0 °

CCP4 map header:

mode	Image stored as Reals
Å/pix. X/Y/Z	1.48	1.48	1.48
M x/y/z	220	220	220
origin x/y/z	0.000	0.000	0.000
length x/y/z	325.600	325.600	325.600
α/β/γ	90.000	90.000	90.000
MAP C/R/S	1	2	3
start NC/NR/NS	8	17	8
NC/NR/NS	220	220	220
D min/max/mean	-0.023	4.238	0.000

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Supplemental data

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Supplemental map: submit-120-p002.map

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Supplemental map: submit-120-p003.map

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Supplemental map: submit-120-p004.map

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Supplemental map: submit-120-p005.map

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Supplemental map: submit-120-p006.map

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Supplemental map: submit-120-p007.map

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Supplemental map: submit-120-p008.map

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Supplemental map: submit-120-p009.map

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Supplemental map: submit-120-p010.map

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Supplemental map: submit-120-p011.map

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Supplemental map: submit-120-p012.map

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Supplemental map: submit-120-p013.map

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Supplemental map: submit-120-p014.map

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Supplemental map: submit-120-p015.map

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Supplemental map: submit-120-p016.map

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Supplemental map: submit-120-p017.map

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Supplemental map: submit-120-p018.map

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Supplemental map: submit-120-p019.map

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Supplemental map: submit-120-p020.map

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Supplemental map: submit-120-p021.map

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Supplemental map: submit-120-p022.map

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Supplemental map: submit-120-p023.map

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Supplemental map: submit-120-p024.map

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Supplemental map: submit-120-p025.map

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Supplemental map: submit-120-p026.map

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Supplemental map: submit-120-p027.map

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Supplemental map: submit-120-p028.map

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Supplemental map: submit-120-p029.map

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Supplemental map: submit-120-p030.map

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Supplemental map: submit-120-p031.map

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Supplemental map: submit-120-p032.map

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Supplemental map: submit-120-p033.map

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Supplemental map: submit-120-p034.map

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Supplemental map: submit-120-p035.map

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Supplemental map: submit-120-p036.map

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Supplemental map: submit-120-p037.map

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Supplemental map: submit-120-p038.map

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Supplemental map: submit-120-p039.map

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Supplemental map: submit-120-p040.map

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Supplemental map: submit-120-p041.map

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Supplemental map: submit-120-p042.map

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Supplemental map: submit-120-p043.map

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Supplemental map: submit-120-p044.map

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Supplemental map: submit-120-p045.map

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Supplemental map: submit-120-p046.map

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Supplemental map: submit-120-p047.map

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Supplemental map: submit-120-p048.map

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Supplemental map: submit-120-p049.map

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Supplemental map: submit-120-p050.map

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Supplemental map: submit-120-p051.map

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Supplemental map: submit-120-p052.map

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Supplemental map: submit-120-p053.map

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Supplemental map: submit-120-p054.map

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Supplemental map: submit-120-p055.map

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Supplemental map: submit-120-p056.map

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Supplemental map: submit-120-p057.map

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Supplemental map: submit-120-p058.map

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Supplemental map: submit-120-p059.map

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Supplemental map: submit-120-p060.map

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Supplemental map: submit-120-p061.map

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Supplemental map: submit-120-p062.map

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Supplemental map: submit-120-p063.map

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Supplemental map: submit-120-p064.map

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Supplemental map: submit-120-p065.map

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Supplemental map: submit-120-p066.map

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Supplemental map: submit-120-p073.map

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Supplemental map: submit-120-p077.map

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Supplemental map: submit-120-p078.map

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Supplemental map: submit-120-p079.map

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Supplemental map: submit-120-p080.map

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Supplemental map: submit-120-p082.map

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Supplemental map: submit-120-p084.map

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Supplemental map: submit-120-p085.map

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Supplemental map: submit-120-p086.map

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Supplemental map: submit-120-p087.map

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Supplemental map: submit-120-p088.map

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Supplemental map: submit-120-p089.map

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Supplemental map: submit-120-p090.map

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Supplemental map: submit-120-p091.map

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Supplemental map: submit-120-p092.map

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Supplemental map: submit-120-p093.map

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Supplemental map: submit-120-p094.map

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Supplemental map: submit-120-p095.map

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Supplemental map: submit-120-p096.map

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Supplemental map: submit-120-p097.map

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Supplemental map: submit-120-p099.map

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Supplemental map: submit-120-p106.map

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Supplemental map: submit-120-p107.map

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Supplemental map: submit-120-p108.map

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Supplemental map: submit-120-p109.map

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Supplemental map: submit-120-p110.map

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Supplemental map: submit-120-p111.map

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Supplemental map: submit-120-p113.map

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Supplemental map: submit-120-p115.map

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Supplemental map: submit-120-p117.map

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Supplemental map: submit-120-p118.map

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Supplemental map: submit-120-p119.map

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Supplemental map: submit-120-p120.map

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Sample components

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Entire : Human IgG1

Entire	Name: Human IgG1Immunoglobulin G
Components	Sample: Human IgG1Immunoglobulin G Protein or peptide: immunoglobulin G subclass 1

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Supramolecule #1000: Human IgG1

Supramolecule	Name: Human IgG1 / type: sample / ID: 1000 / Oligomeric state: monomer / Number unique components: 1
Molecular weight	Experimental: 150 KDa / Theoretical: 150 KDa

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Macromolecule #1: immunoglobulin G subclass 1

Macromolecule	Name: immunoglobulin G subclass 1 / type: protein_or_peptide / ID: 1 / Name.synonym: IgG1 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No / Database: NCBI
Source (natural)	Organism: Homo sapiens (human) / synonym: human
Molecular weight	Experimental: 150 KDa / Theoretical: 150 KDa

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Experimental details

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Structure determination

Method	negative staining
Processing	electron tomography
Aggregation state	particle

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Sample preparation

Concentration	0.01 mg/mL
Buffer	pH: 7.4 Details: 1X Dulbeccos phosphate-buffered saline (Invitrogen, La Jolla, CA), 2.7 mM KCl, 1.46 mM KH2PO4, 136.9 mM NaCl, 8.1 mM Na2HPO4
Staining	Type: NEGATIVE Details: Antibody was diluted to 0.01 mg/mL with deionized water. Aliquots of about 3uL were applied to grids. Grids were washed with deionized water three times, then washed with 1% uranyl formate ...Details: Antibody was diluted to 0.01 mg/mL with deionized water. Aliquots of about 3uL were applied to grids. Grids were washed with deionized water three times, then washed with 1% uranyl formate three times before being blotting to dryness [optimized negative-staining EM specimen preparation protocol as described in Zhang L. and Ren G., Journal of Lipid Research, (2010) 51, 1228-1236; (2011) 52, 175-84; and BBA (2013) 1830, 2150-9.]
Grid	Details: 200 mesh glow-discharged thin carbon-coated EM grids (Cu-200CN, Pacific Grid-Tech, USA)
Vitrification	Cryogen name: NONE / Instrument: OTHER

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Electron microscopy

Microscope	ZEISS LIBRA120PLUS
Electron beam	Acceleration voltage: 120 kV / Electron source: LAB6
Electron optics	Calibrated magnification: 80000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 80000
Sample stage	Specimen holder model: OTHER / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 ° / Tilt series - Axis1 - Angle increment: 1.5 °
Temperature	Min: 280 K / Max: 300 K
Date	Feb 1, 2014
Image recording	Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 81 / Average electron dose: 250 e/Å² / Bits/pixel: 16

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Image processing

CTF correction	Details: each tilt image
Final reconstruction	Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: OTHER / Software - Name: Spider, EMAN1, EMAN2 / Details: Each particle was reconstructed individually. / Number images used: 81
Details	Maps were reconstructed using individual-particle electron tomography (IPET) and the Focus ET Reconstruction Algorithm.{eulerAnglesDetails}: theta -60 to 60 degrees

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Atomic model buiding 1

Initial model	PDB ID: 1igt Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C / Chain - #3 - Chain ID: D
Software	Name: Chimera, NAMD
Details	The new structure was obtained by target molecular dynamics simulation using rigid body docking results.
Refinement	Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation

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+Supplemental map: submit-120-p002.map

+Supplemental map: submit-120-p003.map

+Supplemental map: submit-120-p004.map

+Supplemental map: submit-120-p005.map

+Supplemental map: submit-120-p006.map

+Supplemental map: submit-120-p007.map

+Supplemental map: submit-120-p008.map

+Supplemental map: submit-120-p009.map

+Supplemental map: submit-120-p010.map

+Supplemental map: submit-120-p011.map

+Supplemental map: submit-120-p012.map

+Supplemental map: submit-120-p013.map

+Supplemental map: submit-120-p014.map

+Supplemental map: submit-120-p015.map

+Supplemental map: submit-120-p016.map

+Supplemental map: submit-120-p017.map

+Supplemental map: submit-120-p018.map

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+Supplemental map: submit-120-p020.map

+Supplemental map: submit-120-p021.map

+Supplemental map: submit-120-p022.map

+Supplemental map: submit-120-p023.map

+Supplemental map: submit-120-p024.map

+Supplemental map: submit-120-p025.map

+Supplemental map: submit-120-p026.map

+Supplemental map: submit-120-p027.map

+Supplemental map: submit-120-p028.map

+Supplemental map: submit-120-p029.map

+Supplemental map: submit-120-p030.map

+Supplemental map: submit-120-p031.map

+Supplemental map: submit-120-p032.map

+Supplemental map: submit-120-p033.map

+Supplemental map: submit-120-p034.map

+Supplemental map: submit-120-p035.map

+Supplemental map: submit-120-p036.map

+Supplemental map: submit-120-p037.map

+Supplemental map: submit-120-p038.map

+Supplemental map: submit-120-p039.map

+Supplemental map: submit-120-p040.map

+Supplemental map: submit-120-p041.map

+Supplemental map: submit-120-p042.map

+Supplemental map: submit-120-p043.map

+Supplemental map: submit-120-p044.map

+Supplemental map: submit-120-p045.map

+Supplemental map: submit-120-p046.map

+Supplemental map: submit-120-p047.map

+Supplemental map: submit-120-p048.map

+Supplemental map: submit-120-p049.map

+Supplemental map: submit-120-p050.map

+Supplemental map: submit-120-p051.map

+Supplemental map: submit-120-p052.map

+Supplemental map: submit-120-p053.map

+Supplemental map: submit-120-p054.map

+Supplemental map: submit-120-p055.map

+Supplemental map: submit-120-p056.map

+Supplemental map: submit-120-p057.map

+Supplemental map: submit-120-p058.map

+Supplemental map: submit-120-p059.map

+Supplemental map: submit-120-p060.map

+Supplemental map: submit-120-p061.map

+Supplemental map: submit-120-p062.map

+Supplemental map: submit-120-p063.map

+Supplemental map: submit-120-p064.map

+Supplemental map: submit-120-p065.map

+Supplemental map: submit-120-p066.map

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